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Updated: Sep 27, 2026
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Somatic Mutation Profile in Normal Tissue Adjacent to Tumor in Colorectal Carcinoma Patients: Functional Effect on
Farzana Jasmine1, Daniil Vasiljevs1, Armando Almazan1
1Institute for Population and Precision Health (IPPH), University of Chicago, Chicago, IL 60637, USA.
Abstract:
Background: The somatic mutation (SM) profile of normal colon tissue in colorectal carcinoma (CRC) patients is not well-known. We examined (a) SMs in resected normal colonic tissue adjacent to tumors from non-metastatic CRC patients, (b) identified potentially malignant mutations, and (c) their functional effects and utility for precision medicine. Materials and Methods: Surgically resected fresh paired tumor and adjacent normal colon tissues from 61 patients were used as sources of tissue DNA. Whole blood (WB) DNA was used as a germline reference. Next-generation sequencing using a custom hybridization capture panel was performed on each. Differential gene expression was assessed and stratified by mutation status in normal tissue. Results: Compared to WB DNA, similar numbers of SMs were detected in tumor and adjacent normal colon tissue. Of all SMs found in adjacent tissue, more than 23% of those same mutations were also detected in the matched tumor. Of the 61 patients, 57 (93.4%) had at least one potentially malignant non-synonymous SM in their normal tissue. The most frequently involved genes were BRCA2 (67% of the patients), KMT2C (64%), DHFR (49%), APC (41%), MAP3K1 (41%), PIK3CA (39%), PTEN (39%), ARID1A (38%), and MSH6 (38%). The use of WB as a germline reference was important, as using only adjacent normal tissue as a reference caused false negatives for mutations shared between tumor and normal tissue. Mutation status in normal tissue was associated with differential gene expressions in matched tumors. APC mutations were associated with more marked down-regulation of APC, SLC26A3, SELENBP1, KRT20, and CXCL14, and more marked up-regulation of MMP1, MMP12, MTHFD1L and MTHFD2, the latter two suggesting the folate pathway as a potential therapeutic target. Conclusions: For the first time, we document a comprehensive SM profile of normal colon tissue adjacent to tumors in CRC patients and observe its functional effect on differential gene expression in matched tumor tissue to identify potential therapeutic applications in precision medicine.
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