Contribution of allelic imbalance to colorectal cancer.

Palin K, Pitkänen E, Turunen M, Sahu B, Pihlajamaa P, Kivioja T, Kaasinen E, Välimäki N, Hänninen UA, Cajuso T, Aavikko M, Tuupanen S, Kilpivaara O, van den Berg L, Kondelin J, Tanskanen T, Katainen R, Grau M, Rauanheimo H, Plaketti RM, Taira A, Sulo P, Hartonen T, Dave K, Schmierer B, Botla S, Sokolova M, Vähärautio A, Gladysz K, Ongen H, Dermitzakis E, Bramsen JB, Ørntoft TF, Andersen CL, Ristimäki A, Lepistö A, Renkonen-Sinisalo L, Mecklin JP, Taipale J, Aaltonen LA

Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]

Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.

NGI Stockholm (Genomics Applications) [Service]

NGI Stockholm (Genomics Production) [Service]

QC bibliography QC xrefs

PubMed 30202008

DOI 10.1038/s41467-018-06132-1

Crossref 10.1038/s41467-018-06132-1

10.1038/s41467-018-06132-1

pmc PMC6131244

EGAS00001002966 [High-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed)]

EGAS00001003010 [Somatic mutations of 256 whole-genome sequenced colorectal tumors]

PRJEB25645 [CRISPR/Cas9 knockout and activation screening of colorectal cancer allelic imbalance target genes]

https://doi.org/10.5281/zenodo.1222172 [Contribution of allelic imbalance to colorectal cancer]