the fine-scale architecture of structural variants in 17 mouse genomes17个老鼠基因组结构变异的精细结构.pdfVIP

The fine-scale architecture of structural variants in 17 mouse genomes Yalcin et al. Yalcin et al. Genome Biology 2012, 13:R18 /2012/13/3/R18 (20 March 2012) Yalcin et al. Genome Biology 2012, 13:R18 /2012/13/3/R18 RESEARCH Open Access The fine-scale architecture of structural variants in 17 mouse genomes 1,2* 3 1 1 3 3 Binnaz Yalcin , Kim Wong , Amarjit Bhomra , Martin Goodson , Thomas M Keane , David J Adams and Jonathan Flint 1 Abstract Background: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. Results: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. Conclusions: An integrative approach