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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes.
F1000Res. 2015; 4:17.F

Abstract

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.

Authors+Show Affiliations

The Donnelly Centre, University of Toronto, Toronto, ON, M5S3E1, Canada.The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G0A4, Canada.The Donnelly Centre, University of Toronto, Toronto, ON, M5S3E1, Canada.Department of Laboratory Medicine and Pathobiology, University of Toronto; Program in Genetics and Genome Biology & Department of Paediatric Laboratory Medicine The Hospital for Sick Children, Toronto, ON, M5G1X8, Canada.The Donnelly Centre, University of Toronto, Toronto, ON, M5S3E1, Canada. Department of Computer Science, University of Toronto, Toronto, ON, M5S3G4, Canada. Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

25901276

Citation

Ammar, Ron, et al. "Long Read Nanopore Sequencing for Detection of HLA and CYP2D6 Variants and Haplotypes." F1000Research, vol. 4, 2015, p. 17.
Ammar R, Paton TA, Torti D, et al. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Res. 2015;4:17.
Ammar, R., Paton, T. A., Torti, D., Shlien, A., & Bader, G. D. (2015). Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. F1000Research, 4, 17. https://doi.org/10.12688/f1000research.6037.2
Ammar R, et al. Long Read Nanopore Sequencing for Detection of HLA and CYP2D6 Variants and Haplotypes. F1000Res. 2015;4:17. PubMed PMID: 25901276.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. AU - Ammar,Ron, AU - Paton,Tara A, AU - Torti,Dax, AU - Shlien,Adam, AU - Bader,Gary D, Y1 - 2015/01/21/ PY - 2015/05/13/accepted PY - 2017/9/8/entrez PY - 2015/1/21/pubmed PY - 2015/1/21/medline KW - DNA KW - haplotype KW - nanopore KW - pharmacogenomics KW - sequencing SP - 17 EP - 17 JF - F1000Research JO - F1000Res VL - 4 N2 - 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. SN - 2046-1402 UR - https://www.unboundmedicine.com/medline/citation/25901276/Long_read_nanopore_sequencing_for_detection_of_HLA_and_CYP2D6_variants_and_haplotypes_ L2 - https://f1000research.com/articles/10.12688/f1000research.6037.2/doi DB - PRIME DP - Unbound Medicine ER -
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