Methods for placing, accepting, and filling orders for products and services

Abstract

Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.

What is claimed is:  
     
         1 . A method for providing to a consumer, assays configured to detect presence or expression of genetic material, said method comprising: 
 providing a web-based user interface configured to receive an order for one or more stock assays;    providing a web-based user interface configured to receive a request for design of one or more custom assays and an order for said custom assays; and    delivering to the consumer at least one custom or stock assay in response to an order for said one on more custom or stock assay placed by the consumer.    
     
     
         2 . A method in accordance with  claim 1 , further comprising providing a web-based gene exploration platform configured to provide information to assist a consumer in selecting one or both of a stock assay and a custom assay.  
     
     
         3 . A method in accordance with  claim 2  wherein said information is genomic and biomedical information from at least one public or private source.  
     
     
         4 . A method in accordance with  claim 1 , wherein providing a user interface configured to receive an order for stock assays comprises providing a graphical user interface.  
     
     
         5 . A method in accordance with  claim 4 , further comprising providing a graphical user interface configured for the consumer to perform at least one search for at least one information item used to identify genetic material for a stock assay.  
     
     
         6 . A method in accordance with  claim 5 , wherein the at least one information item used to identify the genetic material is a gene identification item selected from the group consisting of gene symbol, gene name, RefSeq accession number, Panther function, Panther process, GO function, GO process, GO identifier, Applied Biosystems identifier, Celera gene identifier (hCG), Celera transcript identifier (hCT), Celera protein identifier (hCP), LocusLink identifier, GenBank nucleotide identifier, GenBank protein identifier, species identifier, chromosome identifier, haplotype identifier, cytoband identifier, RefSeq GI identifier, and combinations thereof.  
     
     
         7 . A method in accordance with  claim 5 , wherein said at least one search comprises a batch search.  
     
     
         8 . A method in accordance with  claim 5 , wherein the search for at least one information item comprises a gene classification search.  
     
     
         9 . A method in accordance with  claim 8 , wherein the gene classification search comprises a molecular function search.  
     
     
         10 . A method in accordance with  claim 8 , wherein the gene classification search comprises a biological process search.  
     
     
         11 . A method in accordance with  claim 4 , further comprising providing reference information to the consumer concerning genetic material that is detectable by an assay that is ordered by the consumer.  
     
     
         12 . A method in accordance with  claim 11 , wherein the reference information is selected from the group consisting of RefSeq identifier, LocusLink gene name, molecular function, biological process, Celera identification number, gene location, and combinations thereof.  
     
     
         13 . A method in accordance with  claim 4  wherein the graphical user interface is configured to receive an order for at least one SNP assay.  
     
     
         14 . A method in accordance with  claim 13  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 40,000 SNP assays.  
     
     
         15 . A method in accordance with  claim 14  wherein each SNP assay is configured to detect presence of one of at least 40,000 pairs of SNP alleles located in gene regions.  
     
     
         16 . A method in accordance with  claim 15  wherein each of the 40,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         17 . A method in accordance with  claim 13  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 100,000 SNP assays.  
     
     
         18 . A method in accordance with  claim 17  wherein each SNP assay is configured to detect presence of one of at least 100,000 pairs of SNP alleles located in gene regions.  
     
     
         19 . A method in accordance with  claim 18  wherein each of the 100,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         20 . A method in accordance with  claim 13  wherein providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         21 . A method in accordance with  claim 20  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         22 . A method in accordance with  claim 13 , wherein said providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         23 . A method in accordance with  claim 4  wherein the graphical user interface is configured to receive an order for at least one gene expression assay.  
     
     
         24 . A method in accordance with  claim 23  wherein the graphical user interface is configured to receive an order for at least one gene expression assay from a group of at least 10,000 gene expression assays.  
     
     
         25 . A method in accordance with  claim 23  wherein said providing a graphical user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         26 . A method in accordance with  claim 1 , wherein providing a user interface configured to receive a request for design of one or more custom assays and an order for said custom assays comprises providing a graphical user interface configured to receive a request for design of one or more custom assays and an order for said custom assays.  
     
     
         27 . A method in accordance with  claim 26  wherein providing a user interface configured to receive an order for one or more stock assays comprises providing a graphical user interface configured to receive an order for one or more stock assays.  
     
     
         28 . A method in accordance with  claim 1 , wherein said user interface configured to receive orders for custom assays includes a file-receiving interface configured to receive from the consumer a submission file containing information suitable for use in designing at least one of said custom assays.  
     
     
         29 . A method in accordance with  claim 28 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to the target of the custom assay requested by the consumer.  
     
     
         30 . A method in accordance with  claim 28 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to target coordinates of the custom assay requested by the consumer.  
     
     
         31 . A method in accordance with  claim 29 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing information relating to the identity of the consumer requesting a custom assay.  
     
     
         32 . A method in accordance  claim 28 , further comprising providing a submission file builder configured to assist the consumer in preparing said submission file for ordering custom assays.  
     
     
         33 . A method in accordance  claim 32  wherein the file builder provides for electronically validating at least a portion of the submission file.  
     
     
         34 . A method in accordance with  claim 33 , wherein the electronic validation comprises detecting typographical errors in the submission file.  
     
     
         35 . A method in accordance with  claim 34  further comprising prompting the user to correct detected typographical errors in the submission file.  
     
     
         36 . A method in accordance with  claim 33  wherein the electronic validation comprises generating an error log providing information related to whether the submission file is properly formatted.  
     
     
         37 . A method in accordance with  claim 32 , wherein the submission file builder includes a sequence checker to verify correctness of at least a portion of the information contained in the submission file.  
     
     
         38 . A method in accordance with  claim 37 , further comprising providing an electronic shopping basket configured to store an order received from the consumer, said file submission program being operable to upload the submission file to said shopping basket.  
     
     
         39 . A method in accordance with  claim 26  wherein the assays configured to detect presence of genetic material are assays configured to detect presence of at least one SNP allele.  
     
     
         40 . A method in accordance with  claim 39  wherein providing a user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         41 . A method in accordance with  claim 40  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         42 . A method in accordance with  claim 39 , wherein providing a user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         43 . A method in accordance with  claim 26  wherein assays configured to detect presence of genetic material are assays configured to detect expression of at least one gene.  
     
     
         44 . A method in accordance with  claim 1  wherein said delivering to a consumer at least one assay further comprises delivering information concerning said assay.  
     
     
         45 . A method in accordance with  claim 44  wherein said delivering information concerning said assay comprises delivering at least one datasheet.  
     
     
         46 . A method in accordance with  claim 44  wherein delivering information concerning said assay comprises delivering said information on a machine-readable medium.  
     
     
         47 . A method in accordance with  claim 46  wherein said delivering information concerning said assay further comprises delivering at least one datasheet.  
     
     
         48 . A method in accordance with  claim 46  wherein said machine-readable medium is a compact disk.  
     
     
         49 . A method in accordance with  claim 1  wherein said delivering to the consumer at least one custom or stock assay comprises delivering the at least one custom or stock assay in a single tube.  
     
     
         50 . A method in accordance with  claim 49  wherein said delivering to the consumer at least one custom or stock assay in a single tube comprises delivering to the consumer at least one probe and two primers.  
     
     
         51 . A method in accordance with  claim 50  wherein the at least one custom or stock assay in a single tube is a SNP assay comprising a separate probe for each of two alleles and two primers.  
     
     
         52 . A method in accordance with  claim 50  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         53 . A method in accordance with  claim 52  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         54 . A method in accordance with  claim 52  wherein the probe further comprises at least one minor groove binder.  
     
     
         55 . A method in accordance with  claim 50  wherein said delivering to the consumer at least one custom or stock assay in a single tube further comprises delivering at least one custom or stock assay in a single tube and PCR reagents.  
     
     
         56 . A method in accordance with  claim 50  wherein said delivering to the consumer at least one custom or stock assay in a single tube further comprises delivering to the consumer at least one custom or stock assay in a single tube and a universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         57 . A method in accordance with  claim 49  wherein the single tube further comprises a bar code identifier.  
     
     
         58 . A method in accordance with  claim 57  wherein the bar code is a two-dimension bar code  
     
     
         59 . A method in accordance with  claim 49  wherein the single tube further comprises an identifier which is a human-readable Assay number  
     
     
         60 . A method in accordance with  claim 1  further comprising manufacturing assays.  
     
     
         61 . A method in accordance with  claim 60  further comprising performing pre-processing selection, designing primers and probes, and performing in silico quality control prior to said manufacturing.  
     
     
         62 . A method in accordance with  claim 61  wherein the assay is a gene expression assay and wherein each said user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         63 . A method in accordance with  claim 62  wherein said performing pre-processing selection comprises identifying optimal sequence regions which do not contain any single nucleotide polymorphisms or repeat sequences.  
     
     
         64 . A method in accordance with  claim 63  wherein identifying optimal sequence regions comprises utilizing at least one method selected from the group consisting of masking single nucleotide polymorphisms and repeat sequences in the at least one expressed transcript or portion thereof to avoid designing probes and primers thereon, mapping the at least one expressed transcript or portion thereof against at least two genomic databases to identify discrepancies to avoid designing probes and primers thereon, identifying exon-exon boundaries for expressed transcripts of multi-exon genes in order to design probes or primers thereon, and combinations thereof.  
     
     
         65 . A method in accordance with  claim 64  wherein identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         66 . A method in accordance with  claim 64  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding inclusion of single nucleotide polymorphisms or repeat sequences in probe and primer sequences, avoiding inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, constructing either or both of probes and primers on exon-exon boundaries for multi-exon genes, and combinations thereof.  
     
     
         67 . A method in accordance with  claim 62  wherein said designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size, and low incidence of primer-dimer formation.  
     
     
         68 . A method in accordance with  claim 61  wherein said performing in silico quality control comprises determining quality of designed probes and primers utilizing scoring methods selected from the group consisting of transcript BLAST scoring, genome BLAST scoring, scoring size of intron across which a probe spans for multi-exon genes, and combinations thereof.  
     
