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PMID: 25948246 Published · ppublish English Journal Article Review

Haplotype-resolved genome sequencing: experimental methods and applications.

Nature reviews. Genetics ·Vol. 16 ·No. 6 ·2015-06-00 ·Pages 344-58

Snyder MW, Adey A, Kitzman JO, Shendure J

Abstract

Human genomes are diploid and, for their complete description and interpretation, it is necessary not only to discover the variation they contain but also to arrange it onto chromosomal haplotypes. Although whole-genome sequencing is becoming increasingly routine, nearly all such individual genomes are mostly unresolved with respect to haplotype, particularly for rare alleles, which remain poorly resolved by inferential methods. Here, we review emerging technologies for experimentally resolving (that is, 'phasing') haplotypes across individual whole-genome sequences. We also discuss computational methods relevant to their implementation, metrics for assessing their accuracy and completeness, and the relevance of haplotype information to applications of genome sequencing in research and clinical medicine.

MeSH Terms
Animals Computer Simulation Genome, Human Haplotypes High-Throughput Nucleotide Sequencing Humans Linkage Disequilibrium Models, Genetic Sequence Analysis, DNA
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Snyder Matthew W
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Adey Andrew
Department of Molecular and Medical Genetics, Oregon Health &Sciences University, Portland, Oregon 97239, USA.
Kitzman Jacob O
1] Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA. [2] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Shendure Jay
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
DOI
10.1038/nrg3903
Published
2015-06-00
Epub
2015-00-07
Pages
344-58
Language
English
Region
England
NLM ID
100962779
Subset
IM
External Links
PubMed source DOI: 10.1038/nrg3903 View journal details
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