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

Abstract

AIMTo study cancer hotspot mutations by next-generation sequencing (NGS) in stool DNA from patients with different gastrointestinal tract (GIT) neoplasms.METHODSStool 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® 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.RESULTSNGS 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.CONCLUSIONOur results show that in addition to colorectal neoplasms, mutations can also be assayed from stool specimens of patients with gastric neoplasms.

Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin

“…Gene mutation analysis of host DNA from stool samples. Data regarding hotspot mutations in KRAS, NRAS, HRAS, and TP53 genes in DNA from stool samples of Finnish patients was collected from previously published results (15). Gene mutation information was available for 79/83 CRC patients; TP53 mutations were seen in 13, NRAS in 6, KRAS in 3 and no mutations in HRAS patients (all RAS mutations were found in 9 patients).…”

“…DNA isolated from stool samples of both Finnish and Iranian CRC patients were studied for hotspot mutations in 22 cancer-related genes by targeted next generation sequencing using Ion AmpliSeq Colon and Lung Cancer panel v2 (Thermo Fisher Scientific, Waltham, MA, USA). DNA samples were sequenced on Ion Personal Genome Machine System (Thermo Fisher Scientific, Waltham, MA, USA) as previously described (15).…”

A Simple and Highly Specific MassARRAY-Based Stool DNA Assay to Prioritize Follow-up Decisions in Fecal Immunochemical Test-Positive Individuals

“…Of them, 54% (7 variants) were located in APC, TP53 , and PIK3CA . Recently, Youssef et al [16] used NGS to survey the mutation patterns in 87 CRC stool samples, and found 20 mutations in 11 genes. Of them, APC and TP53 were the most frequently mutated genes.…”

Tissue gene mutation profiles in patients with colorectal cancer and their clinical implications

“…NGS provides sequencing data in quantities orders of magnitude higher than Sanger sequencing, and with much greater sensitivity (9). NGS has been used for detection of gene mutations in CRC using DNA from tissue sections, blood and stool (10)(11)(12)(13)(14)(15). Pooling of large quantities of data of gene mutations from tumor tissues and determining their associations with the clinicopathological characteristics may provide important information regarding the pathogenesis of CRC, and thus novel approaches for clinical intervention.…”