     
         69 . A method in accordance with  claim 61  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         70 . A method in accordance with  claim 69  wherein said pre-selected scoring criteria comprises assigning high transcript BLAST scoring for matching to self and no other transcript, assigning high genome BLAST scoring for matching to self and no other genome region and assigning high scoring for intron size greater than 10 kilobases and wherein a high assay design scoring is assigned for designed assays scoring all three of high transcript BLAST scoring, high genome BLAST scoring and high intron size scoring.  
     
     
         71 . A method in accordance with  claim 61  wherein the assay is a SNP assay and wherein each said user interface configured to receive orders for assays is configured to receive, from the consumer, criteria relating to at least one gene region containing at least one SNP.  
     
     
         72 . A method in accordance with  claim 71  wherein said performing pre-processing selection comprises identifying optimal sequence regions which contain neither repeat sequences nor any SNPs other than a SNP for which the assay is designed.  
     
     
         73 . A method in accordance with  claim 72  wherein said identifying optimal sequence regions comprises using one or more methods selected from the group consisting of masking any SNPs other than the at least one SNP for which the assay is to be designed and repeat sequences in the at least one gene region to avoid constructing probes and primers thereon, mapping the at least one SNP against at least two genomic databases to identify discrepancies to avoid constructing probes and primers thereon, and combinations thereof.  
     
     
         74 . A method in accordance with  claim 73  wherein said identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         75 . A method in accordance with  claim 73  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of any SNPs other than the at least one SNP for which the assay is to be designed, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, and combinations thereof.  
     
     
         76 . A method in accordance with  claim 70  wherein designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         77 . A method in accordance with  claim 71  wherein said performing in silico quality control comprises determining the quality of designed probes and primers by genome BLAST scoring.  
     
     
         78 . A method in accordance with  claim 77  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         79 . A method in accordance with  claim 78  wherein pre-selected scoring criteria comprises assigning high genome BLAST scoring for matching to self and no other genome region.  
     
     
         80 . A method in accordance with  claim 60  further comprising quality control testing of the manufactured assays according to pre-selected quality control criteria.  
     
     
         81 . A method in accordance with  claim 80  wherein quality control testing comprises one or more testing procedures selected from the group consisting of synthesis yield testing, analytical quality control testing, functional testing, validation testing, and combinations thereof, wherein each of the one or more testing procedures is performed according to pre-selected quality control criteria.  
     
     
         82 . A method in accordance with  claim 81  wherein synthesis yield testing comprises testing the manufactured assays using PAGE or HPLC.  
     
     
         83 . A method in accordance with  claim 81  wherein the pre-selected quality control criteria for synthesis yield testing is about 90% (w/w) product yield.  
     
     
         84 . A method in accordance with  claim 83  wherein the pre-selected quality control criteria for synthesis yield testing is about 95% (w/w) product yield.  
     
     
         85 . A method in accordance with  claim 81  wherein analytical quality control testing comprises testing the manufactured assays using mass spectrometry.  
     
     
         86 . A method in accordance with  claim 85  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 5% greater or lesser than calculated mass.  
     
     
         87 . A method in accordance with  claim 86  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 2% greater or lesser than calculated mass.  
     
     
         88 . A method in accordance with 81 wherein the manufactured assays are SNP assays and functional testing comprises performing PCR reactions of manufactured assays against from about 10 to about 20 genomic DNA samples.  
     
     
         89 . A method in accordance with  claim 88  wherein the pre-selected quality control criteria for functional testing comprises detecting presence of both alleles.  
     
     
         90 . A method in accordance with  claim 81  wherein the manufactured assay is a gene expression assay and functional testing comprises performing designed assay RT-PCR.  
     
     
         91 . A method in accordance with  claim 90  wherein the manufactured assay is a multi-exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of genomic DNA.  
     
     
         92 . A method in accordance with  claim 90  wherein the manufactured assay is a single exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of non-transcribed genomic DNA.  
     
     
         93 . A method in accordance with  claim 81  wherein the manufactured assay is a SNP assay and validation testing comprises performing designed assay PCR against about 90 human genomic samples.  
     
     
         94 . A method in accordance with  claim 93  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 10%.  
     
     
         95 . A method in accordance with  claim 94  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 15%.  
     
     
         96 . A method in accordance with  claim 81  wherein the manufactured assay is a gene expression and validation testing comprises performing designed assay PCR against a pool of at least about 10 human cDNA samples.  
     
     
         97 . A method in accordance with  claim 96  wherein the human cDNA samples are from different individuals.  
     
     
         98 . A method in accordance with  claim 96  wherein the human cDNA samples are from different cell lines.  
     
     
         99 . A method in accordance with  claim 96  wherein the pre-selected quality control criteria for validation testing comprises detection of amplified transcript at a threshold of less than 35 PCR cycles.  
     
     
         100 . A method in accordance with  claim 59  wherein said manufacturing comprises high-throughput manufacturing.  
     
     
         101 . A system for providing to a consumer, assays configured to detect presence or expression of genetic material, said system comprising: 
 a web-based user interface configured to receive an order for one or more stock assays;    a web-based user interface configured to receive a request for design of one or more custom assays and an order for said custom assays; and    a system for delivering to the consumer at least one custom or stock assay in response to an order for said one custom or stock assay placed by the consumer.    
     
     
         102 . A system in accordance with  claim 101 , further comprising a gene web-based gene exploration platform configured to provide information to assist a consumer in selecting one or both of a stock assay and a custom assay.  
     
     
         103 . A system in accordance with  claim 102  wherein said information is genomic and biomedical information from at least one public or private source.  
     
     
         104 . A system in accordance with  claim 101 , wherein the user interface configured to receive an order for stock assays comprises a graphical user interface.  
     
     
         105 . A system in accordance with  claim 104 , further comprising a graphical user interface configured for the consumer to perform at least one search for at least one information item used to identify genetic material for a stock assay.  
     
     
         106 . A system in accordance with  claim 105 , wherein the at least one information item used to identify the genetic material is a gene identification item selected from the group consisting of gene symbol, gene name, RefSeq accession number, Panther function, Panther process, GO function, GO process, GO identifier, Applied Biosystems identifier, Celera gene identifier (hCG), Celera transcript identifier (hCT), Celera protein identifier (hCP), LocusLink identifier, GenBank nucleotide identifier, GenBank protein identifier, species identifier, chromosome identifier, haplotype identifier, cytoband identifier, RefSeq GI identifier, and combinations thereof.  
     
     
         107 . A system in accordance with  claim 105 , wherein said at least one search comprises a batch search.  
     
     
         108 . A system in accordance with  claim 105 , wherein the at least one information item comprises a gene classification search.  
     
     
         109 . A system in accordance with  claim 108 , wherein the gene classification search comprises a molecular function search.  
     
     
         110 . A system in accordance with  claim 108 , wherein the gene classification search comprises a biological process search.  
     
     
         111 . A system in accordance with  claim 104 , further comprising a web-based user interface configured to provide reference information to the consumer concerning genetic material that is detectable by an assay that is ordered by the consumer.  
     
     
         112 . A system in accordance with  claim 111 , wherein the reference information is selected from the group consisting of RefSeq identifier, LocusLink gene name, molecular function, biological process, Celera identification number, gene location, and combinations thereof.  
     
     
         113 . A system in accordance with  claim 104  wherein the graphical user interface is configured to receive an order for at least one SNP assay.  
     
     
         114 . A system in accordance with  claim 113  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 40,000 SNP assays.  
     
     
         115 . A system in accordance with  claim 114  wherein each SNP assay is configured to detect presence of one of at least 40,000 pairs of SNP alleles located in gene regions.  
     
     
         116 . A system in accordance with  claim 115  wherein each of the 40,000 pairs of SNP alleles are spaced a part by about 10 kilobases within gene regions.  
     
     
         117 . A system in accordance with  claim 114  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 100,000 SNP assays.  
     
     
         118 . A system in accordance with  claim 116  wherein each SNP assay is configured to detect presence of one of at least 100,000 pairs of SNP alleles located in gene regions.  
     
     
         119 . A system in accordance with  claim 118  wherein each of the 100,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         120 . A system in accordance with  claim 113  wherein providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         121 . A system in accordance with  claim 120  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         122 . A system in accordance with  claim 113 , wherein said providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         123 . A system in accordance with  claim 114  wherein the graphical user interface is configured to receive an order for at least one gene expression assay.  
     
     
         124 . A system in accordance with  claim 123  wherein the graphical user interface is configured to receive an order for at least one gene expression assay from a group of at least 10,000 gene expression assays.  
     
     
         125 . A system in accordance with  claim 123  wherein said graphical user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         126 . A system in accordance with  claim 101 , wherein said user interface configured to receive a request for design of one or more custom assays and an order for said custom assays comprises a graphical user interface configured to receive a request for design of one or more custom assays and an order for said custom assays.  
     
     
         127 . A system in accordance with  claim 126  wherein the user interface configured to receive an order for one or more stock assays comprises a graphical user interface configured to receive an order for one or more stock assays.  
     
     
         128 . A system in accordance with  claim 101 , wherein said user interface configured to receive orders for custom assays includes a file-receiving interface configured to receive, from the consumer, a submission file containing information suitable for use in designing at least one of said custom assays.  
     
     
         129 . A system in accordance with  claim 128 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to the target of the custom assay requested by the consumer.  
     
     
         130 . A system in accordance with  claim 129 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to the target coordinates of the custom assay requested by the consumer.  
     
     
         131 . A system in accordance with  claim 128 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing information relating to the identity of the consumer requesting a custom assay.  
     
     
         132 . A system in accordance  claim 128 , further comprising a submission file builder configured to assist the consumer in preparing said submission file for ordering custom assays.  
     
     
         133 . A system in accordance  claim 132  wherein the file builder provides for electronically validating at least a portion of the submission file.  
     
     
         134 . A system in accordance with  claim 133 , wherein the electronic validation comprises detecting typographical errors in the submission file.  
     
     
         135 . A system in accordance with  claim 134  further comprising a system configured to prompt the user to correct detected typographical errors in the submission file.  
     
