Systems and methods for ordering, performing, and reporting genetic screening

Abstract

The present invention provides computer-implemented systems and methods for ordering, performing, and reporting transgenic and targeted mutagenesis screening of genomic DNA. The methods are performed by a remote user's computer, a web site computer and a laboratory computer. The remote user, in communication with another computer, requests a screening of biological samples that are disposed in a multi-well plate. The remote user designates on his computer a variety of parameters necessary to perform the testing and identifies the location of samples in the multi-well plate. A computer at the laboratory receives this information and uses it to perform testing, and to prepare a sample test report that is returned to the remote user. A computer intermediate to the user's computer and the laboratory computer, such as a web site computer, may be used. The laboratory computer is configured to extract information from the remote user's electronic communication and transmit that information electronically to a supplier to order reagents necessary for the testing.

1 . A method of requesting and receiving a sample outcome report for genomic DNA screening of a plurality of biological samples sent by a remote user to a screening laboratory, the remote user providing screening parameters via an electronic communications link to the screening laboratory, the method comprising: 
 (a) transmitting an access request from a remote user to a screening laboratory via an electronic communications link;    (b) receiving an access enabling response from the screening laboratory by the remote user via an electronic communications link, the access enabling response including the screening parameters;    (c) selecting screening parameters by the remote user to provide selected screening parameter selections;    (d) transmitting the selected screening parameter selections from the remote user to the screening laboratory via an electronic communications link;    (e) transmitting a plurality of biological samples from the remote user to the screening laboratory wherein transmitting a plurality of biological samples involves the step of placing one of each of the plurality of biological samples in a corresponding well of a multi-well plate; and    (f) receiving a sample outcome report for a plurality of biological samples from the screening laboratory by the remote user via an electronic communications link, wherein the electronic communications link is the Internet.    
     
     
         2 . The method of  claim 1  wherein the multi-well plate is a 96 well plate.  
     
     
         3 . The method of  claim 1  further comprising the step of correlating each of the plurality of biological samples with a well of the multi-well plate.  
     
     
         4 . The method of  claim 1  wherein the step of receiving an access enabling response includes a sample identification and designation section.  
     
     
         5 . The method of  claim 4  wherein the sample identification and designation section indicates a well plate having a plurality of wells, each well having an associated well position.  
     
     
         6 . The method of  claim 4 , wherein the sample identification and designation section presents an x-y orientation of a plurality of wells, the orientation defining a plurality of rows and a plurality of columns.  
     
     
         7 . The method of  claim 6 , further comprising the step of designating individual ones of the x-y orientation of a plurality of wells.  
     
     
         8 . The method of  claim 1  wherein the step of receiving an access enabling response includes a survey of work section for entering at least one screening parameter selection.  
     
     
         9 . The method of  claim 1  further comprising the step of designating each of the plurality of biological samples in the multi-well plate.  
     
     
         10 . The method of  claim 1 , further comprising the step of designating a control sample of the plurality of biological samples.  
     
     
         11 . The method of  claim 1 , further comprising the step of designating a plate accession number of the multi-well plate.  
     
     
         12 . The method of  claim 1  further comprising the step of designating which sample of the plurality of biological samples is placed into each well of the multi-well plate.  
     
     
         13 . The method of  claim 1  wherein access request includes an account identifier and a password.  
     
     
         14 . The method of  claim 1  wherein the screening parameter selections include a selectable marker.  
     
     
         15 . The method of  claim 1  wherein the screening parameter selections include data indicative of a number of lines to be tested.  
     
     
         16 . The method of  claim 1  where the screening parameter selections include a probe sequence.  
     
     
         17 . The method of  claim 1  wherein the screening parameter selections include a designated control.  
     
     
         18 . The method of  claim 1  wherein the screening parameter selections include a designated genetic sequence.  
     
     
         19 . The method of  claim 1  wherein the screening parameter selections include a target genetic sequence.  
     
     
         20 . The method of  claim 1  wherein the sample outcome report includes a pictorial representation of screening results.  
     
     
         21 . The method of  claim 17  wherein the sample outcome report identifies the designated control.  
     
     
         22 . The method of  claim 21  wherein the sample outcome report includes a quantitative analysis of each of the plurality of biological samples in comparison to the designated control.  
     
     
         23 . The method of  claim 21  wherein the sample outcome report includes a qualitative analysis of each of the plurality of biological samples in comparison to the designated control.  
     
     
         24 . The method of  claim 1  wherein the sample outcome report includes a well location of each of the plurality of biological samples in the multi-well plate.  
     
