title: Haplotype-resolved genome sequencing: experimental methods and applications.
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.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Snyder
authors.affiliation: Department of Molecular and Medical Genetics, Oregon Health &Sciences University, Portland, Oregon 97239, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Adey
authors.affiliation: 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.
authors.forename: Jacob O
authors.initials: JO
authors.lastname: Kitzman
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D000818:Animals; D003198:Computer Simulation; D015894:Genome, Human; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D017422:Sequence Analysis, DNA