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

Paula J. P. de Vree; Elzo de Wit; Mehmet Yilmaz; Monique van de Heijning; Petra Klous; Marjon J. A. M. Verstegen; Yi Wan; Hans Teunissen; Peter H. L. Krijger; Geert Geeven; Paul P. Eijk; Daoud Sie; Bauke Ylstra; Lorette O. M. Hulsman; Marieke F. van Dooren; Laura J. C. M. van Zutven; Ans van den Ouweland; Sjef Verbeek; Ko Willems van Dijk; Marion Cornelissen; Atze T. Das; Ben Berkhout; Birgit Sikkema-Raddatz; Eva van den Berg; Pieter van der Vlies; Desiree Weening; Johan T. den Dunnen; Magdalena Matusiak; Mohamed Lamkanfi; Marjolijn J. L. Ligtenberg; Petra ter Brugge; Jos Jonkers; John A. Foekens; John W. Martens; Rob van der Luijt; Hans Kristian Ploos van Amstel; Max van Min; Erik Splinter; Wouter de Laat; B. Ben

doi:https://doi.org/10.1038/nbt.2959

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

Paula J. P. de Vree, Elzo de Wit, Mehmet Yilmaz, Monique van de Heijning, Petra Klous, Marjon J. A. M. Verstegen, Yi Wan, Hans Teunissen, Peter H. L. Krijger, Geert Geeven, Paul P. Eijk, Daoud Sie, Bauke Ylstra, Lorette O. M. Hulsman, Marieke F. van Dooren, Laura J. C. M. van Zutven, Ans van den Ouweland, Sjef Verbeek, Ko Willems van Dijk, Marion CornelissenAtze T. Das, Ben Berkhout, Birgit Sikkema-Raddatz, Eva van den Berg, Pieter van der Vlies, Desiree Weening, Johan T. den Dunnen, Magdalena Matusiak, Mohamed Lamkanfi, Marjolijn J. L. Ligtenberg, Petra ter Brugge, Jos Jonkers, John A. Foekens, John W. Martens, Rob van der Luijt, Hans Kristian Ploos van Amstel, Max van Min, Erik Splinter, Wouter de Laat, B. Ben

Research output: Contribution to journal › Article › Academic › peer-review

191 Citations (Scopus)

Abstract

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

Original language	English
Pages (from-to)	1019-1025
Journal	Nature biotechnology
Volume	32
Issue number	10
DOIs	https://doi.org/10.1038/nbt.2959
Publication status	Published - 2014

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https://doi.org/10.1038/nbt.2959

Cite this

de Vree, P. J. P., de Wit, E., Yilmaz, M., van de Heijning, M., Klous, P., Verstegen, M. J. A. M., Wan, Y., Teunissen, H., Krijger, P. H. L., Geeven, G., Eijk, P. P., Sie, D., Ylstra, B., Hulsman, L. O. M., van Dooren, M. F., van Zutven, L. J. C. M., van den Ouweland, A., Verbeek, S., van Dijk, K. W., ... Ben, B. (2014). Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nature biotechnology, 32(10), 1019-1025. https://doi.org/10.1038/nbt.2959

@article{0c33df50ee4f4f1aa345535417a0f53e,

title = "Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping",

abstract = "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",

author = "{de Vree}, {Paula J. P.} and {de Wit}, Elzo and Mehmet Yilmaz and {van de Heijning}, Monique and Petra Klous and Verstegen, {Marjon J. A. M.} and Yi Wan and Hans Teunissen and Krijger, {Peter H. L.} and Geert Geeven and Eijk, {Paul P.} and Daoud Sie and Bauke Ylstra and Hulsman, {Lorette O. M.} and {van Dooren}, {Marieke F.} and {van Zutven}, {Laura J. C. M.} and {van den Ouweland}, Ans and Sjef Verbeek and {van Dijk}, {Ko Willems} and Marion Cornelissen and Das, {Atze T.} and Ben Berkhout and Birgit Sikkema-Raddatz and {van den Berg}, Eva and {van der Vlies}, Pieter and Desiree Weening and {den Dunnen}, {Johan T.} and Magdalena Matusiak and Mohamed Lamkanfi and Ligtenberg, {Marjolijn J. L.} and {ter Brugge}, Petra and Jos Jonkers and Foekens, {John A.} and Martens, {John W.} and {van der Luijt}, Rob and {van Amstel}, {Hans Kristian Ploos} and {van Min}, Max and Erik Splinter and {de Laat}, Wouter and B. Ben",

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de Vree, PJP, de Wit, E, Yilmaz, M, van de Heijning, M, Klous, P, Verstegen, MJAM, Wan, Y, Teunissen, H, Krijger, PHL, Geeven, G, Eijk, PP, Sie, D , Ylstra, B, Hulsman, LOM, van Dooren, MF, van Zutven, LJCM, van den Ouweland, A, Verbeek, S, van Dijk, KW, Cornelissen, M , Das, AT , Berkhout, B, Sikkema-Raddatz, B, van den Berg, E, van der Vlies, P, Weening, D, den Dunnen, JT, Matusiak, M, Lamkanfi, M, Ligtenberg, MJL, ter Brugge, P, Jonkers, J, Foekens, JA, Martens, JW, van der Luijt, R, van Amstel, HKP, van Min, M, Splinter, E, de Laat, W & Ben, B 2014, 'Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping', Nature biotechnology, vol. 32, no. 10, pp. 1019-1025. https://doi.org/10.1038/nbt.2959

TY - JOUR

T1 - Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

AU - de Vree, Paula J. P.

AU - de Wit, Elzo

AU - Yilmaz, Mehmet

AU - van de Heijning, Monique

AU - Klous, Petra

AU - Verstegen, Marjon J. A. M.

AU - Wan, Yi

AU - Teunissen, Hans

AU - Krijger, Peter H. L.

AU - Geeven, Geert

AU - Eijk, Paul P.

AU - Sie, Daoud

AU - Ylstra, Bauke

AU - Hulsman, Lorette O. M.

AU - van Dooren, Marieke F.

AU - van Zutven, Laura J. C. M.

AU - van den Ouweland, Ans

AU - Verbeek, Sjef

AU - van Dijk, Ko Willems

AU - Cornelissen, Marion

AU - Das, Atze T.

AU - Berkhout, Ben

AU - Sikkema-Raddatz, Birgit

AU - van den Berg, Eva

AU - van der Vlies, Pieter

AU - Weening, Desiree

AU - den Dunnen, Johan T.

AU - Matusiak, Magdalena

AU - Lamkanfi, Mohamed

AU - Ligtenberg, Marjolijn J. L.

AU - ter Brugge, Petra

AU - Jonkers, Jos

AU - Foekens, John A.

AU - Martens, John W.

AU - van der Luijt, Rob

AU - van Amstel, Hans Kristian Ploos

AU - van Min, Max

AU - Splinter, Erik

AU - de Laat, Wouter

AU - Ben, B.

PY - 2014

Y1 - 2014

N2 - 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

AB - 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

U2 - https://doi.org/10.1038/nbt.2959

DO - https://doi.org/10.1038/nbt.2959

M3 - Article

C2 - 25129690

SN - 1087-0156

VL - 32

SP - 1019

EP - 1025

JO - Nature biotechnology

JF - Nature biotechnology

IS - 10

ER -