     
         25 . The method of  claim 1  wherein the sample outcome report includes a copy number for each of the plurality of biological samples.  
     
     
         26 . The method of  claim 1  wherein the sample outcome report includes an accession number of the well plate.  
     
     
         27 . The method of  claim 1  further comprising the step of electronically showing the remote user a well plate having a plurality of wells, each of the wells having a corresponding well plate location on the multi-well plate.  
     
     
         28 . A computer-implemented method of electronically ordering transgenic or targeted mutagenic screening for a plurality of biological samples by electronic communications between a website and a remote user computer, the method comprising the steps of: 
 (a) transmitting an account identifier and password from the remote user's computer to the website to gain access to the website;    (b) designating at the remote user's computer a plurality of biological samples for transgenic or targeted mutagenic screening;    (c) designating at the remote user's computer the location of the plurality of biological samples in the plurality of wells; and    (d) designating a genetic sequence to be screened for each of the plurality of biological samples.    
     
     
         29 . The method of  claim 28  further comprising the step of showing on the remote user's computer a well plate having a plurality of wells.  
     
     
         30 . The method of  claim 28 , further comprising the step of providing the number of the plurality of biological samples in the plurality of wells in the well plate.  
     
     
         31 . The method of  claim 28 , further comprising the step of designating a control sample.  
     
     
         32 . The method of  claim 31  wherein the step of designating the control sample includes the step of identifying the zygosity of the control sample.  
     
     
         33 . The method of  claim 31  wherein the step of designating the control sample includes the step of identifying a copy number of the control sample.  
     
     
         34 . The method of  claim 31  wherein the step of designating the control sample includes the step of identifying mosaic nature of the control sample.  
     
     
         35 . The method of  claim 28 , further comprising the step of designating a probe sequence complimentary to a portion of the designated genetic sequence.  
     
     
         36 . The method of  claim 28 , further comprising the steps of: 
 (a) transmitting results of the step of designating the location of the plurality of biological samples in the plurality of wells to the website;    (b) transmitting results of the step of designating the genetic sequence of the plurality of biological samples to the website; and    (c) transmitting the corresponding plurality of biological samples in the well plate to the screening laboratory.    
     
     
         37 . The method of  claim 28 , wherein the step of showing includes the step of showing a corresponding row and column identifier for each of the plurality of wells.  
     
     
         38 . A method of screening genomic DNA in a plurality of biological samples, wherein the samples are to be sent by a remote user for ultimate arrival at a screening laboratory, wherein the screening is for a designated genetic sequence, and further wherein the remote user provides screening parameters via the Internet to a screening website, the method comprising: 
 (a) transmitting an access enabling response from the screening website to the remote user via the Internet, the access enabling response including screening parameters;    (b) receiving selected screening parameter selections via the Internet from the remote user;    (c) receiving the plurality of biological samples in a multi-well plate;    (d) conducting screening of the plurality of biological samples according to the selected screening parameters with the reagents to obtain screening results; and    (e) transmitting screening results for the designated genetic sequence to the remote user via the Internet.    
     
     
         39 . The method of step  38  further comprising the step of transmitting a request via the Internet to a supplier to obtain reagents conforming to the screening parameter selections.  
     
     
         40 . The method of  claim 38  wherein the screening parameter selections include a selectable marker.  
     
     
         41 . The method of  claim 38  wherein the plurality of biological samples in a multi-well plate include at least two lines, and further wherein the screening parameter selections include identification of the at least two lines.  
     
     
         42 . The method of  claim 38  wherein the screening parameter selections include a probe sequence.  
     
     
         43 . The method of  claim 38  wherein the screening parameter selections include a designated control.  
     
     
         44 . The method of  claim 43  wherein the designated control is a biological sample having the designated genetic sequence.  
     
     
         45 . The method of  claim 38  wherein the step of conducting screening includes the step of treating the plurality of biological samples with a lysis buffer to obtain cellular debris including genomic DNA.  
     
     
         46 . The method of  claim 45 , wherein the step of conducting screening further includes the step of separating the genomic DNA from the cellular debris of the plurality of biological samples using magnetic particles.  
     
     
         47 . The method of  claim 38  wherein the reagents are labeled probes specific for a portion of the designated genetic sequence.  
     
     
         48 . The method of  claim 38  wherein the request to a supplier is generated to an order manager.  
     
