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bioRxiv · 10.1101/112367

Pan-cancer scale landscape of simple somatic mutations

Zhou, N.·Gallego, B.·Bao, J.·Tsafnat, G.
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Abstract

Genome is the carrier of somatic mutations during the development of cancer. The catalogue of simple somatic mutations (SSM) is a subgroup of somatic mutations. It includes single base substitutions, small deletions and insertions of <= 200 bp, and multiple base substitutions of <= 200 bp. The comprehensive landscape of SSM has not been studied. After analysed 46,692,922 SSM of 10,878 samples, we proposed a pan-cancer scale landscape of SSM for 60 cancer projects in ICGC. In addition, the whole genome sequencing (WGS) and whole exome sequencing (WXS) techniques were compared according to the landscape of SSM. The result indicates numbers of SSM vary dramatically in different cancers. WGS can detect 10 times more single base substitutions and insertions than WXS. In terms of WXS, it called 10 times more deletions than insertions. Multiple base substitutions have not been well studied so they were just observed in a few cancer projects. Cancers generally show high prevalence of C > T substitutions at NpCpG trinucleotide contexts. Skin cancer showed distinct mutational spectra. Breast cancer, bladder cancer, and cervical cancer were found to have similar mutational spectra. Acute myeloid leukemia and lung cancer from South Korea, and colorectal cancer from China show high density of single base substitutions per mega base in chromosome Y. To sum up, our study and findings will be thought provoking in studying SSM in cancer.

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Zhou, N., Gallego, B., Bao, J., Tsafnat, G.. 2017-02-28. Pan-cancer scale landscape of simple somatic mutations. https://doi.org/10.1101/112367

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