A Bayesian ensemble approach with a disease gene network predicts damaging effects of missense variants of human cancers

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Large-scale sequencing of cancer genomes has revealed many novel mutations and inter-tumoral heterogeneity. Therefore, prioritizing variants according to their potential deleterious effects has become essential. We constructed a disease gene network and proposed a Bayesian ensemble approach that integrates diverse sources to predict the functional effects of missense variants. We analyzed 23,336 missense disease mutations and 36,232 neutral polymorphisms of 12,039 human proteins. The results showed successful improvement of prediction accuracy in both sensitivity and specificity, and we demonstrated the utility of the method by applying it to somatic mutations obtained from colorectal and breast cancer cell lines. The candidate genes with predicted deleterious mutations as well as known cancer genes were significantly enriched in many KEGG pathways related to carcinogenesis, supporting genetic homogeneity of cancer at the pathway level. The breast cancer-specific network increased the prediction accuracy for breast cancer mutations. This study provides a ranked list of deleterious mutations and candidate cancer genes and suggests that mutations affecting cancer may occur in important pathways and should be interpreted on the phenotype-related network or pathway. A disease gene network may be of value in predicting functional effects of novel disease-specific mutations.
Publisher
SPRINGER
Issue Date
2013-01
Language
English
Article Type
Article
Keywords

ACTIVATING TRANSCRIPTION FACTOR-2; MESSENGER-RNA EXPRESSION; BREAST-CANCER; MAMMARY-TUMORS; COLORECTAL-CANCER; SOMATIC MUTATIONS; PROTEIN FUNCTION; UP-REGULATION; COLON-CANCER; CTEN

Citation

HUMAN GENETICS, v.132, no.1, pp.15 - 27

ISSN
0340-6717
DOI
10.1007/s00439-012-1218-7
URI
http://hdl.handle.net/10203/103816
Appears in Collection
BiS-Journal Papers(저널논문)
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