System and methods for indel identification using short read sequencing
View Patent ↗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.
1. A computer implemented method of nucleic acid sequence analysis, comprising:
receiving first nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise a first non-overlapping pairwise sequence and a second non-overlapping pairwise sequence separated by an intervening sequence length;
receiving second nucleic acid sequence information comprising at least one reference sequence;
performing a computer assisted mapping operation for the mate pair sequences in which the first non-overlapping pairwise sequence and the second non-overlapping pairwise sequence for a respective mate pair are aligned to the at least one reference sequence using a processor by the steps of:
performing a first mapping operation using a processor to align the first non-overlapping pairwise sequence of the mate pair sequences to the at least one reference sequence with a first selected mismatch constraint,
identifying mate pair sequences having first non-overlapping pairwise sequences which are aligned to the at least one reference sequence while satisfying the selected mismatch constraint,
designating a window region within the at least one reference sequence for the identified mate pair sequences based on the alignment of the first non-overlapping pairwise sequence to the at least one reference sequence,
performing a second mapping operation using a processor to align the second non-overlapping pairwise sequence to the window region of the reference sequence with a second selected mismatch constraint,
identifying mate pair sequences with first and second non-overlapping pairwise sequences that have mapped to the at least one reference sequence 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 first nucleic acid sequence information comprises paired read sequence information separated by the intervening sequence whose length is within a known range.
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 component implemented on a computing device configured to:
receive first nucleic acid sequence information for one or more mate pair sequences, wherein mate pair sequences comprise a first non-overlapping pairwise sequence and a second non-overlapping pairwise sequence separated by an intervening sequence length and further configured to receive second nucleic acid sequence information for at least one reference sequence;
perform a mapping operation for the mate pair sequences in which the first non-overlapping pairwise sequence and the second non-overlapping pairwise sequence for a respective mate pair are aligned to the at least one reference sequence by the steps of:
performing a first mapping operation aligning the first non-overlapping pairwise sequence of the mate pair sequences to the at least one reference sequence with a first selected mismatch constraint,
identifying mate pair sequences having first non-overlapping pairwise sequences which are aligned to the at least one reference sequence while satisfying the selected mismatch constraint,
designating a window region within the at least one reference sequence for the identified mate pair sequences based on the alignment of the first non-overlapping pairwise sequence to the at least one reference sequence,
performing a second mapping operation to align the second non-overlapping pairwise sequence to the window region of the reference sequence with a second selected mismatch constraint,
identify mate pair sequences with first and second non-overlapping pairwise sequences that have mapped to the at least one reference sequence 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 component 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 first nucleic acid sequence information comprises paired read sequence information separated by the intervening sequence whose length is within a known range.
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 non-transitory computer-readable medium, the computer-readable medium being readable to execute a method of nucleic acid sequence analysis, the method comprising:
receiving first nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise a first non-overlapping pairwise sequence and a second non-overlapping pairwise sequence separated by an intervening sequence length;
receiving second nucleic acid sequence information comprising at least one reference sequence;
performing a computer assisted mapping operation for the mate pair sequences in which the first non-overlapping pairwise sequence and the second non-overlapping pairwise sequence for a respective mate pair are aligned to the at least one reference sequence by the steps of:
performing a first mapping operation aligning the first non-overlapping pairwise sequence of mate pair sequences to the at least one reference sequence with a first selected mismatch constraint,
identifying mate pair sequences having first non-overlapping pairwise sequences which are aligned to the at least one reference sequence while satisfying the selected mismatch constraint,
designating a window region within the at least one reference sequence for the mate pair sequences based on the alignment of the first non-overlapping pairwise sequence to the at least one reference sequence,
performing a second mapping operation to align the second non-overlapping pairwise sequence to the window region of the reference sequence with a second selected mismatch constraint,
identifying mate pair sequences with first and second non-overlapping pairwise sequences that have mapped to the at least one reference sequence 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 first nucleic acid sequence information comprises paired read sequence information separated by the intervening sequence whose length is within a known range.
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.