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.

1 .- 19 . (canceled) 
     
     
         20 . A system for producing for a consumer an assay configured to detect a presence or an expression of genetic material, the system comprising:
 a computer system configured to:
 cause a display of a web-based user interface configured to receive an input of a request for design of a custom assay kit comprising a primer having a primer sequence, 
 generate a submission file comprising the request, and 
 generate a design of the custom assay kit including the custom primer based on the submission file and in accordance with criteria selected from one or more of:
 avoiding inclusion of one or both of a single nucleotide polymorphism or a repeat in the primer sequence, 
 avoiding inclusion of a region of discrepancy between at least two genomic databases in the primer sequence, and 
 including the primer sequence on an exon-exon boundary of a multi-exon gene; and 
 
 a system for manufacturing the custom assay kit including the primer according to the design generated. 
   
     
     
         21 . The system of  claim 20 , wherein the computer system is further configured to
 output a gene exploration platform configured to provide to the consumer a comparison of information relating to the custom assay kit to information relating to one or more stock assay kits.   
     
     
         22 . The system of  claim 21 , wherein the gene exploration platform is further configured to provide the consumer with at least one of a computational tool to view and analyze gene structure and function, a genome structure map; and a protein classified by at least one of a family, a function, a process, and a cellular location. 
     
     
         23 . The system of  claim 21 , wherein the gene exploration platform is further configured to provide the consumer with at least one of a chromosome map report, a scaffold report, a sequence report, a gene list, a chromosome map display, a biomolecule report, and a human gene mutation database report. 
     
     
         24 . The system of  claim 21 , wherein the gene exploration platform is further configured to provide a genome navigation facility whereby the consumer can navigate a genome by at least one of searching a genome map and searching a genome assembly. 
     
     
         25 . The system of  claim 21 , wherein the gene exploration platform is further configured to provide a genome navigation facility whereby the consumer can navigate a genome by searching by a gene ID, a gene symbol, and a RefSeq ID. 
     
     
         26 . The system of  claim 21 , wherein the gene exploration platform is further configured to provide a genome navigation facility whereby the consumer can navigate a genome by searching by at least one of a cytogenetic band, by a position on a chromosome, for a STS marker, and for a region between two BACs. 
     
     
         27 . The system of  claim 20 , wherein the computer system is further configured to perform in silico quality control prior to manufacture of the custom assay, the custom assay is a gene expression assay, and the web-based user interface is further configured to receive, from the consumer, relating to at least one expressed transcript or portion thereof. 
     
     
         28 . The system of  claim 20 , wherein the custom assay kit further includes a probe comprising a probe sequence. 
     
     
         29 . The system of  claim 20 , wherein:
 the web-based user interface is further configured to receive input of a target nucleic acid sequence to be analyzed using the assay, and   the computer systems if further configured to generate the design of the custom assay kit based on input of the target nucleic acid sequence input.   
     
     
         30 . The system of  claim 20 , wherein the custom assay kit is configured to be used in a polymerase chain reaction assay. 
     
     
         31 . The system of  claim 20 , wherein the custom assay kit is configured to be used in a gene expression assay. 
     
     
         32 . A method for producing a custom assay kit comprising a custom primer, the custom assay kit configured to detect a presence or an expression of genetic material, the method comprising:
 causing a display of a web-based user interface configured to receive from a consumer an input of a request for design of a custom assay comprising a primer having a primer sequence;   generating a submission file based on the request;   designing the custom assay kit, including the primer, based on the submission file and in accordance with criteria selected from one or more of:
 avoiding inclusion of a single nucleotide polymorphism or a repeat sequence in the primer sequence, 
 avoiding inclusion of a region of discrepancy between at least two genomic databases in the primer sequence, and 
 including the primer sequence on an exon-exon boundary of a multi-exon gene; and 
   manufacturing the custom assay kit comprising the primer based on the designing.   
     
     
         33 . The method of  claim 32 , further comprising performing in silico quality control prior to the manufacturing, wherein the custom assay is a gene expression assay and the web-based user interface is further configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof. 
     
     
         34 . The method of  claim 32 , wherein the designing further comprises utilizing specifications comprising at least one of T m , GC content, buffer and salt conditions, oligonucleotide concentration, low oligonucleotide secondary structure, amplicon size, and low incidence of primer-dimer formation. 
     
     
         35 . The method of  claim 32 , further comprising performing quality control testing of the manufactured custom assay according to pre-selected quality control criteria, wherein the quality control testing comprises at least one of synthesis yield testing, analytical quality control testing, functional testing, and validation testing. 
     
     
         36 . The method of  claim 35 , wherein the synthesis yield testing comprises testing the manufactured custom assay using PAGE or HPLC, and the pre-selected quality control criteria for the synthesis yield testing is about 90% (w/w) product yield. 
     
     
         37 . The method of  claim 35 , wherein the analytical quality control testing comprises testing the manufactured custom assay using mass spectrometry, and 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. 
     
     
         38 . The method of  claim 35 , wherein the manufactured custom assay is a multi-exon gene expression assay, the functional testing comprises performing designed assay RT-PCR, and the pre-selected quality control criteria for the functional testing comprises detectable amplification of a transcript in accordance with assay design in absence of detectable amplification of genomic DNA. 
     
     
         39 . The method of  claim 35 , wherein the manufactured custom assay is a gene expression assay and the validation testing comprises performing designed assay PCR against a pool of at least about 10 human cDNA samples. 
     
     
         40 . The method of  claim 39 , wherein the pre-selected quality control criteria for the validation testing comprises detection of an amplified transcript at a threshold of less than 35 PCR cycles.