Targeted sequencing-based analyses of candidate gene variants in ulcerative colitis-associated colorectal neoplasia.

British Journal of Cancer
Sanjiban ChakrabartyKapaettu Satyamoorthy

Abstract

Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma. Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia. Findings from the study are also compared with previously published genome wide and exome sequencing data in inflammatory bowel disease-associated and sporadic colorectal carcinoma. Next-generation sequencing analysis identified 1107 mutations in 275 genes in UCHR subjects. In addition to TP53 (17%) and KRAS (22%) mutations, recurrent mutations in APC (33%), ACVR2A (61%), ARID1A (44%), RAF1 (39%) and MTOR (61%) were observed in UCHR subjects. In addition, APC, FGFR3, FGFR2 and PIK3CA driver mutations were identified in UCHR subjects. Recurrent mutations in ARID1A (44%), SMARCA4 (17%), MLL2 (44%), MLL3 (67%), SETD2 (17%) and TET2 (50%) g...Continue Reading

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Citations

Aug 2, 2019·Digestive Diseases and Sciences·Kristin E BurkeJames M Richter
Dec 18, 2019·Journal of Oral Pathology & Medicine : Official Publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology·Chinchu JayaprakashKapaettu Satyamoorthy
Feb 2, 2021·International Journal of Cancer. Journal International Du Cancer·Satu Mäki-NevalaPäivi Peltomäki
Feb 26, 2021·Journal of Oncology·Ke ChenJiliang Wang
Oct 15, 2020·Journal of Cancer Research and Clinical Oncology·Sannia SjöstedtChristian von Buchwald
Jun 5, 2021·Mutation Research. Reviews in Mutation Research·Ruihua WangKaren Poon
Jul 3, 2021·Cancers·Mehmet YalchinAilsa Hart
Aug 5, 2021·Inflammatory Bowel Diseases·Giuseppe BiscagliaOrazio Palmieri

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Methods Mentioned

BETA
biopsies
Assay
PCR
chip
deamination
histone acetylation

Software Mentioned

Maftools
GSEA
Integrative Genomic Viewer
CIRCOS
Variant Effect Scoring Tool
Torrent Suite
Coverage Analysis Plugin
Ion Reporter
Ion Torrent Variant Caller Plugin
Ensembl74

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