Introduction

The rapid growth of sequencing technologies has greatly contributed to our understanding of human genetics. Yet, despite this growth, mainstream technologies have not been fully able to resolve the diploid nature of the human genome. Here we describe statistically aided, long-read haplotyping (SLRH), a rapid, accurate method that uses a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, as little as 30 Gbp of additional sequencing data are needed to phase genotypes identified by 50× coverage whole-genome sequencing. Using SLRH, we phase 99% of single-nucleotide variants in three human genomes into long haplotype blocks 0.2-1 Mbp in length. We apply our method to determine allele-specific methylation patterns in a human genome and identify hundreds of differentially methylated regions that were previously unknown. SLRH should facilitate population-scale haplotyping of human genomes.

Publications

  1. Whole-genome haplotyping using long reads and statistical methods.
    Cite this
    Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M, 2014-03-01 - Nature biotechnology

Credits

  1. Volodymyr Kuleshov
    Developer

    Illumina, Inc., United States of America

  2. Dan Xie
    Developer

    Department of Genetics, Stanford University School of Medicine, United States of America

  3. Rui Chen
    Developer

    Department of Genetics, Stanford University School of Medicine, United States of America

  4. Dmitry Pushkarev
    Developer

    Illumina, Inc., United States of America

  5. Zhihai Ma
    Developer

    Department of Genetics, Stanford University School of Medicine, United States of America

  6. Tim Blauwkamp
    Developer

    Illumina, Inc., United States of America

  7. Michael Kertesz
    Developer

    Illumina, Inc., United States of America

  8. Michael Snyder
    Investigator

    Department of Genetics, Stanford University School of Medicine, United States of America

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Summary
AccessionBT006010
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByMichael Snyder