Document Type
Article
Publication Date
8-12-2023
Abstract
Recently, worldwide incidences of young adult aggressive colorectal cancer (CRC) have rapidly increased. Of these incidences diagnosed as familial Lynch syndrome (LS) CRC, outcomes are extremely poor. In this study, we seek novel familial germline variants from a large pedigree Tunisian family with 12 LS-affected individuals to identify putative germline variants associated with varying risk of LS. Whole-genome sequencing analysis was performed to identify known and novel germline variants shared between affected and non-affected pedigree members. SNPs, indels, and structural variants (SVs) were computationally identified, and their oncological influence was predicted using the Genetic Association of Complex Diseases and Disorders, OncoKB, and My Cancer Genome databases. Of 94 germline familial variants identified with predicted functional impact, 37 SNPs/indels were detected in 28 genes, 2 of which (MLH1 and PRH1-TAS2R14) have known association with CRC and 4 others (PPP1R13B, LAMA5, FTO, and NLRP14) have known association with non-CRC cancers. In addition, 48 of 57 identified SVs overlap with 43 genes. Three of these genes (RELN, IRS2, and FOXP1) have a known association with non-CRC digestive cancers and one (RRAS2) has a known association with non-CRC cancer. Our study identified 83 novel, predicted functionally impactful germline variants grouped in three “variant risk clusters” shared in three familiarly associated LS groups (high, intermediate and low risk). This variant characterization study demonstrates that large pedigree investigations provide important evidence supporting the hypothesis that different “variant risk clusters” can convey different mechanisms of risk and oncogenesis of LS-CRC even within the same pedigree.
Recommended Citation
Barbirou, Mouadh; Miller, Amanda A.; Mezlini, Amel; Bouhaouala-Zahar, Balkiss; and Tonellato, Peter J., "Variant Characterization of a Representative Large Pedigree Suggests “Variant Risk Clusters” Convey Varying Predisposition of Risk to Lynch Syndrome" (2023). Department of Medical Oncology Faculty Papers. Paper 248.
https://jdc.jefferson.edu/medoncfp/248
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Supplementary Materials
Language
English
Comments
This article is the author's final published version in Cancers, Volume 15, Issue 16, 2023, Article number 4074.
The published version is available at https://doi.org/10.3390/cancers15164074. Copyright © 2023 by the authors. Licensee MDPI, Basel, Switzerland.