Methods and systems for determining haplotypes and phasing of haplotypes

Abstract

The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.

1 - 20 . (canceled) 
     
     
         21 . A system for determining one or more haplotypes of a nucleic acid sample, comprising:
 a sequencing instrument that sequences individual fragments of a first modified nucleic acid molecule with a first pattern of synthetic polymorphisms and a second modified nucleic acid molecule with a second pattern of synthetic polymorphisms to generate sequence reads of the first and second modified nucleic acid molecules; and   a processor configured to perform a method comprising:
 receiving the sequence reads of the first and second modified nucleic acid molecules; 
 matching the first pattern of synthetic polymorphisms with the second pattern of synthetic polymorphisms; 
 aligning the first and second modified nucleic acid molecules based on the matched pattern of synthetic polymorphisms; and 
 determining one or more haplotypes of the nucleic acid sample based at least in part on the aligned first and second modified nucleic acid molecules. 
   
     
     
         22 . The system of  claim 21 , wherein the processor is configured to perform a method comprising identifying a phase of the subset of the individual fragments based on the aligned first and second modified nucleic acid molecules. 
     
     
         23 . The system of  claim 21 , wherein the processor is configured to perform a method comprising determining a sequence of the nucleic acid sample. 
     
     
         24 . The system of  claim 21 , wherein the nucleic acid sample comprises one or more naturally-occurring polymorphisms. 
     
     
         25 . The system of  claim 21 , wherein the synthetic polymorphisms comprise single nucleotide polymorphisms. 
     
     
         26 . The system of  claim 25 , wherein the single nucleotide polymorphisms replace native nucleotides at a site of incorporation. 
     
     
         27 . The system of  claim 26 , wherein said plurality of single nucleotide polymorphisms comprises a plurality of modified nucleotides. 
     
     
         28 . The system of  claim 27 , wherein the modified nucleotides are selected from the group consisting of 8-oxoguanine, isocytosine, isoguanine and dPTP. 
     
     
         29 . The system of  claim 21 , wherein the individual fragments comprise several different nucleotide types along the length of the nucleic acid. 
     
     
         30 . The system of  claim 29 , wherein at least two haplotypes are bi-allelic for first and second nucleotide types along the length of a nucleic acid in the nucleic acid sample. 
     
     
         31 . The system of  claim 21 , wherein the sequencing instrument sequences individual fragments by a method selected from the group consisting of: sequencing by synthesis, sequencing by hybridization, sequencing by ligation, single molecule sequencing, nanopore sequencing, pyrosequencing and polymerase chain reaction. 
     
     
         32 . The system of  claim 21 , wherein the processor is configured to perform a method comprising identifying the synthetic polymorphisms. 
     
     
         33 . The system of  claim 32 , wherein the processor is configured to perform a method comprising removing identified synthetic polymorphisms from the sequence. 
     
     
         34 . The system of  claim 21 , wherein the nucleic acid sample comprises tandem repeats. 
     
     
         35 . The system of  claim 21 , wherein the haplotypes are located on different individual fragments of the nucleic acid sample. 
     
     
         36 . The system of  claim 21 , wherein one or more of the individual fragments further comprises an adapter sequence. 
     
     
         37 . The system of  claim 21 , wherein the sequence reads of the first and second modified nucleic acid molecules overlap. 
     
     
         38 . The system of  claim 37 , wherein the overlap comprises a plurality of nucleotides. 
     
     
         39 . The system of  claim 21 , wherein aligning further comprises consensus calling of nucleotides in the nucleic acid molecule. 
     
     
         40 . The system of  claim 24 , wherein the processor is configured to perform a method comprising generating a report of the one or more naturally-occurring polymorphisms.