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

de Vree, P. J. P., de Wit, E., Yilmaz, M., de Heijning, M. V., 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., Cornelissen, M., Das, A. T., Berkhout, B., Sikkema-Raddatz, B., van den Berg, E., van der Vlies, P., Weening, D., den Dunnen, J. T., Matusiak, M., Lamkanfi, M., Ligtenberg, M. J. L., ter Brugge, P., Jonkers, J., Foekens, J. A., Martens, J. W., van der Luijt, R., van Amstel, H. K. P., van Min, M., Splinter, E. & de Laat, W., Oct-2014, In : Nature Biotechnology. 32, 10, p. 1019-1025.e2 9 p.

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

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DOI

  • 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

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 languageEnglish
Pages (from-to)1019-1025.e2
Number of pages9
JournalNature Biotechnology
Volume32
Issue number10
Publication statusPublished - Oct-2014

    Keywords

  • COMPLEX CHROMOSOMAL REARRANGEMENTS, INFLAMMASOME ACTIVATION, GENETIC-VARIATION, 4C TECHNOLOGY, GENOME, DISEASE, TUMORS, CONFORMATION, ENRICHMENT, EXPRESSION

ID: 16261257