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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
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Journal Article
Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
2015
Overview
Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information. Phasing short read data typically requires supplemental statistical phasing based on known haplotype structure in the population or parental genotypic data. Here we demonstrate that the MinION nanopore sequencer is capable of producing very long reads to resolve both variants and haplotypes of
HLA-A
,
HLA-B
and
CYP2D6
genes important in determining patient drug response in sample NA12878 of CEPH/UTAH pedigree 1463, without the need for statistical phasing. Long read data from a single 24-hour nanopore sequencing run was used to reconstruct haplotypes, which were confirmed by HapMap data and statistically phased Complete Genomics and Sequenom genotypes. Our results demonstrate that nanopore sequencing is an emerging standalone technology with potential utility in a clinical environment to aid in medical decision-making.
Publisher
F1000Research,F1000 Research Ltd
Subject
