Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data

Oncotarget
Duarte Mendes OliveiraAntonia Rizzuto

Abstract

The objective of this study was to determine the feasibility to detect copy number alterations in colon cancer samples using Next Generation Sequencing data and to elucidate the association between copy number alterations in specific genes and the development of cancer in different colon segments. We report the successful detection of somatic changes in gene copy number in 37 colon cancer patients by analysis of sequencing data through Amplicon CNA Algorithm. Overall, we have found a total of 748 significant copy number alterations in 230 significant genes, of which 143 showed CN losses and 87 showed CN gains. Validation of results was performed on 20 representative genes by quantitative qPCR and/or immunostaining. By this analysis, we have identified 4 genes that were subjected to copy number alterations in tumors arising in all colon segments (defined "common genes") and the presence of copy number alterations in 14 genes that were significantly associated to one specific site (defined "site-associated genes"). Finally, copy number alterations in ASXL1, TSC1 and IL7R turned out to be clinically relevant since the loss of TSC1 and IL7R was associated with advanced stages and/or reduced survival whereas copy number gain of ASXL...Continue Reading

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Citations

May 31, 2019·Molecular & Cellular Proteomics : MCP·Sara R SavageBing Zhang
Jan 31, 2020·Frontiers in Genetics·Zhiqiang ChangWenyuan Zhao
Dec 30, 2018·European Journal of Medicinal Chemistry·Meiyang XiHaopeng Sun
Aug 9, 2019·Molecular & Cellular Proteomics : MCP·Sara R SavageBing Zhang
Aug 11, 2020·Molecular Therapy. Methods & Clinical Development·Zhiqiang ChangYan Xu

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BETA
surgical resection
pull-down
PCR
light microscopy

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