Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

Abstract

Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA-PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakagefusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers.

Discovery of recurrent structural variants in nasopharyngeal carcinoma

“…This first characterization of NPC by deep whole genome sequencing demonstrated effective structural variant discovery with our approach, which involved (1) generation of high-complexity, long-insert mate-pair libraries by a novel combination of methods; (Williams et al 2012) and tumor genomes (Hillmer et al 2011), our study achieves the deepest-to date-physical coverage (7503) as well as high sequence coverage (583) with a single mate-pair library. The great degree of physical coverage afforded by long-insert mate-pair libraries facilitated our proof-of-concept demonstration that structural variants can be discovered even in very low-tumor content samples: In the case of NPC-5421, two of three gene fusion variants were inferred from the mate pair data to be present at only 6% allele frequency; both were validated by Sanger sequencing.…”

“…For technical reasons, it is difficult to obtain deep genome coverage with inserts exceeding 600 bp using this approach. Much larger inserts can be produced by circularizing large DNA fragments of up to 10 kb (Fullwood et al 2009;Hillmer et al 2011), and subsequent isolation of a short fragment that contains both ends (mate pairs). Large-insert and fosmid mate-pair libraries offer several attractive features that make them well-suited for analysis of structural variation (Raphael et al 2003;International Human Genome Sequencing Consortium 2004;Tuzun et al 2005;Kidd et al 2008;Hampton et al 2011;Williams et al 2012).…”

The tandem duplicator phenotype as a distinct genomic configuration in cancer

“…A catalog of somatic structural variation data was compiled from a number of WGS studies, comprising a total of 277 tumor samples, as listed in Dataset S1 (4,9,10,(15)(16)(17)(18)(19)(20)(21)(22). We manually curated the available structural variation information (relative orientation and mapping coordinates of the discordant mate-pair or paired-end read clusters) from every individual study to classify each reported somatic event into one of the four basic rearrangements: deletion, TD, inversion, or interchromosomal translocation (49).…”

“…Previous attempts at describing the genomic features of the TDP have relied on a basic TD count or on the proportion of TDs relative to the total number of structural variations in a cancer genome (10,15). These approaches lack in robustness, because they are prone to be influenced by observer and technical biases, such as sequencing coverage, and are not able to discriminate between the genome-wide TD prevalence that characterizes the TDP vs. abnormal TD accumulation in a few functional genomic loci, previously described in association with focal amplification (9,16). Our proposed metric to calculate the TDP score is described in the main text.…”

Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations

“…In our experiments, we used an insert size of 3 kb, which provides a good balance between resolution and the ability to detect breakpoints across repetitive regions. 14,30 We estimated the resolution that can be reached based on clustering analysis by calculating the distribution of the sizes of deletions predicted by our analysis (Supplementary Figure S5). This shows that the majority of deletions is smaller than 10 kb and the lower detection limit is B1 kb.…”