     
         136 . A system in accordance with  claim 133  wherein the electronic validation comprises generating an error log providing information related to whether the submission file is properly formatted.  
     
     
         137 . A system according to  claim 132 , wherein the submission file builder includes a sequence checker to verify correctness of at least a portion of the information contained in the submission file for which the custom assay is to be designed.  
     
     
         138 . A system according to  claim 137 , further comprising an electronic shopping basket configured to store an order received from the consumer, said file submission program being operable to upload the submission file to said shopping basket.  
     
     
         139 . A system in accordance with  claim 126  wherein the assays configured to detect presence of genetic material are assays configured to detect presence of at least one SNP allele.  
     
     
         140 . A system in accordance with  claim 139  wherein the user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         141 . A system in accordance with  claim 140  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         142 . A system in accordance with  claim 139 , wherein the user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         143 . A system in accordance with  claim 126  wherein assays configured to detect presence of genetic material are assays configured to detect expression of at least one gene.  
     
     
         144 . A system in accordance with  claim 101  wherein said system for delivering to a consumer at least one assay further comprises a system for delivering information concerning said assay.  
     
     
         145 . A system in accordance with  claim 144  wherein said system for delivering information concerning said assay comprises a system for delivering at least one datasheet.  
     
     
         146 . A system in accordance with  claim 144  wherein said system for delivering information concerning said assay comprises a system for delivering said information on a machine-readable medium.  
     
     
         147 . A system in accordance with  claim 146  wherein said system for delivering information concerning said assay further comprises a system for delivering at least one datasheet.  
     
     
         148 . A system in accordance with  claim 146  wherein said machine-readable medium is a compact disk.  
     
     
         149 . A system in accordance with  claim 101  wherein said system for delivering for the consumer at least one custom or stock assay comprises a system for delivering the at least one custom or stock assay in a single tube.  
     
     
         150 . A system in accordance with  claim 149  wherein said at least one custom or stock assay in a single tube comprises at least one probe and two primers.  
     
     
         151 . A system in accordance with  claim 150  wherein the at least one custom or stock assay in a single tube is a SNP assay comprising a separate probe for each of two alleles and two primers.  
     
     
         152 . A system in accordance with  claim 150  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         153 . A system in accordance with  claim 152  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         154 . A system in accordance with  claim 152  wherein the probe further comprises at least one minor groove binder.  
     
     
         155 . A system in accordance with  claim 150  wherein said system for delivering for the consumer at least one custom or stock assay further comprises a system for delivering for the consumer at least one custom or stock assay in a single tube and PCR reagents.  
     
     
         156 . A system in accordance with  claim 155  wherein said system for delivering to the consumer at least one custom or stock assay further comprises a system for delivering to the consumer at least one custom or stock assay in a single tube and a universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         157 . A system in accordance with  claim 149  wherein the single tube further comprises a bar code identifier.  
     
     
         158 . A system in accordance with  claim 157  wherein the bar code is a two-dimension bar code.  
     
     
         159 . A system in accordance with  claim 149  wherein the single tube further comprises an identifier which is a human-readable Assay number  
     
     
         160 . A system in accordance with  claim 101  further comprising a facility for manufacturing assays.  
     
     
         161 . A system in accordance with  claim 160  further comprising a system for performing pre-processing selection, a system for designing primers and probes, and a system for performing in silico quality control prior to said manufacturing.  
     
     
         162 . A system in accordance with  claim 161  wherein the assay is a gene expression assay and wherein each said user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         163 . A system in accordance with  claim 161  wherein said system for performing pre-processing selection comprises a component for identifying optimal sequence regions which do not contain any single nucleotide polymorphisms or repeat sequences.  
     
     
         164 . A system in accordance with  claim 163  wherein the component for identifying optimal sequence regions comprises components selected from the group consisting of a component for masking single nucleotide polymorphisms and repeat sequences in the at least one expressed transcript or portion thereof to avoid designing probes and primers thereon, a component for mapping the at least one expressed transcript or portion thereof against at least two genomic databases to identify discrepancies to avoid designing probes and primers thereon, a component for identifying exon-exon boundaries for expressed transcripts of multi-exon genes in order to design probes or primers thereon and combinations thereof.  
     
     
         165 . A system in accordance with  claim 164  wherein the component for identifying optimal sequence regions comprises a component for masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         166 . A system in accordance with  claim 164  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of single nucleotide polymorphisms or repeat sequences in probe and primer sequences, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, constructing either or both of probes and primers on exon-exon boundaries for multi-exon genes, and combinations thereof.  
     
     
         167 . A system in accordance with  claim 162  wherein said system for designing probes and primers utilizes specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         168 . A system in accordance with  claim 161  wherein said system for performing in silico quality control comprises a component for determining the quality of designed probes and primers utilizing scoring systems selected from the group consisting of transcript BLAST scoring, genome BLAST scoring, scoring the size of intron across which a probe spans for multi-exon genes and combinations thereof.  
     
     
         169 . A system in accordance with  claim 161  further comprising a system for manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         170 . A system in accordance with  claim 169  wherein said pre-selected scoring criteria comprises high transcript BLAST scoring for matching to self and no other transcript, high genome BLAST scoring for matching to self and no other genome region and high scoring for intron size greater than 10 kilobases and wherein high assay design scoring comprises high scoring for all three of high transcript BLAST scoring, high genome BLAST scoring and high intron size scoring.  
     
     
         171 . A system in accordance with  claim 161  wherein the assay is a SNP assay and wherein each said user interface configured to receive orders for assays is configured to receive, from the consumer, criteria relating to at least one gene region containing at least one SNP.  
     
     
         172 . A system in accordance with  claim 171  wherein said system for performing pre-processing selection comprises a component for identifying optimal sequence regions which contain neither repeat sequences nor any SNPs other than a SNP for which the assay is designed.  
     
     
         173 . A system in accordance with  claim 172  wherein said component for identifying optimal sequence regions comprises systems selected from the group consisting of masking any SNPs other than the at least one SNP for which the assay is to be designed and repeat sequences in the at least one gene region to avoid a component for designing probes and primers thereon, mapping the at least one SNP against at least two genomic databases to identify discrepancies to avoid constructing probes and primers thereon, and combinations thereof.  
     
     
         174 . A system in accordance with  claim 173  wherein said identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         175 . A system in accordance with  claim 173  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of any SNPs other than the at least one SNP for which the assay is to be designed, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, and combinations thereof.  
     
     
         176 . A system in accordance with  claim 170  wherein probes and primers are designed utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         177 . A system in accordance with  claim 171  wherein said system for performing in silico quality control comprises a system for determining the quality of designed probes and primers by genome BLAST scoring.  
     
     
         178 . A system in accordance with  claim 177  further comprising a system configured to manufacture designed probes and primers having pre-selected scoring criteria.  
     
     
         179 . A system in accordance with  claim 178  wherein pre-selected scoring criteria comprises high genome BLAST scoring for matching to self and no other genome region.  
     
     
         180 . A system in accordance with  claim 160  further comprising a system configured to perform quality control testing of the manufactured assay according to pre-selected quality control criteria.  
     
     
         181 . A system in accordance with  claim 180  wherein quality control testing comprises testing systems are selected from the group consisting of a synthesis yield testing system, an analytical quality control testing system, a functional testing system, a validation testing system and combinations thereof wherein each of the one or more testing systems is performed according to pre-selected quality control criteria.  
     
     
         182 . A system in accordance with  claim 181  wherein the synthesis yield testing system comprises a system for testing the manufactured assay using PAGE or HPLC.  
     
     
         183 . A system in accordance with  claim 181  wherein the pre-selected quality control criteria for the synthesis yield testing system is about 90% (w/w) product yield.  
     
     
         184 . A system in accordance with  claim 183  wherein the pre-selected quality control criteria for the synthesis yield testing system is about 95% (w/w) product yield.  
     
     
         185 . A system in accordance with  claim 181  wherein the analytical quality control testing system comprises a system for testing the manufactured assays using mass spectrometry.  
     
     
         186 . A system in accordance with  claim 185  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 5% greater or lesser than calculated mass.  
     
     
         187 . A system in accordance with  claim 186  wherein the pre-selected quality control criteria for the synthesis yield testing system is such that determined mass is not more than 2% greater or lesser than calculated mass.  
     
     
         188 . A system in accordance with  181  wherein the manufactured assays are SNP assays and the system for functional testing comprises a system for performing PCR reactions of manufactured assays against from about 10 to about 20 genomic DNA samples.  
     
     
         189 . A system in accordance with  claim 188  wherein the pre-selected quality control criteria for the functional testing system comprises detection presence of both alleles.  
     
     
         190 . A system in accordance with  claim 181  wherein the manufactured assay is a gene expression assay and system for functional testing comprises a system for performing designed assay RT-PCR.  
     
     
         191 . A system in accordance with  claim 190  wherein the manufactured assay is a multi-exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of genomic DNA.  
     
     
         192 . A system in accordance with  claim 190  wherein the manufactured assay is a single exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of non-transcribed genomic DNA.  
     
     
         193 . A system in accordance with  claim 191  wherein the manufactured assay is a SNP assay and the system for validation testing comprises a system for performing designed assay PCR against about 90 human genomic samples.  
     
     
         194 . A system in accordance with  claim 193  wherein the pre-selected quality control criteria for the system for validation testing comprises detecting a minor allele frequency of at least 10%.  
     
     
         195 . A system in accordance with  claim 194  wherein the pre-selected quality control criteria for the system for validation testing comprises detecting a minor allele frequency of at least 15%.  
     
     
         196 . A system in accordance with  claim 181  wherein the manufactured assay is a gene expression and the system for validation testing comprises a system for performing designed assay PCR against a pool of at least about 10 human cDNA samples.  
     
     
         197 . A system in accordance with  claim 196  wherein the human cDNA samples are from different individuals.  
     
     
         198 . A system in accordance with  claim 196  wherein the human cDNA samples are from different cell lines.  
     
     
         199 . A system in accordance with  claim 196  wherein the pre-selected quality control criteria for the system for validation testing comprises detection of amplified transcript at a threshold of less than 35 PCR cycles.  
     
