Long-span PET mapping reveals characteristic patterns of #SVs in… cancer [v norm] genomes, but no MEIs or small events
The described study used long paired-end-tags (PET) to analyze and compare SVs in cancer and normal genomes. It determined the prevalence of different types of SVs in normal and cancer sample. Overall, the results are interesting and convincing on a qualitative level; however, for the reasons outlined below, more precise and quantitative delineation of the observed effects is highly desirable.
1) Small sample size of normal genomes (only 2 normal genomes)
2) Validation rate was low (< 77%) for everything except deletions, and for singletons it was even lower. .
3) Long PET is not good for finding smaller events (few kbps). Thus, this analysis missed smaller scale SVs and cancer rearrangements.
4) While there is a discussion about breakpoints and associated repeats, it is not very informative as breakpoint locations were not determined to basepair resolution.
5) No MEI were considered — particularly, no cancer MEI were considered in the analysis, while recently it was found that somatic retrotransposition occurs in cancer (Lee et al., PMID: 22745252)..
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes –
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.
Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.