Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

被引：199

作者：

de Vree, Paula J. P. ^{[1
,2
]}

de Wit, Elzo ^{[1
,2
,3
]}

Yilmaz, Mehmet ^{[3
]}

de Heijning, Monique van ^{[3
]}

Klous, Petra ^{[3
]}

Verstegen, Marjon J. A. M. ^{[1
,2
]}

Wan, Yi ^{[1
,2
]}

Teunissen, Hans ^{[1
,2
]}

Krijger, Peter H. L. ^{[1
,2
]}

Geeven, Geert ^{[1
,2
]}

Eijk, Paul P. ^{[4
]}

Sie, Daoud ^{[4
]}

Ylstra, Bauke ^{[4
]}

Hulsman, Lorette O. M. ^{[5
]}

van Dooren, Marieke F. ^{[5
]}

van Zutven, Laura J. C. M. ^{[5
]}

van den Ouweland, Ans

Verbeek, Sjef ^{[6
,7
]}

van Dijk, Ko Willems ^{[6
,7
]}

Cornelissen, Marion ^{[8
]}

Das, Atze T. ^{[8
]}

Ben Berkhout ^{[8
]}

Sikkema-Raddatz, Birgit ^{[9
]}

van den Berg, Eva ^{[9
]}

van der Vlies, Pieter ^{[9
]}

Weening, Desiree ^{[9
]}

den Dunnen, Johan T. ^{[10
]}

Matusiak, Magdalena ^{[11
,12
]}

Lamkanfi, Mohamed ^{[11
,12
]}

Ligtenberg, Marjolijn J. L. ^{[13
]}

ter Brugge, Petra ^{[14
,15
]}

Jonkers, Jos ^{[14
,15
]}

Foekens, John A. ^{[16
]}

Martens, John W. ^{[16
]}

van der Luijt, Rob ^{[17
]}

van Amstel, Hans Kristian Ploos ^{[17
]}

van Min, Max ^{[3
]}

Splinter, Erik ^{[3
]}

de Laat, Wouter ^{[1
,2
,3
]}

机构：

[1] KNAW, Hubrecht Inst, Utrecht, Netherlands

[2] Univ Med Ctr Utrecht, Utrecht, Netherlands

[3] Cergentis BV, Utrecht, Netherlands

[4] Vrije Univ Amsterdam Med Ctr, Dept Pathol, Amsterdam, Netherlands

[5] Erasmus MC, Dept Clin Genet, Rotterdam, Netherlands

[6] Leiden Univ, Med Ctr, Dept Human Genet, Leiden, Netherlands

[7] Leiden Univ, Med Ctr, Dept Endocrinol, Leiden, Netherlands

[8] Univ Amsterdam, Acad Med Ctr, Ctr Infect & Immun Amsterdam CINIMA, Dept Med Microbiol,Lab Expt Virol, NL-1105 AZ Amsterdam, Netherlands

[9] Univ Groningen, Univ Med Ctr Groningen, Dept Genet, Groningen, Netherlands

[10] Leiden Univ, Med Ctr, Ctr Human & Clin Genet, Leiden Genome Technol Ctr, Leiden, Netherlands

[11] VIB, Dept Med Prot Res, Ghent, Belgium

[12] Univ Ghent, Dept Biochem, B-9000 Ghent, Belgium

[13] Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6525 ED Nijmegen, Netherlands

[14] Netherlands Canc Inst, Div Mol Pathol, Amsterdam, Netherlands

[15] Netherlands Canc Inst, Canc Genom Ctr, Amsterdam, Netherlands

[16] Erasmus Univ, Med Ctr, Erasmus MC Canc Inst, Dept Med Oncol, Rotterdam, Netherlands

[17] Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands

来源：

NATURE BIOTECHNOLOGY | 2014年 / 32卷 / 10期

关键词：

COMPLEX CHROMOSOMAL REARRANGEMENTS; INFLAMMASOME ACTIVATION; GENE-EXPRESSION; ENRICHMENT; MUTATIONS;

D O I：

10.1038/nbt.2959

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：

Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. We show that, unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. This enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, including BRCA1 and BRCA2, and enables haplotyping. We show that TLA can also be used to uncover insertion sites and sequences of integrated transgenes and viruses. TLA therefore promises to be a useful method in genetic research and diagnostics when comprehensive or allele-specific genetic information is needed.

引用

页码：1019 / +

页数：9

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