Gene mutations in stool from gastric and colorectal neoplasia patients by next-generation sequencing

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http://hdl.handle.net/10138/230818

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Youssef , O , Sarhadi , V , Ehsan , H , Böhling , T , Carpelan-Holmström , M , Koskensalo , S , Puolakkainen , P , Kokkola , A & Knuutila , S 2017 , ' Gene mutations in stool from gastric and colorectal neoplasia patients by next-generation sequencing ' , World Journal of Gastroenterology , vol. 23 , no. 47 , pp. 8291-8299 . https://doi.org/10.3748/wjg.v23.i47.8291

Title: Gene mutations in stool from gastric and colorectal neoplasia patients by next-generation sequencing
Author: Youssef, Omar; Sarhadi, Virinder; Ehsan, Homa; Böhling, Tom; Carpelan-Holmström, Monika; Koskensalo, Selja; Puolakkainen, Pauli; Kokkola, Arto; Knuutila, Sakari
Contributor: University of Helsinki, Medicum
University of Helsinki, Medicum
University of Helsinki, HUSLAB
University of Helsinki, Clinicum
University of Helsinki, Department of Surgery
University of Helsinki, Clinicum
University of Helsinki, II kirurgian klinikka
University of Helsinki, Medicum
Date: 2017-12-21
Language: eng
Number of pages: 9
Belongs to series: World Journal of Gastroenterology
ISSN: 1007-9327
URI: http://hdl.handle.net/10138/230818
Abstract: AIM To study cancer hotspot mutations by next-generation sequencing (NGS) in stool DNA from patients with different gastrointestinal tract (GIT) neoplasms. METHODS Stool samples were collected from 87 Finnish patients diagnosed with various gastric and colorectal neoplasms, including benign tumors, and from 14 healthy controls. DNA was isolated from stools by using the PSP (R) Spin Stool DNA Plus Kit. For each sample, 20 ng of DNA was used to construct sequencing libraries using the Ion AmpliSeq Cancer Hotspot Panel v2 or Ion AmpliSeq Colon and Lung Cancer panel v2. Sequencing was performed on Ion PGM. Torrent Suite Software v.5.2.2 was used for variant calling and data analysis. RESULTS NGS was successful in assaying 72 GIT samples and 13 healthy controls, with success rates of the assay being 78% for stomach neoplasia and 87% for colorectal tumors. In stool specimens from patients with gastric neoplasia, five hotspot mutations were found in APC, CDKN2A and EGFR genes, in addition to seven novel mutations. From colorectal patients, 20 mutations were detected in AKT1, APC, ERBB2, FBXW7, KIT, KRAS, NRAS, SMARCB1, SMO, STK11 and TP53. Healthy controls did not exhibit any hotspot mutations, except for two novel ones. APC and TP53 were the most frequently mutated genes in colorectal neoplasms, with five mutations, followed by KRAS with two mutations. APC was the most commonly mutated gene in stools of patients with premalignant/benign GIT lesions. CONCLUSION Our results show that in addition to colorectal neoplasms, mutations can also be assayed from stool specimens of patients with gastric neoplasms.
Subject: Stool DNA
next-generation sequencing
Mutations
Gastric neoplasia
Colorectal neoplasia
TUMOR-SUPPRESSOR GENE
APC GENE
ADENOMATOUS POLYPOSIS
STROMAL TUMOR
CANCER
ADENOCARCINOMA
CARCINOMA
KRAS
FREQUENT
GROWTH
3121 General medicine, internal medicine and other clinical medicine
3111 Biomedicine
3126 Surgery, anesthesiology, intensive care, radiology
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