     
         200 . A system in accordance with  claim 159  wherein said manufacturing comprises high-throughput manufacturing.  
     
     
         201 . A method for constructing a system for providing to a consumer, assays configured to detect presence or expression of genetic material, said method comprising: 
 providing a web-based user interface configured to receive an order for one or more stock assays;    providing a web-based user interface configured to receive a request for design of one or more custom assays and an order for said custom assays; and    providing a system for delivering to the consumer at least one custom or stock assay in response to an order for said one custom or stock assay placed by the consumer.    
     
     
         202 . A method in accordance with  claim 201  further comprising providing a web-based gene exploration platform configured to provide information to assist a consumer in selecting one or both of a stock assay and a custom assay.  
     
     
         203 . A method in accordance with  claim 202  wherein said information is genomic and biomedical information from at least one public or private source.  
     
     
         204 . A method in accordance with  claim 201 , wherein providing a user interface configured to receive an order for stock assays comprises providing a graphical user interface.  
     
     
         205 . A method in accordance with  claim 204 , further comprising providing a graphical user configured interface for the consumer to perform at least one search for at least one information item used to identify genetic material for a stock assay.  
     
     
         206 . A method in accordance with  claim 204 , wherein the at least one information item used to identify the genetic material is a gene identification item selected from the group consisting of gene symbol, gene name, RefSeq accession number, Panther function, Panther process, GO function, GO process, GO identifier, Applied Biosystems identifier, Celera gene identifier (hCG), Celera transcript identifier (hCT), Celera protein identifier (hCP), LocusLink identifier, GenBank nucleotide identifier, GenBank protein identifier, species identifier, chromosome identifier, haplotype identifier, cytoband identifier, RefSeq GI identifier, and combinations thereof.  
     
     
         207 . A method in accordance with  claim 204 , wherein said at least one search comprises a batch search.  
     
     
         208 . A method in accordance with  claim 204 , wherein the at least one information item comprises a gene classification search.  
     
     
         209 . A method in accordance with  claim 208 , wherein the gene classification search comprises a molecular function search.  
     
     
         210 . A method in accordance with  claim 209 , wherein the gene classification search comprises a biological process search.  
     
     
         211 . A method in accordance with  claim 204 , further comprising providing a system for supplying reference information to the consumer concerning genetic material that is detectable by an assay that is ordered by the consumer.  
     
     
         212 . A method in accordance with  claim 211 , wherein the reference information is selected from the group consisting of RefSeq identifier, LocusLink gene name, molecular function, biological process, Celera identification number, gene location, and combinations thereof.  
     
     
         213 . A method in accordance with  claim 205  wherein the graphical user interface is configured to receive an order for at least one SNP assay.  
     
     
         214 . A method in accordance with  claim 213  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 40,000 SNP assays.  
     
     
         215 . A method in accordance with  claim 214  wherein each SNP assay is configured to detect presence of one of at least 40,000 pairs of SNP alleles located in gene regions.  
     
     
         216 . A method in accordance with  claim 215  wherein each of the 40,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         217 . A method in accordance with  claim 214  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 100,000 SNP assays.  
     
     
         218 . A method in accordance with  claim 217  wherein each SNP assay is configured to detect presence of one of at least 100,000 pairs of SNP alleles located in gene regions.  
     
     
         219 . A method in accordance with  claim 218  wherein each of the 100,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         220 . A method in accordance with  claim 213  wherein providing the graphical user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         221 . A method in accordance with  claim 220  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         222 . A method in accordance with  claim 213 , wherein said providing the graphical user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         223 . A method in accordance with  claim 214  wherein the graphical user interface is configured to receive an order for at least one gene expression assay.  
     
     
         224 . A method in accordance with  claim 223  wherein the graphical user interface is configured to receive an order for at least one gene expression assay from a group of at least 10,000 gene expression assays.  
     
     
         225 . A method in accordance with  claim 223  wherein said providing a user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         226 . A method in accordance with  claim 201 , wherein providing a user interface configured to receive a request for design of one or more custom assays and an order for said custom assays comprises providing a graphical user interface configured to receive a request for design of one or more custom assays and an order for said custom assays.  
     
     
         227 . A method in accordance with  claim 226  wherein providing a user interface configured to receive an order for one or more stock assays comprises providing a graphical user interface configured to receive an order for one or more stock assays.  
     
     
         228 . A method in accordance with  claim 201 , wherein said user interface configured to receive orders for custom assays includes a file-receiving interface configured to receive, from the consumer, a submission file containing information suitable for use in designing at least one of said custom assays.  
     
     
         229 . A method in accordance with  claim 228 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to the target of the custom assay requested by the consumer.  
     
     
         230 . A method in accordance with  claim 229 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to target coordinates of the custom assay requested by the consumer.  
     
     
         231 . A method in accordance with  claim 228 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing information relating to the identity of the consumer requesting a custom assay.  
     
     
         232 . A method in accordance  claim 228 , further comprising providing a submission file builder configured to assist the consumer in preparing said submission file for ordering custom assays.  
     
     
         233 . A method in accordance  claim 232  wherein the file builder provides for electronically validating at least a portion of the submission file.  
     
     
         234 . A method in accordance with  claim 233 , wherein the electronic validation comprises detecting typographical errors in the submission file.  
     
     
         235 . A method in accordance with  claim 234  further comprising a providing a prompt for the user to correct detected typographical errors in the submission file.  
     
     
         236 . A method in accordance with  claim 233  wherein the electronic validation comprises generating an error log providing information related to whether the submission file is properly formatted.  
     
     
         237 . A method in accordance with  claim 232 , wherein the submission file builder includes a sequence checker to verify correctness of at least a portion of the information contained in the submission file for which the custom assay is to be designed.  
     
     
         238 . A method for providing assays to a consumer as set forth in  claim 237 , further comprising a shopping basket for storing an order generated by the consumer, said file submission program being operable to upload the submission file to said shopping basket.  
     
     
         239 . A method in accordance with  claim 226  wherein assays configured to detect presence of genetic material are assays to detect presence of at least one SNP allele.  
     
     
         240 . A method in accordance with  claim 239  wherein providing a user interface configured to receive orders for assays includes providing an providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         241 . A method in accordance with  claim 240  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         242 . A method in accordance with  claim 239 , wherein providing a user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         243 . A method in accordance with  claim 226  wherein assays configured to detect presence of genetic material are assays configured to detect expression of at least one gene.  
     
     
         244 . A method in accordance with  claim 201  wherein said system delivering to a consumer at least one assay further comprises delivering information concerning said assay.  
     
     
         245 . A method in accordance with  claim 244  wherein said system for delivering information concerning said assay comprises delivering at least one datasheet.  
     
     
         246 . A method in accordance with  claim 244  wherein said system for delivering information concerning said assay comprises delivering said information on a machine-readable medium.  
     
     
         247 . A method in accordance with  claim 246  wherein said system for delivering information concerning said assay further comprises a system for delivering at least one datasheet.  
     
     
         248 . A method in accordance with  claim 246  wherein said machine-readable medium is a compact disk.  
     
     
         249 . A method in accordance with  claim 201  wherein said system for delivering to the consumer at least one custom or stock assay comprises a system for delivering the at least one custom or stock assay in a single tube.  
     
     
         250 . A method in accordance with  claim 249  wherein the at least one custom or stock assay in a single tube comprises at least one probe and two primers.  
     
     
         251 . A method in accordance with  claim 250  wherein the at least one custom or stock assay in a single tube is a SNP assay comprising a probe for each of two alleles and two primers.  
     
     
         252 . A method in accordance with  claim 250  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         253 . A method in accordance with  claim 252  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         254 . A method in accordance with  claim 252  wherein the probe further comprises at least one minor groove binder.  
     
     
         255 . A method in accordance with  claim 250  wherein said delivering to the consumer at least one custom or stock assay in a single tube further comprises delivering at least one custom assay in a single tube and PCR reagents.  
     
     
         256 . A method in accordance with  claim 255  wherein said delivering to the consumer at least one custom or stock assay in response to an order for said one custom or stock assay placed by the consumer further comprises delivering to the consumer one custom or stock assay in a single tube and universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         257 . A method in accordance with  claim 249  wherein the single tube further comprises a bar code identifier.  
     
     
         258 . A method in accordance with  claim 257  wherein the bar code is a two-dimension bar code.  
     
     
         259 . A method in accordance with  claim 249  wherein the single tube further comprises an identifier which is a human-readable Assay number.  
     
     
         260 . A method in accordance with  claim 201  further comprising providing a facility for manufacturing assays.  
     
     
         261 . A method in accordance with  claim 260  further comprising providing a system for performing pre-processing selection, a system for designing primers and probes, and a system for performing in silico quality control prior to said manufacturing.  
     
     
         262 . A method in accordance with  claim 261  wherein the assay is a gene expression assay and wherein each said user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         263 . A method in accordance with  claim 262  wherein said performing pre-processing selection comprises identifying optimal sequence regions which do not contain any single nucleotide polymorphisms or repeat sequences.  
     
     
         264 . A method in accordance with  claim 263  wherein identifying optimal sequence regions comprises utilizing at least one method selected from the group consisting of masking single nucleotide polymorphisms and repeat sequences in the at least one expressed transcript or portion thereof to avoid designing probes and primers thereon, mapping the at least one expressed transcript or portion thereof against at least two genomic databases to identify discrepancies to avoid designing probes and primers thereon, identifying exon-exon boundaries for expressed transcripts of multi-exon genes in order to design probes or primers thereon and combinations thereof.  
     
     
         265 . A method in accordance with  claim 264  wherein identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         266 . A method in accordance with  claim 264  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding inclusion of single nucleotide polymorphisms or repeat sequences in probe and primer sequences, avoiding inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, constructing either or both of probes and primers on exon-exon boundaries for multi-exon genes and combinations thereof.  
     
