Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location.

PloS One
Xiaoyang RuanWilliam C Reinhold

Abstract

Runs of homozygosity (ROH) represents extended length of homozygotes on a long genomic distance. In oncology, it is known as loss of heterozygosity (LOH) if identified exclusively in cancer cell rather than in matched control cell. Studies have identified several genomic regions which show consistent ROH in different kinds of carcinoma. To query whether this consistency can be observed on broader spectrum, both in more cancer types and in wider genomic regions, we investigated ROH patterns in the National Cancer Institute 60 cancer cell line panel (NCI-60) and HapMap Caucasian healthy trio families. Using results from Affymetrix 500 K SNP arrays, we report a genome wide significant association of ROH regions between the NCI-60 and HapMap samples, with much a higher level of ROH (11 fold) in the cancer cell lines. Analysis shows that more severe ROH found in cancer cells appears to be the extension of existing ROH in healthy state. In the HapMap trios, the adult subgroup had a slightly but significantly higher level (1.02 fold) of ROH than did the young subgroup. For several ROH regions we observed the co-occurrence of fragile sites (FRAs). However, FRA on the genome wide level does not show a clear relationship with ROH regions.

Associated Datasets

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Citations

Feb 26, 2015·Pharmacogenomics·Nifang Niu, Liewei Wang
Jul 18, 2014·PloS One·William C ReinholdYves Pommier
Jan 24, 2015·Journal of Molecular Endocrinology·Timon VandammeKen Op de Beeck
Nov 4, 2016·Mobile DNA·John G ZampellaKathleen H Burns
Sep 20, 2017·Molecular Carcinogenesis·Brooke R DrulinerLisa Boardman
Jun 7, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·William C ReinholdYves Pommier

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Methods Mentioned

BETA
genotyping

Software Mentioned

GeneGO
CellMiner
Unix
R
Affymetrix Power Tool ( APT )
dChip
pennCNV
PLINK

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