SYSTEM AND METHODS FOR INDEL IDENTIFICATION USING SHORT READ SEQUENCING

• US 20080189049A1
• Filed: 02/05/2008
• Published: 08/07/2008
• Est. Priority Date: 02/05/2007
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: ZHANG, Zheng
• Granted Patent: US 8,165,821 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• 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

Abstract

Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.

Claims

1. A method of nucleic acid sequence analysis, comprising:

receiving nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length;

receiving nucleic acid sequence information comprising at least one reference sequence;

performing a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of;

performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;

performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;

identifying non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations;

and,

outputting the results of the mapping operations.

2. The method of claim 1, wherein the second mapping operation further identifies indels with respect to the reference sequence by determining a difference between an expected intervening sequence length between the non-overlapping pairwise sequences and an observed intervening sequence length between the non-overlapping pairwise sequences.

3. The method of claim 2, wherein the indel comprises an insertion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

4. The method of claim 2, wherein the indel comprises a deletion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

5. The method of claim 1, wherein the non-overlapping sequence information comprises paired read sequence information separated by the intervening sequence whose distance is approximately known.

6. The method of claim 5, wherein each of the paired read sequences has a length of between approximately 10 and 75 bases.

7. The method of claim 5, wherein the intervening sequence has a length of between approximately 2 kilobases and 15 kilobases.

8. A system for nucleic acid sequence analysis, comprising:

a data analysis unit configured to;

receive nucleic acid sequence information for one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length and further configured to receive nucleic acid sequence information for at least one reference sequence;

perform a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of;

performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;

performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;

identify non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations; and

,

a data terminal for displaying the results of the mapping operations generated by the data analysis unit to a user.

9. The system of claim 8, wherein the second mapping operation performed by the data analysis unit further identifies indels with respect to the reference sequence by determining a difference between an expected intervening sequence length between the non-overlapping pairwise sequences and an observed intervening sequence length between the non-overlapping pairwise sequences.

10. The system of claim 9, wherein the indel comprises an insertion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

11. The system of claim 9, wherein the indel comprises a deletion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

12. The system of claim 8, wherein the non-overlapping sequence information comprises paired read sequence information separated by the intervening sequence whose distance is approximately known.

13. The system of claim 12, wherein each of the paired read sequences has a length of between approximately 10 and 75 bases.

14. A computer-readable medium, the computer-readable medium being readable to execute a method of nucleic acid sequence analysis, the method comprising:

receiving nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise non-overlapping pairwise sequences separated by an intervening sequence length;

receiving nucleic acid sequence information comprising at least one reference sequence;

performing a mapping operation for each of the one or more mate pair sequences in which the non-overlapping pairwise sequences are aligned to the at least one reference sequence by the steps of;

performing a first mapping operation aligning the non-overlapping pairwise sequences to the at least one reference sequence with a selected mismatch constraint identifying non-overlapping pairwise sequences for which one of the non-overlapping pairwise sequences align to the at least one reference sequence while satisfying the selected mismatch constraint;

performing a second mapping operation designating a window region of the reference sequence to align the non aligned pairwise sequence with a selected mismatch constraint;

identifying non-overlapping pairwise sequences that are successfully mapped following performing the first and second mapping operations;

and,

outputting the results of the mapping operations.

15. The computer-readable medium of claim 14, wherein the second mapping operation further identifies indels with respect to the reference sequence by determining a difference between an expected intervening sequence length between the non-overlapping pairwise sequences and an observed intervening sequence length between the non-overlapping pairwise sequences.

16. The computer-readable medium of claim 15, wherein the indel comprises an insertion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

17. The computer-readable medium of claim 15, wherein the indel comprises a deletion occurring between the non-overlapping pairwise sequences which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length.

18. The computer-readable medium of claim 14, wherein the non-overlapping sequence information comprises paired read sequence information separated by the intervening sequence whose distance is approximately known.

19. The computer-readable medium of claim 18, wherein each of the paired read sequences has a length of between approximately 10 and 75 bases.

20. The computer-readable medium of claim 19, wherein the intervening sequence has a length of between approximately 2 kilobases and 15 kilobases.