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- Title
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping.
- Authors
de Vree, Paula J P; de Wit, Elzo; Yilmaz, Mehmet; van de Heijning, Monique; Klous, Petra; Verstegen, Marjon J A M; Wan, Yi; Teunissen, Hans; Krijger, Peter H L; Geeven, Geert; Eijk, Paul P; Sie, Daoud; Ylstra, Bauke; Hulsman, Lorette O M; van Dooren, Marieke F; van Zutven, Laura J C M; van den Ouweland, Ans; Verbeek, Sjef; van Dijk, Ko Willems; Cornelissen, Marion
- 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.
- Subjects
HAPLOTYPES; HUMAN genetic variation; TRANSGENES; GENOMES; DOMINANCE (Genetics)
- Publication
Nature Biotechnology, 2014, Vol 32, Issue 10, p1019
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt.2959