Exonic variants undergoing allele-specific selection in cancers
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Updated: Nov 3, 2025

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Qiyuan Li1,2, Yuanyuan Zeng3, Janet Wang4
1Department of Hematology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361102, China.
Background:
Allelic imbalance (AI) in tumors is caused by chromosomal and sub-chromosomal gains and losses.
Results:
We evaluated AI at 109,086 germline exonic SNP loci in four cancer types, and identified a set of SNPs that demonstrate strong tumor allele specificity in AI events. Further analyses demonstrated that these alleles show consistently different frequencies in the cancer population compared to the healthy population and are significantly enriched for predicted protein-damaging variants. Moreover, genes harboring SNPs that demonstrate allele specificity are enriched for cancer-related biological processes and are more likely to be essential in cancer cells.
Conclusions:
In summary, our study provides a unique and complementary method to identify genes and variants that are relevant to carcinogenesis.
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