System and methods for indel identification using short read sequencing

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.

1 . (canceled) 
     
     
         2 . The method of  claim 22 , 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 sequences of a mate pair and an observed intervening sequence length between the non-overlapping sequences of a mate pair. 
     
     
         3 . The method of  claim 2 , wherein the indel comprises an insertion occurring between the non-overlapping sequences of a mate pair 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 sequences of a mate pair which accounts for the difference between the expected intervening sequence length and the observed intervening sequence length. 
     
     
         5 . The method of  claim 22 , 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 .- 20 . (canceled) 
     
     
         21 . A method of nucleic acid sequence analysis, comprising:
 sequencing a first locality from a plurality of nucleic acid fragments to generate first non-overlapping sequences of a plurality of mate pair sequences;   sequencing a second locality from the nucleic acid fragments to generate second non-overlapping sequences of the mate pair sequences, the first and second locality of a nucleic acid fragment corresponds to a first region of a genome and a second region of a genome, the first and second regions separated by an intervening region whose length is within a known range;   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.   
     
     
         22 . A method for nucleic acid sequence analysis, comprising:
 sequencing a first locality and a second locality from at least one nucleic acid fragment to generate first and second non-overlapping sequences, the first locality corresponding to a first region of a genome and the second locality corresponding to a second region of a genome, the first and second regions separated by an intervening region;   receiving a reference nucleic acid sequence information comprising at least one reference sequence;   performing a first mapping operation using a processor to at least partially align the first non-overlapping sequence to the reference nucleic acid sequence,   designating a window region comprising at least a portion of the at least one reference sequence based at least in part upon the alignment of the first non-overlapping sequence to the at least one reference sequence,   performing a second mapping operation using a processor to at least partially align the second non-overlapping sequence to the designated window region of the reference sequence thereby positioning the first and second non-overlapping sequences with respect to one another, and   outputting the results of the mapping operations.   
     
     
         23 . A method for nucleic acid sequence analysis, comprising:
 sequencing at least a portion of a plurality nucleic acid fragments to generate a plurality of sequence reads;   receiving a reference nucleic acid sequence information comprising at least one reference sequence;   mapping the plurality of sequence reads using a processor to at least partially align the sequence reads to the reference nucleic acid sequence;   identifying a first sequence read that partially maps to a first portion of the reference nucleic acid sequence and second sequence read that partially maps to a second portion of the reference nucleic acid sequence;   traversing a shortest path along overlapping sequence reads using a processor to determine a sequence of an indel between the first portion of the reference nucleic acid sequence and the second portion of the reference nucleic acid sequence; and   outputting the sequence of the indel.   
     
     
         24 . The method of  claim 23 , further comprising identifying overlapping sequence reads comprising a sequence read that partially overlaps with the first sequence read and sequence read that overlaps the second sequence read. 
     
     
         25 . The method of  claim 23 , wherein overlapping reads are determined by a match of a minimum number of bases of an overlap region between reads.