Targeted, haplotype-resolved resequencing of long segments of the human genome

被引：25

作者：

Raymond, CK ^{[1
]}

Subramanian, S ^{[1
]}

Paddock, M ^{[1
]}

Qiu, RL ^{[1
]}

Deodato, C ^{[1
]}

Palmieri, A ^{[1
]}

Chang, J ^{[1
]}

Radke, T ^{[1
]}

Haugen, E ^{[1
]}

Kas, A ^{[1
]}

Waring, D ^{[1
]}

Bovee, D ^{[1
]}

Stacy, R ^{[1
]}

Kaul, R ^{[1
]}

Olson, MV ^{[1
]}

机构：

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

来源：

GENOMICS | 2005年 / 86卷 / 06期

关键词：

automation; fosmids; genomic libraries;

D O I：

10.1016/j.ygeno.2005.08.013

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：

Currently, challenges exist to acquire long-range (hundreds of kilobase pairs) phase-discriminated sequence across substantial numbers of individuals. We have developed a straightforward method for isolating and characterizing specific genomic regions in a haplospecific manner. Real-time PCR is carried out to STS content map and genotype pools of fosmid clones arrayed in 384-well microtiter plates. Single-nucleotide polymorphisms, microsatellite markers, and insertion-deletion polymorphisms are used to differentiate the target region into haplotype-specific tiling paths. DNA of clones from these tiling paths is retrieved from the library and either sequenced by standard shotgun methods or amplified in vitro and sequenced by a primer-based, directed method. This approach provides convenient access to complete, haplotype-resolved resequencing data from multiple individuals across tens to hundreds of thousands of basepairs. We illustrate its implementation with a detailed example of more than 400 kbp from the human CFTR region, across 15 individuals, and summarize our experience applying it to many other human loci. (c) 2005 Elsevier Inc. All rights reserved.

引用

页码：759 / 766

页数：8

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