alexa Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Next Generation Sequencing & Applications

Author(s): de Vree PJ, de Wit E, Yilmaz M, van de Heijning M, Klous P,

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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. This article was published in Nat Biotechnol and referenced in Journal of Next Generation Sequencing & Applications

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