     
         267 . A method in accordance with  claim 262  wherein said system for designing probes and primers utilizes specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         268 . A method in accordance with  claim 261  wherein said system for performing in silico quality control comprises a system for determining quality of designed probes and primers utilizing scoring methods selected from the group consisting of transcript BLAST scoring, genome BLAST scoring, scoring the size of intron across which a probe spans for multi-exon genes, and combinations thereof.  
     
     
         269 . A method in accordance with  claim 261  further comprising providing a system for manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         270 . A method in accordance with  claim 269  wherein said pre-selected scoring criteria comprises assigning high transcript BLAST scoring for matching to self and no other transcript, assigning high genome BLAST scoring for matching to self and no other genome region and assigning high scoring for intron size greater than 10 kilobases and wherein a high assay design scoring is assigned for designed assays scoring all three of high transcript BLAST scoring, high genome BLAST scoring and high intron size scoring.  
     
     
         271 . A method in accordance with  claim 261  wherein the assay is a SNP assay and wherein each said user interface configured to receive orders for assays is configured to receive, from the consumer, criteria relating to at least one gene region containing at least one SNP.  
     
     
         272 . A method in accordance with  claim 271  wherein said system for performing pre-processing selection comprises a component for identifying optimal sequence regions which contain neither repeat sequences not any SNPs other than a SNP for which the assay is designed.  
     
     
         273 . A method in accordance with  claim 272  wherein said component for identifying optimal sequence regions comprises using one or more methods selected from the group consisting of a component for masking any SNPs other than the at least one SNP for which the assay is to be designed and repeat sequences in the at least one gene region to avoid constructing probes and primers thereon, a component for mapping the at least one SNP against at least two genomic databases to identify discrepancies to avoid constructing probes and primers thereon, and combinations thereof.  
     
     
         274 . A method in accordance with  claim 273  wherein said component for identifying optimal sequence regions comprises a component for masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         275 . A method in accordance with  claim 273  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of any SNPs other than the at least one SNP for which the assay is to be designed, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, and combinations thereof.  
     
     
         276 . A method in accordance with  claim 270  wherein the system for designing probes and primers comprises a system for utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         277 . A method in accordance with  claim 271  wherein said system for performing in silico quality control comprises a system for determining the probes and primers by genome BLAST scoring.  
     
     
         278 . A method in accordance with  claim 277  further comprising a system for manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         279 . A method in accordance with  claim 278  wherein pre-selected scoring criteria comprises assigning high Genome BLAST scoring for matching to self and no other genome region.  
     
     
         280 . A method in accordance with  claim 260  further comprising quality control testing of the manufactured assays according to pre-selected quality control criteria.  
     
     
         281 . A method in accordance with  claim 280  wherein quality control testing comprises one or more testing procedures selected from the group consisting of synthesis yield testing, analytical quality control testing, functional testing, validation testing and combinations thereof wherein each of the one or more testing procedures is performed according to pre-selected quality control criteria.  
     
     
         282 . A method in accordance with  claim 281  wherein the system for synthesis yield testing comprises a system for testing the manufactured assays using PAGE or HPLC.  
     
     
         283 . A method in accordance with  claim 281  wherein the pre-selected quality control criteria for synthesis yield testing is about 90% (w/w) product yield.  
     
     
         284 . A method in accordance with  claim 283  wherein the pre-selected quality control criteria for synthesis yield testing is about 95% (w/w) product yield.  
     
     
         285 . A method in accordance with  claim 281  wherein analytical quality control testing comprises testing the manufactured assays using mass spectrometry.  
     
     
         286 . A method in accordance with  claim 285  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 5% greater or lesser than calculated mass.  
     
     
         287 . A method in accordance with  claim 286  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 2% greater or lesser than calculated mass.  
     
     
         288 . A method in accordance with  281  wherein the manufactured assays are SNP assays and functional testing comprises performing PCR reactions of manufactured assays against from about 10 to about 20 genomic DNA samples.  
     
     
         289 . A method in accordance with  claim 288  wherein the pre-selected quality control criteria for functional testing comprises detecting presence of both alleles.  
     
     
         290 . A method in accordance with  claim 281  wherein the manufactured assay is a gene expression assay and functional testing comprises performing designed assay RT-PCR.  
     
     
         291 . A method in accordance with  claim 290  wherein the manufactured assay is a multi-exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of genomic DNA.  
     
     
         292 . A method in accordance with  claim 290  wherein the manufactured assay is a single exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of non-transcribed genomic DNA.  
     
     
         293 . A method in accordance with  claim 281  wherein the manufactured assay is a SNP assay and system for validation testing comprises a system for performing designed assay PCR against about 90 human genomic samples.  
     
     
         294 . A method in accordance with  claim 293  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 10%.  
     
     
         295 . A method in accordance with  claim 294  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 15%.  
     
     
         296 . A method in accordance with  claim 281  wherein the manufactured assay is a gene expression and the system for validation testing comprises a system for performing designed assay PCR against a pool of at least about 10 human cDNA samples.  
     
     
         297 . A method in accordance with  claim 296  wherein the human cDNA samples are from different individuals.  
     
     
         298 . A method in accordance with  claim 296  wherein the human cDNA samples are from different cell lines.  
     
     
         299 . A method in accordance with  claim 296  wherein the pre-selected quality control criteria for the system for validation testing comprises a system for detection of amplified transcript at a threshold of less than 35 PCR cycles.  
     
     
         300 . A method in accordance with  claim 259  wherein said manufacturing comprises high-throughput manufacturing.  
     
     
         301 . A kit comprising: 
 one or more assays for detecting presence or expression of genomic material, wherein at least one assay is in a single tube and wherein the at least one assay in a single tube comprises at least one probe, a forward primer and a reverse primer.    
     
     
         302 . A kit in accordance with  claim 301  further comprising an information source comprising at least one member of the group consisting of an E-datasheet, an assay information file, at least one printed datasheet and combinations thereof.  
     
     
         303 . A kit in accordance with  claim 301  wherein the assay is a SNP assay.  
     
     
         304 . A kit in accordance with  claim 301  wherein the assay is gene expression assay.  
     
     
         305 . A kit in accordance with  claim 303  wherein the assay is a SNP assay comprising one probe for each of two alleles and two primers.  
     
     
         306 . A kit in accordance with  claim 305  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         307 . A kit in accordance with  claim 306  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         308 . A kit in accordance with  claim 307  wherein the probe further comprises at least one minor groove binder.  
     
     
         309 . A kit in accordance with  claim 301  further comprising PCR reagents or RT-PCR reagents.  
     
     
         310 . A kit in accordance with  claim 301  further comprising universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         311 . A kit in accordance with  claim 301  wherein the single tube further comprises a bar code identifier.  
     
     
         312 . A kit in accordance with  claim 311  wherein the bar code identifier is a two dimensional bar code identifier.  
     
     
         313 . A kit in accordance with  claim 301  wherein the single tube further comprises a human-readable assay number.  
     
     
         314 . A kit in accordance with  claim 301  wherein the kit comprises a plurality of assays each of which is in a single tube to constitute a plurality of tubes.  
     
     
         315 . A kit in accordance with  claim 314  further comprising a rack configured to hold said plurality of tubes.  
     
     
         316 . A kit in accordance with  claim 315  wherein the rack has a bar-code identification.  
     
     
         317 . A kit in accordance with  claim 301  which comprises at least one printed datasheet containing information on the assay.  
     
     
         318 . A kit in accordance with  claim 301  which comprises at least one machine readable medium containing information on the assay.  
     
     
         319 . A kit in accordance with  claim 318  which comprises at least one datasheet containing information on the assay.  
     
     
         320 . A kit in accordance with  claim 318  wherein the machine readable medium is a compact disk.  
     
     
         321 . A method for building a submission file useful for designing and ordering at least one of SNP genotyping assays and gene expression assays, said assays comprising at least one probe, a forward primer and a reverse primer, said method comprising: 
 providing a graphical user interface configured to receive, from a consumer, information relating to assay design said information comprising information related to at least one target sequence, wherein said information does not include information selected from the group consisting of sequence of the at least one probe, sequence of the forward primer, sequence of the reverse primer and combinations thereof.    
     
     
         322 . A method in accordance with  claim 321  further comprising: 
 electronically validating at least a portion of the information relating to the at least one target sequence and generating validating information related to said validating; and  
 saving the information relating to the at least one target sequence and the validating information in a submission file.  
 
     
     
         323 . A method in accordance with  claim 322 , further comprising uploading the saved submission file to a web-based assay ordering system.  
     
     
         324 . A method in accordance with  claim 323  wherein said electronic validating comprises detecting typographical errors in a target sequence.  
     
     
         325 . A method in accordance with  claim 322 , further comprising prompting the consumer to correct detected typographical errors in the target sequence when such errors are present.  
     
     
         326 . A method in accordance with  claim 322  further comprising generating an error log providing information related to whether the target sequence is properly formatted.  
     
     
         327 . A system for recommending genomic products and services to a consumer, the products and services being used to detect presence or expression of genetic material in a biological sample, the system comprising: 
 a first source of information regarding at least one of presence and expression of genetic material in biological samples;    a second source of information regarding products and services for analyzing genetic material; and    an interface system communicating with said first source of information and said second source of information and operable to recommend to the consumer certain products and services in response to inquires to said first source of information by the consumer.    
     
     
         328 . A system in accordance with  claim 327  further comprising a web-based interface configured to provide access to the first source of information by the consumer.  
     
     
         329 . A system in accordance with  claim 327  wherein the first source of information includes information regarding at least one SNP.  
     
     
         330 . A system in accordance with  claim 329  wherein the first source of information further comprises information regarding identity of the at least one SNP.  
     
     
         331 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of at least one bi-allelic SNP.  
     
     
         332 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of at least one bi-allelic SNP located in a gene region.  
     
     
         333 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of each of a group of at least about 40,000 bi-allelic SNPs locate in gene regions.  
     
     
         334 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of each of a group of about 40,000 bi-allelic SNPS located in gene regions and spaced apart by about 10 kilobases within the gene regions.  
     
     
         335 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of at least about 40,000 bi-allelic SNPs having a minor allele frequency of at least about 10%.  
     
