Target Locus Amplification for hypothesis neutral sequencing and haplotyping of select genomic loci. Targeted Locus Amplification BRCA1/2

Gene function can be affected by many types of genetic changes including single nucleotide variants, small indels and structural variants. Despite rapid developments in targeted gene and whole genome analysis techniques, the robust detection of all relevant variation in and around genes of interest remains a challenge. Here we present a conceptually novel strategy called Targeted Locus Amplification (TLA) that uses physical proximity of neighboring chromosomal parts and requires one, or very few, primer pair(s) to selectively amplify and sequence entire genes. We demonstrate that TLA uncovers all types of genetic variants and show it identifies previously unnoticed chromosomal inversions and gene fusions in clinically relevant genes. The methodology can also be used for the analysis of viral and transgene integration sites and is highly suitable for haplotyping across large chromosomal intervals. TLA therefore promises to be a useful method in genetic research and diagnostics.