Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution

Abstract

For decades, cytogenetic studies have demonstrated that somatically acquired structural rearrangements of the genome are a common feature of most classes of human cancer. However, the characteristics of these rearrangements at sequence-level resolution have thus far been subject to very limited description. One process that is dependent upon somatic genome rearrangement is gene amplification, a mechanism often exploited by cancer cells to increase copy number and hence expression of dominantly acting cancer genes. The mechanisms underlying gene amplification are complex but must involve chromosome breakage and rejoining. We sequenced 133 different genomic rearrangements identified within four cancer amplicons involving the frequently amplified cancer genes MYC, MYCN, and ERBB2. The observed architectures of rearrangement were diverse and highly distinctive, with evidence for sister chromatid breakage-fusion-bridge cycles, formation and reinsertion of double minutes, and the presence of bizarre clusters of small genomic fragments. There were characteristic features of sequences at the breakage-fusion junctions, indicating roles for nonhomologous end joining and homologous recombination-mediated repair mechanisms together with nontemplated DNA synthesis. Evidence was also found for sequence-dependent variation in susceptibility of the genome to somatic rearrangement. The results therefore provide insights into the DNA breakage and repair processes operative in somatic genome rearrangement and illustrate how the evolutionary histories of individual cancers can be reconstructed from large-scale cancer genome sequencing.

Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles

“…They invoke the rescue of individual stalled replication forks by switching the template during strand synthesis or resynthesis to an unrelated template that has only a few base pairs of homology. This results in joining of a strand to an unrelated sequence; it explains the insertion of genomic shards (small fragments of genome from elsewhere in the genome) (Bignell et al 2007), which are often found in the junctions, and are presumed to be the result of abortive attempts to use another template (Hastings et al 2009b); and it specifies that junctions show microhomology between the joined sequences of typically 2 to 5 bp. Our translocations were consistent with this pattern, showing microhomology of 1 to 8 bp at the junctions, and, in two cases, typical genomic shards (Supplemental Table 3).…”

“…2B; Howarth et al 2008). The cloned junctions were at 10,438,664 bp and 9,108,545 bp (Table 1 Table 3), 80 kb away from the breakpoint, typical of the small fragments of distant sequence that are often found inserted in junctions, named ''genomic shards'' (Bignell et al 2007;Hastings et al 2009a). The resulting loss was clear in the SNP6 array-CGH data from Bignell et al (2010) (Supplemental Fig.…”

“…Fragments of DNA from elsewhere in the genome (genomic shards) (Bignell et al 2007) were inserted at two of the junctions (Supplemental Table 3). …”

Whole-genome cancer analysis as an approach to deeper understanding of tumour biology

“…Initial applications of these approaches have been quite successful (Bignell et al, 2007;Campbell et al, 2008). For example, Campbell et al (2008) used Illumina GA technology to attain the precise sequence of several hundred variants, comprising germline and somatic intra-and inter-chromosomal rearrangements in two lung cancer cell lines.…”

Translating insights from the cancer genome into clinical practice

“…Next-generation sequencing technologies that allow the entire genomes of tumour cells to be sequenced will be particularly valuable for discovering fusion genes and other structural rearrange ments. The promise of this approach is illustrated by the remarkable structural complexity found in cancer genomes by using endsequence profiling 23 , genomic-region sequencing 24 or genome-wide parallel paired-end sequencing 25 (Box 1).…”