     
         336 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding a population within which the at least about 40,000 bi-allelic SNP have a minor allele frequency of at least 10%.  
     
     
         337 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding the identity of at least about 40,000 bi-allelic SNPs having a minor allele frequency of at least about 15%.  
     
     
         338 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding identity of each of a group of at least about 100,000 bi-allelic SNPs locate in gene regions.  
     
     
         339 . A system in accordance with  claim 338  wherein the first source of information further comprises information regarding identity of each of a group of at least about 100,000 bi-allelic SNPS located in gene regions and spaced apart by about 10 kilobases within the gene regions.  
     
     
         340 . A system in accordance with  claim 338  wherein the first source of information further comprises information regarding the identity of each of at least about 100,000 bi-allelic SNPs having a minor allele frequency of at least 10%.  
     
     
         341 . A system in accordance with  claim 340  wherein the first source of information further comprises information regarding a population within which the at least about 100,000 bi-allelic SNP have a minor allele frequency of at least 10%.  
     
     
         342 . A system in accordance with  claim 337  wherein the first source of information further comprises information regarding a population within which the at least about 40,000 bi-allelic SNP have a minor allele frequency of at least 15%.  
     
     
         343 . A system in accordance with  claim 327  wherein the first source of information further comprises information regarding at least one expressed gene.  
     
     
         344 . A system in accordance with  claim 343  wherein the first source of information further comprises information regarding identity of the at least one expressed gene.  
     
     
         345 . A system in accordance with  claim 344  wherein the information regarding the identity of at least one expressed gene one gene comprises information regarding the identity of each of a group of at least about 10,000 expressed genes.  
     
     
         346 . A system in accordance with  claim 344  wherein the first source of information further comprises information regarding exons and introns of the at least one expressed gene.  
     
     
         347 . A system in accordance with  claim 344  wherein the first source of information further comprises information regarding intron-exon junction.  
     
     
         348 . A system in accordance with  claim 347  wherein the first source of information further comprises information regarding intron length at the intron-exon junction.  
     
     
         349 . A system in accordance with  claim 327  further comprises a web-based interface configured to provide access to the first source of information by the consumer.  
     
     
         350 . A system in accordance with  claim 327  wherein the second source of information further comprises information regarding SNP assays.  
     
     
         351 . A system in accordance with  claim 327  wherein the second source of information further comprises information regarding instruments for performing PCR or RT-PCR reactions.  
     
     
         352 . A system in accordance with  claim 327  wherein the second source of information further comprises information regarding laboratory information management systems.  
     
     
         353 . A system in accordance with  claim 352  wherein the information regarding laboratory information management systems further comprises in-formation regarding devices configured for use in a laboratory information management system.  
     
     
         354 . A method for providing to a consumer, assays configured to detect presence or expression of genetic material, said method comprising: 
 providing a web-based user interface configured to receive a request for design of one or more custom assays and an order for said custom assays; and    delivering to the consumer at least one custom assay in a single tube in response to an order for said at least one custom assay placed by the, consumer, wherein said assay comprises at least one probe, a forward primer and a reverse primer.    
     
     
         355 . A method in accordance with  claim 354 , further comprising providing a web-based gene exploration platform configured to assist a consumer in selecting a custom assay.  
     
     
         356 . A method in accordance with  claim 355  wherein said information comprises genomic and biomedical information from at least one public or private source.  
     
     
         357 . A method in accordance with  claim 354 , wherein providing a user interface configured to receive a request for design of one or more custom assays and an order for said custom assays comprises providing a graphical user interface configured to receive a request for design of one or more custom assays and an order for said custom assays.  
     
     
         358 . A method in accordance with  claim 354 , wherein said user interface configured to receive orders for custom assays includes a file-receiving interface configured to receive, from the consumer, a submission file containing information suitable for use in designing at least one of said custom assays.  
     
     
         359 . A method in accordance with  claim 358 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to the target of the custom assay requested by the consumer.  
     
     
         360 . A method in accordance with  claim 359 , wherein said file-receiving interface is configured to receive from the consumer a submission file containing sequence information relating to target coordinates of the custom assay requested by the consumer.  
     
     
         361 . A method in accordance with  claim 358 , wherein said file receiving interface is configured to receive from the consumer a submission file containing information relating to the identity of the consumer requesting a custom assay.  
     
     
         362 . A method in accordance  claim 358 , further comprising providing a submission file builder configured to assist the consumer in preparing said submission file for ordering custom assays.  
     
     
         363 . A method in accordance  claim 362  wherein the file builder provides for electronically validating at least a portion of the submission file.  
     
     
         364 . A method in accordance with  claim 363 , wherein the electronic validation comprises detecting typographical errors in the submission file.  
     
     
         365 . A method in accordance with  claim 364  further comprising prompting the consumer to correct detected typographical errors in the submission file.  
     
     
         366 . A method in accordance with  claim 363  wherein the electronic validation comprises generating an error log providing information related to whether the submission file is properly formatted.  
     
     
         367 . A method in accordance with 362, wherein the submission file builder includes a sequence checker to verify correctness of at least a portion of the information contained in the submission file.  
     
     
         368 . A method in accordance with  claim 367 , further comprising providing an electronic shopping basket configured to store an order received from the consumer, said file submission program being operable to upload the submission file to said shopping basket.  
     
     
         369 . A method in accordance with  claim 356  wherein the assays configured to detect presence of genetic material are assays to configured to detect presence of at least one SNP allele.  
     
     
         370 . A method in accordance with  claim 369  wherein providing a user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         371 . A method in accordance with  claim 370  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         372 . A method in accordance with  claim 369 , wherein providing a user interface configured to receive orders for assays includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         373 . A method in accordance with  claim 356  wherein assays configured to detect presence of genetic material are assays configured to detect expression of at least one gene.  
     
     
         374 . A method in accordance with  claim 354  wherein said delivering to a consumer at least one assay further comprises delivering information concerning said assay.  
     
     
         375 . A method in accordance with  claim 374  wherein said delivering information concerning said assay comprises delivering at least one datasheet.  
     
     
         376 . A method in accordance with  claim 374  wherein delivering information concerning said assay comprises delivering said information on a machine-readable medium.  
     
     
         377 . A method in accordance with  claim 376  wherein said delivering information concerning said assay further comprises delivering at least one datasheet.  
     
     
         378 . A method in accordance with  claim 376  wherein said machine-readable medium is a compact disk.  
     
     
         379 . A method in accordance with  claim 354  wherein said delivering to the consumer at least one custom assay comprises delivering the at least one custom assay in a single tube.  
     
     
         380 . A method in accordance with  claim 379  wherein said delivering to the consumer at least one custom assay in a single tube comprises delivering to the consumer at least one probe and two primers.  
     
     
         381 . A method in accordance with  claim 380  wherein the custom assay in a single tube is a SNP assay comprising a separate probe for each of two alleles and two primers.  
     
     
         382 . A method in accordance with  claim 380  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         383 . A method in accordance with  claim 382  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         384 . A method in accordance with  claim 382  wherein the probe further comprises at least one minor groove binder.  
     
     
         385 . A method in accordance with  claim 380  wherein said delivering to the consumer at least one custom assay in a single tube further comprises delivering at least one custom assay in a single tube and PCR reagents.  
     
     
         386 . A method in accordance with  claim 380  wherein said delivering to the consumer at least one custom assay in a single tube further comprises delivering to the consumer at least one custom assay in a single tube and a universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         387 . A method in accordance with  claim 379  wherein the single tube further comprises a bar code identifier.  
     
     
         388 . A method in accordance with  claim 387  wherein the bar code is a two-dimension bar code  
     
     
         389 . A method in accordance with  claim 379  wherein the single tube further comprises an identifier which is a human-readable Assay number  
     
     
         390 . A method in accordance with  claim 354  further comprising manufacturing assays.  
     
     
         391 . A method in accordance with  claim 390  further comprising performing pre-processing selection, designing primers and probes, and performing in silico quality control prior to said manufacturing.  
     
     
         392 . A method in accordance with  claim 391  wherein the assay is a gene expression assay and wherein said user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         393 . A method in accordance with  claim 392  wherein said performing pre-processing selection comprises identifying optimal sequence regions which do not contain any single nucleotide polymorphisms or repeat sequences.  
     
     
         394 . A method in accordance with  claim 393  wherein identifying optimal sequence regions comprises utilizing at least one method selected from the group consisting of masking single nucleotide polymorphisms and repeat sequences in the at least one expressed transcript or portion thereof to avoid designing probes and primers thereon, mapping the at least one expressed transcript or portion thereof against at least two genomic databases to identify discrepancies to avoid designing probes and primers thereon, identifying exon-exon boundaries for expressed transcripts of multi-exon genes in order to design probes or primers thereon and combinations thereof.  
     
     
         395 . A method in accordance with  claim 394  wherein identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         396 . A method in accordance with  claim 394  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding inclusion of single nucleotide polymorphisms or repeat sequences in probe and primer sequences, avoiding inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, constructing either or both of probes and primers on exon-exon boundaries for multi-exon genes and combinations thereof.  
     
     
         397 . A method in accordance with  claim 392  wherein said designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         398 . A method in accordance with  claim 391  wherein said performing in silico quality control comprises determining quality of designed probes and primers utilizing scoring methods selected from the group consisting of transcript BLAST scoring, genome BLAST scoring, scoring size of intron across which a probe spans for multi-exon genes, and combinations thereof.  
     
     
         399 . A method in accordance with  claim 391  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         400 . A method in accordance with  claim 399  wherein said pre-selected scoring criteria comprises assigning high transcript BLAST scoring for matching to self and no other transcript, assigning high genome BLAST scoring for matching to self and no other genome region and assigning high scoring for intron size greater than 10 kilobases and wherein a high assay design scoring is assigned for designed assays scoring all three of high transcript BLAST scoring, high genome BLAST scoring and high intron size scoring.  
     
     
         401 . A method in accordance with  claim 391  wherein the assay is a SNP assay and wherein said user interface configured to receive orders for assays is configured to receive, from the consumer, criteria relating to at least one gene region containing at least one SNP.  
     