     
         49 . A computer-implemented method of processing an order for transgenic or targeted mutagenesis screening of a plurality of biological samples in a multi-well plate by electronic communications between a website and a remote user's computer, the method comprising the steps of: 
 (a) receiving from the remote user's computer a user account identifier and password;    (b) checking validity of the account identifier and password;    (c) receiving from the remote user a designation of a genetic sequence for screening the plurality of biological samples;    (d) receiving a designation from the remote user's computer of a plurality of biological samples for transgenic or targeted mutagenic screening; and    (e) receiving from the remote user's computer a designation of which of the plurality of biological samples was placed into each well of a multi-well plate.    
     
     
         50 . The method of  claim 49  wherein the designated genetic sequence is selected from the group including SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5.  
     
     
         51 . The method of  claim 49  wherein the designated genetic sequence is a transgenic insert.  
     
     
         52 . The method of  claim 49  wherein the designated genetic sequence is a selectable marker.  
     
     
         53 . The method of  claim 49  wherein the designated genetic sequence is a knock-in.  
     
     
         54 . The method of  claim 49  wherein the designated genetic sequence is a knock-out.  
     
     
         55 . The method of  claim 49  further comprising the step of adding labeled probes specific for reference genetic sequence to the plurality of biological samples.  
     
     
         56 . The method of  claim 49  wherein the reference genetic sequence is selected from the group consisting of: SEQ. ID NO: 6, SEQ. ID NO: 7, SEQ. ID NO: 8, SEQ. ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16.  
     
     
         57 . The method of  claim 49  further comprising the step of receiving selected screening parameter selections via the Internet from the remote user.  
     
     
         58 . The method of  claim 57  wherein the screening parameter selections include a selectable marker.  
     
     
         59 . The method of  claim 57  wherein the screening parameter selections include a designation of a plurality of lines to be tested.  
     
     
         60 . The method of  claim 57  where the screening parameter selections includes a probe sequence.  
     
     
         61 . The method of  claim 57  wherein the screening parameter selections include a designated control.  
     
     
         62 . The method of  claim 49  further comprising the step of receiving a designation of a control sample from the remote user via the Internet.  
     
     
         63 . The method of  claim 62  wherein the step of receiving a designation of a control sample includes the step of receiving an identification of a zygosity of the control sample from the remote user via the Internet.  
     
     
         64 . The method of  claim 62  wherein the step of receiving a designation of a control sample includes the step of receiving an identification of a copy number of the control sample from the remote user via the Internet.  
     
     
         65 . The method of  claim 62  wherein the step of receiving a designation of a control sample includes the step of receiving an identification of a mosaic nature of the control sample from the remote user via the Internet.  
     
     
         66 . The method of  claim 49  further comprising the step of receiving a designation of a probe sequence complimentary to a portion of the designated genetic sequence.  
     
     
         67 . The method of  claim 49  further comprising the step of transmitting screening results to the remote user, wherein the screening results are the result of screening the plurality of biological samples.  
     
     
         68 . The method of  claim 67  wherein the step of transmitting screening results includes the step of transmitting a sample outcome report for the plurality of biological samples to the remote user via the Internet.  
     
     
         69 . The method of  claim 68  wherein the sample outcome report includes a pictorial representation of screening results.  
     
     
         70 . The method of  claim 68  wherein the sample outcome report includes a quantitative analysis of each of the plurality of biological samples in comparison to a designated control.  
     
     
         71 . The method of  claim 68  wherein the sample outcome report includes a qualitative analysis of each of the plurality of biological samples in comparison to a designated control.  
     
     
         72 . The method of  claim 70 , wherein the designated control includes the designated genetic sequence.  
     
     
         73 . The method of  claim 68  wherein the sample outcome report includes an accession number of the well plate.  
     
     
         74 . The method of  claim 68  wherein the sample outcome report includes a well location of each of the plurality of biological samples in the well plate.  
     
     
         75 . The method of  claim 68  wherein the sample outcome report includes a copy number for each of the plurality of biological samples.  
     
     
         76 . The method of  claim 50  wherein the designated genetic sequence is selected from the group consisting of SEQ ID NO: 1; SEQ ID NO: 2; SEQ ID NO: 3; SEQ ID NO: 4; and SEQ ID NO: 5.  
     
     
         77 . The method of  claim 49  further comprising the steps of: 
 reviewing the designated genetic sequence; and    designating a portion of the designated genetic sequence as a target genetic sequence.    
     
     
         78 . The method of  claim 77  further comprising the steps of: 
 transmitting the target genetic sequence to a supplier to create a target-binding probe; and    receiving the target-binding probe from the supplier.    
     
     
         79 . The method of  claim 49  wherein the plurality of biological samples comes from a genetic line.  
     
     
         80 . The method of  claim 49 , wherein the plurality of biological samples comes from a plurality of genetic lines.  
     
