Haplotype-resolved genome sequencing of a Gujarati Indian individual

被引：168

作者：

Kitzman, Jacob O. ^{[1
]}

MacKenzie, Alexandra P. ^{[1
]}

Adey, Andrew ^{[1
]}

Hiatt, Joseph B. ^{[1
]}

Patwardhan, Rupali P. ^{[1
]}

Sudmant, Peter H. ^{[1
]}

Ng, Sarah B. ^{[1
]}

Alkan, Can ^{[1
,2
]}

Qiu, Ruolan ^{[1
]}

Eichler, Evan E. ^{[1
,2
]}

Shendure, Jay ^{[1
]}

机构：

[1] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA

[2] Howard Hughes Med Inst, Seattle, WA USA

来源：

NATURE BIOTECHNOLOGY | 2011年 / 29卷 / 01期

基金：

美国国家卫生研究院; 美国国家科学基金会; 加拿大自然科学与工程研究理事会;

关键词：

STRUCTURAL VARIATION; COPY-NUMBER; SHORT-READ; ALGORITHMS;

D O I：

10.1038/nbt.1740

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Haplotype information is essential to the complete description and interpretation of genomes(1), genetic diversity(2) and genetic ancestry(3). Although individual human genome sequencing is increasingly routine(4), nearly all such genomes are unresolved with respect to haplotype. Here we combine the throughput of massively parallel sequencing(5) with the contiguity information provided by large-insert cloning(6) to experimentally determine the haplotype-resolved genome of a South Asian individual. A single fosmid library was split into a modest number of pools, each providing similar to 3% physical coverage of the diploid genome. Sequencing of each pool yielded reads overwhelmingly derived from only one homologous chromosome at any given location. These data were combined with whole-genome shotgun sequence to directly phase 94% of ascertained heterozygous single nucleotide polymorphisms (SNPs) into long haplotype blocks (N50 of 386 kilobases (kbp)). This method also facilitates the analysis of structural variation, for example, to anchor novel insertions(7,8) to specific locations and haplotypes.

引用

页码：59 / +

页数：6

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