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

(2014) NATURE BIOTECHNOLOGY. 32(10). p.1019-1025
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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.
Keywords
TUMORS, DISEASE, EXPRESSION, CONFORMATION, GENOME, GENETIC-VARIATION, 4C TECHNOLOGY, INFLAMMASOME ACTIVATION, COMPLEX CHROMOSOMAL REARRANGEMENTS, ENRICHMENT

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MLA
de Vree, Paula JP, Elzo de Wit, Mehmet Yilmaz, et al. “Targeted Sequencing by Proximity Ligation for Comprehensive Variant Detection and Local Haplotyping.” NATURE BIOTECHNOLOGY 32.10 (2014): 1019–1025. Print.
APA
de Vree, P. J., de Wit, E., Yilmaz, M., van de Heijning, M., Klous, P., Verstegen, M. J., Wan, Y., et al. (2014). Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. NATURE BIOTECHNOLOGY, 32(10), 1019–1025.
Chicago author-date
de Vree, Paula JP, Elzo de Wit, Mehmet Yilmaz, Monique van de Heijning, Petra Klous, Marjon JAM Verstegen, Yi Wan, et al. 2014. “Targeted Sequencing by Proximity Ligation for Comprehensive Variant Detection and Local Haplotyping.” Nature Biotechnology 32 (10): 1019–1025.
Chicago author-date (all authors)
de Vree, Paula JP, Elzo de Wit, Mehmet Yilmaz, Monique van de Heijning, Petra Klous, Marjon JAM Verstegen, Yi Wan, Hans Teunissen, Peter HL Krijger, Geert Geeven, Paul P Eijk, Daoud Sie, Bauke Ylstra, Lorette OM Hulsman, Marieke F van Dooren, Laura JCM 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 JL 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, and Wouter de Laat. 2014. “Targeted Sequencing by Proximity Ligation for Comprehensive Variant Detection and Local Haplotyping.” Nature Biotechnology 32 (10): 1019–1025.
Vancouver
1.
de Vree PJ, de Wit E, Yilmaz M, van de Heijning M, Klous P, Verstegen MJ, et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. NATURE BIOTECHNOLOGY. 2014;32(10):1019–25.
IEEE
[1]
P. J. de Vree et al., “Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping,” NATURE BIOTECHNOLOGY, vol. 32, no. 10, pp. 1019–1025, 2014.
@article{5809560,
  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 JP and de Wit, Elzo and Yilmaz, Mehmet and van de Heijning, Monique and Klous, Petra and Verstegen, Marjon JAM and Wan, Yi and Teunissen, Hans and Krijger, Peter HL and Geeven, Geert and Eijk, Paul P and Sie, Daoud and Ylstra, Bauke and Hulsman, Lorette OM and van Dooren, Marieke F and van Zutven, Laura JCM and van den Ouweland, Ans and Verbeek, Sjef and Willems van Dijk, Ko and Cornelissen, Marion and Das, Atze T and Berkhout, Ben and Sikkema-Raddatz, Birgit and van den Berg, Eva and van der Vlies, Pieter and Weening, Desiree and den Dunnen, Johan T and Matusiak, Magdalena and Lamkanfi, Mohamed and Ligtenberg, Marjolijn JL and ter Brugge, Petra and Jonkers, Jos and Foekens, John A and Martens, John W and van der Luijt, Rob and Ploos van Amstel, Hans Kristian and van Min, Max and Splinter, Erik and de Laat, Wouter},
  issn         = {1087-0156},
  journal      = {NATURE BIOTECHNOLOGY},
  keywords     = {TUMORS,DISEASE,EXPRESSION,CONFORMATION,GENOME,GENETIC-VARIATION,4C TECHNOLOGY,INFLAMMASOME ACTIVATION,COMPLEX CHROMOSOMAL REARRANGEMENTS,ENRICHMENT},
  language     = {eng},
  number       = {10},
  pages        = {1019--1025},
  title        = {Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping},
  url          = {http://dx.doi.org/10.1038/nbt.2959},
  volume       = {32},
  year         = {2014},
}

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