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

• US 10,689,692 B2
• Filed: 09/06/2016
• Issued: 06/23/2020
• Est. Priority Date: 01/25/2002
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Koehler, Ryan T., Livak, Kenneth J., Stevens, Junko, De La Vega, Francisco M., Rhodes, Michael, Bellon, Laurent R., Madden, Dawn, Gilbert, Dennis A., Wang, Yu N., Spier, Eugene G., You, Xiaoqing, Xu, Lily, Heil, Jeremy, Winn-Deen, Emily S., McMullen, Ivy, Eddins, Susan, Smith, Leila G.
• Primary Examiner(s): Brusca, John S
• Application Number:
  US15/256,827
• Publication Number:
  US 20170268051A1
• Time in Patent Office: 1,386 Days
• Field of Search: None
• CPC Class Codes: B01L 2300/021 Identification, e.g. bar codes
• CPC Class Codes: B01L 3/545 for laboratory containers
• CPC Class Codes: B01L 3/5453 for test tubes
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2547/101 by confinement to a single tube/container
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 35/00663 of consumables
• CPC Class Codes: G06Q 30/0621 Item configuration or customization
• CPC Class Codes: G06Q 30/0633 Lists, e.g. purchase orders, compilation or processing
• CPC Class Codes: G06Q 30/0641 Shopping interfaces
• CPC Class Codes: G06Q 50/22 Social work or social welfare, e.g. community support activities or counselling services
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 : Ontologies; Annotations
• CPC Class Codes: G16C 20/60 : In silico combinatorial chemistry
• CPC Class Codes: G16H 10/40 : for data related to laboratory analysis, e.g. patient specimen analysis

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.

Claims

1. A system for providing to 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 first web-based user interface configured to receive a first input of a first order for a stock assay,

cause a display of a second web-based user interface configured to receive a second input of a request for design of a custom assay comprising a probe comprising a probe sequence and a primer comprising a primer sequence and a third input for a second order for the custom assay,

generate a submission file comprising the first order, the request, or the second order, or any combination thereof, and

design the custom assay 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 probe sequence and in the primer sequence,

avoiding inclusion of a region of discrepancy between at least two genomic databases in the probe sequence and in the primer sequence, and

including the probe sequence, the primer sequence, or both on an exon-exon boundary of a multi-exon gene;

a system for delivering to the consumer the custom assay manufactured according to the design, the stock assay, or both.

2. The system of claim 1, 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 second web-based user interface is further configured to receive, from the consumer, criteria relating to at least one expressed transcript or portion thereof.

3. The system of claim 1, wherein the computer system is further configured to

output a gene exploration platform configured to provide information to assist the consumer in selecting one or both of the stock assay and the custom assay.

4. The system of claim 3 further configured to provide links between the gene exploration platform and the first web-based user interface, the second web-based user interface, or both.

5. The system of claim 3, 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.

6. The system of claim 3, 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.

7. The system of claim 3, 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.

8. The system of claim 3, 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.

9. The system of claim 3, 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.

10. A method for providing to a consumer, an assay 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 probe comprising a probe sequence and a primer comprising a primer sequence, and configured to receive from the consumer an input of an order for the custom assay;

generating a submission file comprising the request, the order, or both;

designing the custom assay 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 probe sequence and in the primer sequence,

avoiding inclusion of a region of discrepancy between at least two genomic databases in the probe sequence and in the primer sequence, and

including the probe sequence, the primer sequence, or both on an exon-exon boundary of a multi-exon gene;

manufacturing the custom assay from the designing; and

delivering to the consumer the custom assay.

11. The method of claim 10, wherein the manufacturing comprises high-throughput manufacturing.

12. The method of claim 10 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.

13. The method of claim 10, 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.

14. The method of claim 10 further comprising performing quality control testing of the manufactured assays 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.

15. The method of claim 14 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.

16. The method of claim 14, 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.

17. The method of claim 14, wherein the manufactured 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.

18. The method of claim 14 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.

19. The method of claim 18 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.