A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

Abstract

Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation. We develop a resource based on capillary end-sequencing of 13.8 million fosmid clones from 17 human genomes and characterize the complete sequence of 1,054 large structural variants corresponding to 589 deletions, 384 insertions, and 81 inversions. We analyze the 2,081 breakpoint junctions and infer potential mechanism of origin. Three mechanisms account for the bulk of germline structural variation: microhomology-mediated processes involving short (2–20 bp) stretches of sequence (28%), non-allelic homologous recombination (NAHR) (22%) and L1 retrotransposition (19%). The high quality and long-range continuity of the sequence reveals more complex mutational mechanisms including repeat-mediated inversions and gene conversion that are most often missed by other methods including comparative genomic hybridization, SNP microarrays and next-generation sequencing.

Discovery of recurrent structural variants in nasopharyngeal carcinoma

“…Overall, SMASH breakpoint detection rates were similar to HYDRA, with SMASH more accurately resolving breakpoint coordinates and HYDRA more consistently detecting short insertions. In a separate simulation, we detected breakpoints previously reported as a part of human structural variant resource (Kidd et al 2010; Supplemental Material), demonstrating good performance of SMASH on real-world SVs; here, breakpoint detection was limited by the ability to map variant reads into nonunique regions of the genome. In general, homology of sequences in the immediate neighborhood of breakpoints represents a major challenge for accurate SV detection by variant callers that rely on split reads and readpair discordance.…”

“…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). However, specific detection of somatic structural variants in cancer using these tools typically requires additional downstream custom analysis to enable ''subtraction'' of germline variants from the tumor variant calls (Rausch et al 2012a).…”

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

“…This included a 36-kbp chimpanzee-hyperexpanded segment homologous to human chromosome 2, contained in the chimpanzee clone AC150905, and a 45-kbp gorilla-hyperexpanded segment homologous to human chromosome 10 (19534885-19579478 NCBI35) (Fan et al 2002;Cheng et al 2005;Marques-Bonet et al 2009;Ventura et al 2011). To better define the cap structure organization in both apes and delineate the full extent of these duplications, we performed a series of comparative FISH experiments using a set of overlapping human fosmid clones (Kidd et al 2010) mapping to a 463-kbp region of human chromosome 2 (113840263-114303469) and a 341-kbp region mapping to chromosome 10 (19359773-19700390) (Table 1; Fig. 2).…”

“…Rearrangements were visualized using Miropeats (Parsons 1995) and previously described in-house visualization tools (Kidd et al 2010). …”

Retrotransposons and Complex Diseases: Is it Time for a Retrotransposon- Based “Omics” Profiling approach to Elucidate the Origins of Pathogenesis?

“…In practice, we must still await enlightening responses to such questions. Considering that: (a) a typical genome differs 82% from the reference human genome, counting in the variants single nucleotide polymorphisms (SNPs), short indels, large structural variants and CNVs [13], (b) retrotransposons constitute an important agent for generation of GV, being responsible for 20.5% of the structural variation in humans [14], (c) retrotransposons influence gene expression, as 31% of total protein-coding genes transcription start sites in humans are located within retrotransposon sequences and 14,546 retrotransposonderived regions are identified as enhancers [15,16] and (d) 1.04% of the retrotransposon-generated variants lie within already known risk loci for common and rare human diseases [14], it seems straightforward a demand to determine the genomic landscape of individuals with complex diseases using advanced "omics" approaches. In this manner, it can be determined each individual's "mobilome" the sum of retrotransposon counterpart of the genome further representing a pathogenic "genomic identity card" (GID).…”