     
         402 . A method in accordance with  claim 401  wherein said performing pre-processing selection comprises identifying optimal sequence regions which contain neither repeat sequences nor any SNPs other than a SNP for which the assay is designed.  
     
     
         403 . A method in accordance with  claim 402  wherein said identifying optimal sequence regions comprises using one or more methods selected from the group consisting of masking any SNPs other than the at least one SNP for which the assay is to be designed and repeat sequences in the at least one gene region to avoid constructing probes and primers thereon, mapping the at least one SNP against at least two genomic databases to identify discrepancies to avoid constructing probes-and primers thereon, and combinations thereof.  
     
     
         404 . A method in accordance with  claim 403  wherein said identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         405 . A method in accordance with  claim 403  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of any SNPs other than the at least one SNP for which the assay is to be designed, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, and combinations thereof.  
     
     
         406 . A method in accordance with  claim 400  wherein designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         407 . A method in accordance with  claim 401  wherein said performing in silico quality control comprises determining the quality of designed probes and primers by genome BLAST scoring.  
     
     
         408 . A method in accordance with  claim 407  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         409 . A method in accordance with  claim 408  wherein pre-selected scoring criteria comprises assigning high Genome BLAST scoring for matching to self and no other genome region.  
     
     
         410 . A method in accordance with  claim 390  further comprising quality control testing of the manufactured assays according to pre-selected quality control criteria.  
     
     
         411 . A method in accordance with  claim 410  wherein quality control testing comprises one or more tests selected from the group consisting of synthesis yield testing, analytical quality control testing, functional testing, validation testing and combinations thereof, wherein each of the one or more tests is performed according to pre-selected quality control criteria.  
     
     
         412 . A method in accordance with  claim 411  wherein synthesis yield testing comprises testing the manufactured assays using PAGE or HPLC.  
     
     
         413 . A method in accordance with  claim 411  wherein the pre-selected quality control criteria for synthesis yield testing is about 90% (w/w) product yield.  
     
     
         414 . A method in accordance with  claim 413  wherein the pre-selected quality control criteria for synthesis yield testing is about 95% (w/w) product yield.  
     
     
         415 . A method in accordance with  claim 411  wherein analytical quality control testing comprises testing the manufactured assays using mass spectrometry.  
     
     
         416 . A method in accordance with  claim 415  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 5% greater or lesser than calculated mass.  
     
     
         417 . A method in accordance with  claim 416  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 2% greater or lesser than calculated mass.  
     
     
         418 . A method in accordance with  411  wherein the manufactured assays are SNP assays and functional testing comprises performing PCR reactions of manufactured assays against from about 10 to about 20 genomic DNA samples.  
     
     
         419 . A method in accordance with  claim 418  wherein the pre-selected quality control criteria for functional testing comprises detecting presence of both alleles.  
     
     
         420 . A method in accordance with  claim 411  wherein the manufactured assay is a gene expression assay and functional testing comprises performing designed assay RT-PCR.  
     
     
         421 . A method in accordance with  claim 420  wherein the manufactured assay is a multi-exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of genomic DNA.  
     
     
         422 . A method in accordance with  claim 420  wherein the manufactured assay is a single exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of non-transcribed genomic DNA.  
     
     
         423 . A method in accordance with  claim 411  wherein the manufactured assay is a SNP assay and validation testing comprises performing designed assay PCR against about 90 human genomic samples.  
     
     
         424 . A method in accordance with  claim 423  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 10%.  
     
     
         425 . A method in accordance with  claim 424  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 15%.  
     
     
         426 . A method in accordance with  claim 410  wherein the manufactured assay is a gene expression and validation testing comprises performing designed assay PCR against a pool of at least about 10 human cDNA samples.  
     
     
         427 . A method in accordance with  claim 426  wherein the human cDNA samples are from different individuals.  
     
     
         428 . A method in accordance with  claim 426  wherein the human cDNA samples are from different cell lines.  
     
     
         429 . A method in accordance with  claim 426  wherein the pre-selected quality control criteria for validation testing comprises detection of amplified transcript at a threshold of less than 35 PCR cycles.  
     
     
         430 . A method in accordance with  claim 390  wherein said manufacturing comprises high-throughput manufacturing.  
     
     
         431 . A method for providing to a consumer, assays configured to detect presence or expression of genetic material, said method comprising: 
 providing a web-based user interface configured to receive an order one or more stock assays; and    delivering to the consumer at least one stock assay in a single tube in response to an order for said at least one stock assay placed by the consumer wherein said assay comprises at least one probe, a forward primer and a reverse primer.    
     
     
         432 . A method in accordance with  claim 431 , further comprising providing a web-based gene exploration platform configured to provide information to assist a consumer in selecting a stock assay.  
     
     
         433 . A method in accordance with  claim 432  wherein said information is genomic and biomedical information from at least one public or private source.  
     
     
         434 . A method in accordance with  claim 431 , wherein providing a user interface configured to receive an order for stock assays comprises providing a graphical user interface.  
     
     
         435 . A method in accordance with  claim 434 , further comprising providing a graphical user interface configured for the consumer to perform at least one search for at least one information item used to identify genetic material for a stock assay.  
     
     
         436 . A method in accordance with  claim 435 , wherein the at least one information item used to identify the genetic material is a gene identification item selected from the group consisting of gene symbol, gene name, RefSeq accession number, Panther function, Panther process, GO function, GO process, GO identifier, Applied Biosystems identifier, Celera gene identifier (hCG), Celera transcript identifier (hCT), Celera protein identifier (hCP), LocusLink identifier, GenBank nucleotide identifier, GenBank protein identifier, species identifier, chromosome identifier, haplotype identifier, cytoband identifier, RefSeq GI identifier, and combinations thereof.  
     
     
         437 . A method in accordance with  claim 435 , wherein said at least one search comprises a batch search.  
     
     
         438 . A method in accordance with  claim 435 , wherein the at least one information item comprises a gene classification search.  
     
     
         439 . A method in accordance with  claim 438 , wherein the gene classification search comprises a molecular function search.  
     
     
         440 . A method in accordance with  claim 438 , wherein the gene classification search comprises a biological process search.  
     
     
         441 . A method in accordance with  claim 434 , further comprising providing reference information to the consumer concerning genetic material that is detectable by an assay that is ordered by the consumer.  
     
     
         442 . A method in accordance with  claim 441 , wherein the reference information is selected from the group consisting of RefSeq identifier, LocusLink gene name, molecular function, biological process, Celera identification number, gene location, and combinations thereof.  
     
     
         443 . A method in accordance with  claim 434  wherein the graphical user interface is configured to receive an order for at least one SNP assay.  
     
     
         444 . A method in accordance with  claim 443  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 40,000 SNP assays.  
     
     
         445 . A method in accordance with  claim 444  wherein each SNP assay is configured to detect presence of one of at least 40,000 pairs of SNP alleles located in gene regions.  
     
     
         446 . A method in accordance with  claim 445  wherein each of the 40,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         447 . A method in accordance with  claim 443  wherein the graphical user interface is configured to receive an order for at least one SNP assay from a group of at least 100,000 SNP assays.  
     
     
         448 . A method in accordance with  claim 447  wherein each SNP assay is configured to detect presence of one of at least 100,000 pairs of SNP alleles located in gene regions.  
     
     
         449 . A method in accordance with  claim 448  wherein each of the 100,000 pairs of SNP alleles are spaced apart by about 10 kilobases within gene regions.  
     
     
         450 . A method in accordance with  claim 443  wherein providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to at least one gene region containing the at least one SNP.  
     
     
         451 . A method in accordance with  claim 450  wherein the criteria relating to the at least one gene region containing the at least one SNP comprises excluding assays for SNPs located in 10 kilobases at 5′ end and 10 kilobases at 3′ end of the gene region.  
     
     
         452 . A method in accordance with  claim 443 , wherein said providing the graphical user interface includes providing an interface configured to receive, from the consumer, criteria relating to minor allele frequency.  
     
     
         453 . A method in accordance with  claim 434  wherein the graphical user interface is configured to receive an order for at least one gene expression assay.  
     
     
         454 . A method in accordance with  claim 453  wherein the graphical user interface is configured to receive an order for at least one gene expression assay from a group of at least 10,000 gene expression assays.  
     
     
         455 . A method in accordance with  claim 453  wherein said providing a graphical user interface for ordering assays includes providing an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         456 . A method in accordance with  claim 431  wherein said delivering to a consumer at least one assay further comprises delivering information concerning said assay.  
     
     
         457 . A method in accordance with  claim 456  wherein said delivering information concerning said assay comprises delivering at least one datasheet.  
     
     
         458 . A method in accordance with  claim 456  wherein delivering information concerning said assay comprises delivering said information on a machine-readable medium.  
     
     
         459 . A method in accordance with  claim 458  wherein said delivering information concerning said assay further comprises delivering at least one datasheet.  
     
     
         460 . A method in accordance with  claim 458  wherein said machine-readable medium is a compact disk.  
     
     
         461 . A method in accordance with  claim 431  wherein said delivering to the consumer at least one stock assay comprises delivering the at least one stock assay in a single tube.  
     
     
         462 . A method in accordance with  claim 461  wherein said delivering to the consumer at least one stock assay in a single tube comprises delivering to the consumer at least one probe and two primers.  
     
     
         463 . A method in accordance with  claim 462  wherein the at least one custom or stock assay in a single tube is a SNP assay comprising a separate probe for each of two alleles and two primers.  
     
     
         464 . A method in accordance with  claim 462  wherein the probe comprises at least one fluorophore and at least one fluorescence quencher.  
     
     
         465 . A method in accordance with  claim 464  wherein the fluorescence quencher is a non-fluorescent fluorescence quencher.  
     
     
         466 . A method in accordance with  claim 464  wherein the probe further comprises at least one minor groove binder.  
     
     
         467 . A method in accordance with  claim 462  wherein said delivering to the consumer at least one stock assay in a single tube further comprises delivering at least one stock assay in a single tube and PCR reagents.  
     
