Patent ID: 9181583
Filing Date: 2015-11-10
Classification: C12Q,G16B

Abstract:
1. A method of determining haplotypes in a sample comprising: (a) selectively amplifying a nucleic acid molecule from an individual, said nucleic acid molecule comprising (b) carrying out a sequencing read of a first region of the amplified exon pair, said first region comprising at least a portion of said first exon and a portion of the intron adjacent to said first exon; (c) carrying out a sequencing read of a second region of the amplified exon pair, said second region comprising at least a portion of said second exon and a portion of the intron adjacent to said second exon; (d) performing steps (b) and (c) a plurality of times to generate a plurality of paired sequencing reads of said HLA gene, said plurality of paired sequencing reads comprising sequence information from at least two different haplotypes; (e) partitioning each sequencing read into one of two different haplotypes, wherein partitioning comprises computer implemented steps (f)-(i): (f) randomly selecting a first and second paired sequencing read and designating said reads as haplotype 1 and haplotype 2, respectively; (g) assigning each remaining paired sequencing read in said plurality of paired sequencing reads to said haplotype 1 or said haplotype 2 based on sequence similarity to either haplotype 1 or haplotype 2; (h) computing a consensus sequence for haplotype 1 and a consensus sequence for haplotype 2 using the paired sequence reads assigned to each haplotype; and (i) designating said consensus sequences as haplotypes 1 and 2 and repeating steps (g)-(h) until said consensus sequences no longer change; thereby determining haplotypes in said sample.