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Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing

2014; Springer Nature; Volume: 59; Issue: 12 Linguagem: Inglês

10.1038/jhg.2014.88

1435-232X

Toshifumi Suzuki, Yoshinori Tsurusaki, Mitsuko Nakashima, Noriko Miyake, Hirotomo Saitsu, Satoru Takeda, Naomichi Matsumoto,

Cancer Genomics and Diagnostics

Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.