Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

Abstract

Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that ;16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.

Discovery of recurrent structural variants in nasopharyngeal carcinoma

“…Except for small insertions, SMASH consistently detected breakpoints with allelic frequencies >1.7%. To see if SMASH produces results comparable to other SV algorithms, we compared its breakpoint detection to HYDRA (Quinlan et al 2010;Malhotra et al 2013) on a set of simulated breakpoints (Supplemental Material; Supplemental Table T3). Overall, SMASH breakpoint detection rates were similar to HYDRA, with SMASH more accurately resolving breakpoint coordinates and HYDRA more consistently detecting short insertions.…”

“…Structural variation methods, such as GASV (Sindi et al 2009), SegSeq (Chiang et al 2009), DELLY (Rausch et al 2012b), HYDRA (Quinlan et al 2010), AGE (Abyzov and Gerstein 2011), and others (Lee et al 2008; for review, see Snyder et al 2010;Alkan et al 2011), generally utilize (1) read-pair (RP) discordance, (2) increase or reduction in sequence coverage, (3) split reads that span breakpoints, and (4) exact assembly of breakpoint sequences. These tools were primarily designed for variant detection from a single data set, such as a normal genome, and are suited for cataloguing structural polymorphisms in the human population (Kidd et al 2008(Kidd et al , 2010Mills et al 2011).…”

Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma

“…The likelihood of local hopping of the SB transposon is increased on the chromosome where the transposon concatamer is located (62); thus, all insertions on chromosome 4, the site of the T2/Onc2 donor concatamer, were removed from the dataset before subsequent analysis, unless indicated otherwise. Sfi1 is listed as a singlecopy gene in the reference mouse genome; however, it is estimated that the mouse genome has 20-30 copies of Sfi1 (63). Insertions in multiple different Sfi1 loci are erroneously annotated to a single Sfi1 gene located on chromosome 11; thus, we removed Sfi1 from our lists of CIS genes, because this is a known artifact.…”

Severe ocular phenotypes in Rbp4-deficient mice in the C57BL/6 genetic background

“…Structural variation is widespread in mammalian genomes 34,35 and is an important cause of disease. 36 Genome-wide association studies identified single-nucleotide polymorphisms in several genes, such as GRIA4, KCNQ5, RDH5, LAMA2, BMP2, SIX6, PRSS56, GJD2, RASGRF1, ZC3H11B, and WNT7B, as risk factors for refractive error including myopia.…”