     
         468 . A method in accordance with  claim 462  wherein said delivering to the consumer at least one stock assay in a single tube further comprises delivering to the consumer at least one stock assay in a single tube and a universal master mix, said universal master mix comprising at least one salt, a buffer, and a DNA polymerase.  
     
     
         469 . A method in accordance with  claim 461  wherein the single tube further comprises a bar code identifier.  
     
     
         470 . A method in accordance with  claim 469  wherein the bar code is a two-dimension bar code  
     
     
         471 . A method in accordance with  claim 461  wherein the single tube further comprises an identifier which is a human-readable Assay number  
     
     
         472 . A method in accordance with  claim 431  further comprising manufacturing assays.  
     
     
         473 . A method in accordance with  claim 472  further comprising performing pre-processing selection, designing primers and probes, and performing in silico quality control prior to said manufacturing.  
     
     
         474 . A method in accordance with  claim 473  wherein the assay is a gene expression assay and wherein each said user interface configured to receive orders for assays includes an interface configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.  
     
     
         475 . A method in accordance with  claim 474  wherein said performing pre-processing selection comprises identifying optimal sequence regions which do not contain any single nucleotide polymorphisms or repeat sequences.  
     
     
         476 . A method in accordance with  claim 475  wherein identifying optimal sequence regions comprises utilizing at least one method selected from the group consisting of masking single nucleotide polymorphisms and repeat sequences in the at least one expressed transcript or portion thereof to avoid designing probes and primers thereon, mapping the at least one expressed transcript or portion thereof against at least two genomic databases to identify discrepancies to avoid designing probes and primers thereon, identifying exon-exon boundaries for expressed transcripts of multi-exon genes in order to design probes or primers thereon and combinations thereof.  
     
     
         477 . A method in accordance with  claim 476  wherein identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         478 . A method in accordance with  claim 476  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding inclusion of single nucleotide polymorphisms or repeat sequences in probe and primer sequences, avoiding inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, constructing either or both of probes and primers on exon-exon boundaries for multi-exon genes and combinations thereof.  
     
     
         479 . A method in accordance with  claim 474  wherein designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         480 . A method in accordance with  claim 473  wherein said performing in silico quality control comprises determining the quality of designed probes and primers utilizing scoring methods selected from the group consisting of transcript BLAST scoring, genome BLAST scoring, scoring the size of intron across which a probe spans for multi-exon genes and combinations thereof.  
     
     
         481 . A method in accordance with  claim 473  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         482 . A method in accordance with  claim 481  wherein said pre-selected scoring criteria comprises assigning high transcript BLAST scoring for matching to self and no other transcript, assigning high genome BLAST scoring for matching to self and no other genome region and assigning high scoring for intron size greater than 10 kilobases and wherein a high assay design scoring is assigned for designed assays scoring all three of high transcript BLAST scoring, high genome BLAST scoring and high intron size scoring.  
     
     
         483 . A method in accordance with  claim 473  wherein the assay is a SNP assay and wherein each said user interface configured to receive orders for assays is configured to receive, from the consumer, criteria relating to at least one gene region containing at least one SNP.  
     
     
         484 . A method in accordance with  claim 483  wherein said performing pre-processing selection comprises identifying optimal sequence regions which contain neither repeat sequences nor any SNPs other than a SNP for which the assay is designed.  
     
     
         485 . A method in accordance with  claim 484  wherein said identifying optimal sequence regions comprises using one or more methods selected from the group consisting of masking any SNPs other than the at least one SNP for which the assay is to be designed and repeat sequences in the at least one gene region to avoid constructing probes and primers thereon, mapping the at least one SNP against at least two genomic databases to identify discrepancies to avoid constructing probes and primers thereon, and combinations thereof.  
     
     
         486 . A method in accordance with  claim 485  wherein said identifying optimal sequence regions comprises masking repeat sequences selected from the group consisting of di-nucleotide repeats, tri-nucleotide repeats, Alu restriction site repeats, long interspersed nuclear elements, and short interspersed nuclear elements.  
     
     
         487 . A method in accordance with  claim 485  wherein said probes and primers are designed in accordance with criteria selected from the group consisting of avoiding the inclusion of any SNPs other than the at least one SNP for which the assay is to be designed, avoiding the inclusion of regions of discrepancy between at least two genomic databases in probe and primer sequence, and combinations thereof.  
     
     
         488 . A method in accordance with  claim 482  wherein designing probes and primers comprises utilizing specifications selected from the group consisting of T m , GC content, buffer and salt conditions, oligonucleotide concentration in assay, low secondary structure of oligonucleotide, amplicon size and low incidence of primer-dimer formation.  
     
     
         489 . A method in accordance with  claim 482  wherein said performing in silico quality control comprises determining the quality of designed probes and primers by genome BLAST scoring.  
     
     
         490 . A method in accordance with  claim 489  further comprising manufacturing designed probes and primers having pre-selected scoring criteria.  
     
     
         491 . A method in accordance with  claim 480  wherein pre-selected scoring criteria comprises assigning high Genome BLAST scoring for matching to self and no other genome region.  
     
     
         492 . A method in accordance with  claim 472  further comprising quality control testing of the manufactured assays according to pre-selected quality control criteria.  
     
     
         493 . A method in accordance with  claim 492  wherein quality control testing comprises one or more testing procedures selected from the group consisting of synthesis yield testing, analytical quality control testing, functional testing, validation testing and combinations thereof, wherein each of the one or more testing procedures is performed according to pre-selected quality control criteria.  
     
     
         494 . A method in accordance with  claim 493  wherein synthesis yield testing comprises testing the manufactured assays using PAGE or HPLC.  
     
     
         495 . A method in accordance with  claim 493  wherein the pre-selected quality control criteria for synthesis yield testing is about 90% (w/w) product yield.  
     
     
         496 . A method in accordance with  claim 495  wherein the pre-selected quality control criteria for synthesis yield testing is about 95% (w/w) product yield.  
     
     
         497 . A method in accordance with  claim 493  wherein analytical quality control testing comprises testing the manufactured assays using mass spectrometry.  
     
     
         498 . A method in accordance with  claim 497  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 5% greater or lesser than calculated mass.  
     
     
         499 . A method in accordance with  claim 498  wherein the pre-selected quality control criteria for synthesis yield testing is such that determined mass is not more than 2% greater or lesser than calculated mass.  
     
     
         500 . A method in accordance with  493  wherein the manufactured assays are SNP assays and functional testing comprises performing PCR reactions of manufactured assays against from about 10 to about 20 genomic DNA samples.  
     
     
         501 . A method in accordance with  claim 500  wherein the pre-selected quality control criteria for functional testing comprises detecting presence of both alleles.  
     
     
         502 . A method in accordance with  claim 493  wherein the manufactured assay is a gene expression assay and functional testing comprises performing designed assay RT-PCR.  
     
     
         503 . A method in accordance with  claim 502  wherein the manufactured assay is a multi-exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of genomic DNA.  
     
     
         504 . A method in accordance with  claim 502  wherein manufactured assay is a single exon gene expression assay and the pre-selected quality control criteria for functional testing comprises detectable amplification of transcript in accordance with assay design in absence of detectable amplification of non-transcribed genomic DNA.  
     
     
         505 . A method in accordance with  claim 493  wherein the manufactured assay is a SNP assay and validation testing comprises performing designed assay PCR against about 90 human genomic samples.  
     
     
         506 . A method in accordance with  claim 505  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 10%.  
     
     
         507 . A method in accordance with  claim 506  wherein the pre-selected quality control criteria for validation testing comprises detecting a minor allele frequency of at least 15%.  
     
     
         508 . A method in accordance with  claim 492  wherein the manufactured assay is a gene expression and validation testing comprises performing designed assay PCR against a pool of at least about 10 human cDNA samples.  
     
     
         509 . A method in accordance with  claim 508  wherein the human cDNA samples are from different individuals.  
     
     
         510 . A method in accordance with  claim 508  wherein the human cDNA samples are from different cell lines.  
     
     
         511 . A method in accordance with  claim 508  wherein the pre-selected quality control criteria for validation testing comprises detection of amplified transcript at a threshold of less than 35 PCR cycles.  
     
     
         512 . A method in accordance with  claim 511  wherein said manufacturing comprises high-throughput manufacturing.  
     
     
         513 . A web portal configured to provide: 
 an interface configured to accept orders for one or more stock assays;    an interface configured to accept orders for one or more custom assays;    a gene exploration platform configured to provide information to assist a user in selecting one or both of a stock assay and a custom assay.    
     
     
         514 . A web site in accordance with  claim 513  further configured to provide links between said gene exploration platform and said interface to accept orders for stock assays, and between said gene exploration platform and said interface to accept orders for custom assays.  
     
     
         515 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide access to a set of genomic and biomedical data from at least one public or private source.  
     
     
         516 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a user with at least one member of the set consisting of: computational tools to view and analyze gene structure and function; genome structure maps; proteins classified by at least one of family, function, process, and cellular location; and combinations thereof.  
     
     
         517 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a chromosome map report.  
     
     
         518 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a scaffold report.  
     
     
         519 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a sequence report.  
     
     
         520 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a gene list.  
     
     
         521 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a chromosome map display.  
     
     
         522 . A web site in accordance with  claim 513  wherein said gene exploration platform is further configured to provide a biomolecule report.  
     
     
         523 . A web site in accordance with  claim 522  wherein said biomolecule report contains at least one view selected from the group consisting of a protein view, an mRNA view, and a chromosome view, and combinations thereof.  
     
     
         524 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a human gene mutation database report.  
     
     
         525 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by at least one of searching a genome map or searching a genome assembly.  
     
     
         526 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by searching by a member of the group consisting of gene ID, gene symbol, and RefSeq ID.  
     
     
         527 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by searching by cytogenetic band.  
     
     
         528 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by searching by position on a chromosome.  
     
     
         529 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by searching for STS markers.  
     
     
         530 . A web site in accordance with  claim 513  wherein said gene exploration platform is configured to provide a genome navigation facility whereby a user can navigate a genome by searching for a region between two BACs.