     
         81 . A process for screening a plurality of biological samples in a multi-well plate at a screening laboratory, the process comprising the steps of: 
 receiving an electronic communication from a remote user, the communication including screening parameter selections;    entering the screening parameter selections into a laboratory information management system of the screening laboratory;    receiving the multi-well plate at the screening laboratory; and    screening genomic DNA isolated from the plurality of biological samples at the screening laboratory.    
     
     
         82 . The process of  claim 81  wherein the step of receiving an electronic communication from a remote user includes the step of receiving the electronic communication directly from the remote user.  
     
     
         83 . The process of  claim 81  wherein the step of receiving an electronic communication from a remote user includes the step of receiving the electronic communication indirectly from the remote user.  
     
     
         84 . The process of  claim 81  wherein the step of receiving electronic communication from a remote user includes the step of receiving a designation of an electronic accession number of the multi-well plate, and further wherein the step of entering the screening parameter selections includes the step of entering the designated electronic accession number into the laboratory information management system.  
     
     
         85 . The process of  claim 81  wherein the step of receiving the multi-well plate includes the step of electronically scanning an actual accession number on the plate.  
     
     
         86 . The process of  claim 85  wherein the step of electronically scanning includes the step of barcode scanning the actual accession number on the plate.  
     
     
         87 . The process of  claim 86 , wherein the step of barcode scanning the actual accession number includes the step of entering the barcode scanned accession number into the laboratory information management system.  
     
     
         88 . The process of  claim 85  further comprising the step of comparing the actual accession number with the designated accession number previously entered by the remote user when the remote user ordered genetic scanning.  
     
     
         89 . The process of  claim 88  further comprising the step of electronically communicating an arrival of the multi-well plate at the laboratory to the remote user after the step of comparing.  
     
     
         90 . The process of  claim 88  further comprising the steps of posting an arrival of the multi-well plate at the laboratory on a web site after the step of comparing, wherein the remote user has password protected access to the web site.  
     
     
         91 . The process of  claim 88  further comprising the step of the e-mailing the remote user of an arrival of the plurality of biological samples in the multi-well plate at the laboratory after the step of comparing multi-well plate accession numbers.  
     
     
         92 . The process of  claim 81  wherein the step of receiving an electronic communication from a remote user includes the step of receiving the electronic communication from the remote user at the laboratory.  
     
     
         93 . The process of  claim 81  wherein the screening parameter selections include a selectable marker.  
     
     
         94 . The process of  claim 81  wherein the screening parameter selections include identifying the number of lines to be tested.  
     
     
         95 . The process of  claim 81  wherein the screening parameter selections include a designated control.  
     
     
         96 . The process of  claim 81  wherein the screening parameter selections include a designated genetic sequence.  
     
     
         97 . The process of  claim 96  further comprising the step of electronically transmitting the designated genetic sequence to a supplier.  
     
     
         98 . The process of  claim 81  further comprising the steps of: 
 receiving an electronic designation of a control sample from the remote user; and    receiving the control sample at the laboratory.    
     
     
         99 . The process of  claim 98 , wherein the step of receiving the control sample at the laboratory includes the step of receiving the control sample from the remote user.  
     
     
         100 . The process of  claim 98  wherein the step of receiving an electronic designation of a control sample includes the step of receiving an electronic identification of the zygosity of the control sample from the remote user via the Internet.  
     
     
         101 . The process of  claim 98  wherein the step of receiving an electronic designation of a control sample includes the step of receiving an electronic identification of a copy number of the control sample from the remote user via the Internet.  
     
     
         102 . The process of  claim 98  wherein the step of receiving an electronic designation of a control sample includes the step of receiving an electronic identification of a mosaic nature of the control sample from the remote user via the Internet.  
     
     
         103 . The process of  claim 98  further comprising the step of receiving an electronic designation of a probe sequence complimentary to a portion of the designated genetic sequence.  
     
     
         104 . The process of  claim 81  wherein each of the plurality of biological samples is a tissue sample and further wherein each is contained in the corresponding well of a plurality of wells of the multi-well plate, the method further comprising the steps of: 
 adding lysis buffer to each of the plurality of wells containing a tissue sample to lysis the tissue; and    producing cellular debris including genomic DNA mixed with lysis buffer in each of the plurality of wells.    
     
     
         105 . The process of  claim 104  further comprising the step of transferring the genomic DNA from each of the plurality of wells to a corresponding well in a second multi-well plate.  
     
     
         106 . The process of  claim 105  further comprising the step of adding magnetic particles to each corresponding well in the second multi-well plate.