التفاصيل البيبلوغرافية
| العنوان: |
Custom design method for resequencing arrays |
| Document Number: |
20050032074 |
| تاريخ النشر: |
February 10, 2005 |
| Appl. No: |
10/658879 |
| Application Filed: |
September 09, 2003 |
| مستخلص: |
A method is described that receives user-selected sequence and provides a custom array designed for resequencing the user-selected sequence. The system determines probes corresponding to the sequence and to possible variants of the sequence and generates a custom probe array design. The system then displays the custom probe array design to the user via a graphical user interface and receives a user acceptance of the design. The system provides the user with the accepted custom probe array. The system may also enable a number of users to share space on a custom probe array. Another optional feature is to enable a number of users to share in ordering portions of a lot of catalog probe arrays to take advantage of economies of scale from lot-size purchases. |
| Inventors: |
Shah, Nila A. (Cupertino, CA, US); Warrington, Janet A. (Los Altos, CA, US); Zhou, Xue Mei (San Jose, CA, US); Mittmann, Michael P. (Palo Alto, CA, US); Mei, Rui (Santa Clara, CA, US) |
| Assignees: |
Affymetrix, INC. (Santa Clara, CA, US) |
| Claim: |
1. A computerized method for designing a resequencing array to resequence a user selected sequence comprising: receiving a user design request comprising a user selected sequence; producing an array design for resequencing said user selected sequence; outputting said array design to said user; receiving acceptance for said array design from said user; outputting a file that is useful for controlling a nucleic acid synthesizer during the construction of an array comprising said array design; synthesizing at least one copy of said array; and providing said at least one copy of said array to said user. |
| Claim: |
2. The method of claim 1 wherein said nucleic acid synthesizer is maskless. |
| Claim: |
3. The method of claim 1 wherein said user design request comprises a sequence file. |
| Claim: |
4. The method of claim 1 wherein said user design request is received over the internet. |
| Claim: |
5. The method of claim 1 wherein the array further comprises user selected control probes. |
| Claim: |
6. A method for a provider of nucleic acid arrays to provide a user with an array for resequencing a user selected nucleic acid wherein the method comprises: receiving a sequence computer file from said user wherein the sequence computer file comprises the sequence of the user selected nucleic acid; preparing a design for a resequencing array for the selected sequence; outputting said design into a design computer file; providing said design computer file to said user; receiving approval for said design from said user; outputting an instruction computer file wherein said instruction computer file provides instructions to a nucleic acid synthesizer for synthesis of an array comprising said design; synthesizing said array; and providing said user with said array. |
| Claim: |
7. The method of claim 6 wherein after receiving from said user said sequence computer file the provider analyzes the sequence to remove repetitive sequences. |
| Claim: |
8. The method of claim 6 wherein said provider identifies ambiguous sequence within said user selected nucleic acid sequence by: obtaining analogous sequence from at least one other source; comparing the sequence from said file to said sequence from at least one other source; identifying bases that are different and removes ambiguity by comparing the sequence from two or more sources. |
| Claim: |
9. The method of claim 6 wherein said provider provides said user with computer executable code for identifying ambiguous sequence within a selected sequence and for resolving the ambiguity of the identified ambiguous sequence. |
| Claim: |
10. The method of claim 6 wherein said provider also provides said user with the sequence of primers that may be used to amplify said user selected sequence. |
| Claim: |
11. The method of claim 10 wherein said provider further provides a graphical user interface for said user to order primers with the provided sequence from a third party on the internet. |
| Claim: |
12. The method of claim 6 wherein said user selected sequence is identified by said user in an association study or a linkage study wherein said sequence is associated with a phenotype. |
| Claim: |
13. The method of claim 6 wherein said user first identifies said user selected sequence as being associated with a phenotype using a genotyping array that genotypes more than 10,000 different human polymorphisms. |
| Claim: |
14. The method of claim 6 wherein said sequence computer file is received by the provider over the Internet. |
| Claim: |
15. The method of claim 6 wherein said design computer file is provided to the user over the Internet. |
| Claim: |
16. A method for providing resequencing arrays to a user comprising: using a computer to design one or more resequencing arrays for one or more regions of a genome of interest; providing users with a list of available designs for resequencing arrays; receiving an order from a user for a specific design from said list of available designs wherein said specific design is for an array to resequence a selected sequence; outputting an instruction computer file for said specific design to a nucleic acid synthesizer; synthesizing an array using said instruction computer file; and providing the array or arrays to said user. |
| Claim: |
17. The method of claim 16 further comprising providing primer sequences to the user, wherein said primer sequences may be used to amplify at least one region of said selected sequence. |
| Claim: |
18. The method of claim 16 wherein said genome of interest is the human genome. |
| Claim: |
19. The method of claim 16 wherein said selected sequence comprises at least one complete chromosome. |
| Claim: |
20. The method of claim 16 wherein said list of available designs is provided to said user over the Internet. |
| Current U.S. Class: |
435006/000 |
| رقم الانضمام: |
edspap.20050032074 |
| قاعدة البيانات: |
USPTO Patent Applications |