Abstract 4376: Next-generation sequencing of gastric cancer samples from Rwanda: a feasibility study
Authors: Mary D. Chamberlin, Francine B. De Abreu, Torrey L. Gallagher
Journal: Cancer Research (2017)

Abstract Background: Gastric cancer is associated with high morbidity and mortality around the world. In developing countries, patients often present with advanced disease creating a challenge for effective treatment. Next generation sequencing is identifying mutations in more than 50% of gastric cancers in developed countries. Chronic infections and other geographic differences may lead to variations in somatic mutations that could lead to different approaches to treatment. In this pilot study we sought to determine if an overseas collaboration between the University of Rwanda College of Medicine and Health Sciences and the Geisel School of Medicine at Dartmouth was feasible and effective at determining molecular profiles of gastric cancer. Methods: Patients referred for endoscopy at University Teaching Hospital of Kigali, Rwanda were consented to participate prior to the procedure. Biopsy tissues were processed for routine pathologic assessment and those confirmed as gastric adenocarcinoma were included. Formalin-fixed paraffin embedded tissues, H&amp;E stained slides and tissue blocks were transported from Rwanda to New Hampshire, USA by visiting professors participating in the Human Resources for Health Program between May 2015 and July 2016. DNA and RNA from 39 samples were extracted using at least 7 FFPE unstained slides according to AllPrep RNA/DNA FFPE Kit Protocol. Library preparation was performed using 5 ng gDNA using the Pillar NGS SLIMampTM Lung and Colon Hot Spot Panel. Library quanitification was performed using Qubit, and samples with at least 4 nM were normalized, pooled and sequenced on the v3 cartridge on the Illumina's MiSeq system. For data analysis, FASTq files were uploaded to Pillar Biosciences, where sequence alignment, annotation, and variant classification were performed. Results: Eighteen samples had insufficient tissue for nucleic acid extraction. Of the 39 samples processed for sequencing, 17 had low library quantification due to low DNA concentration or poor quality. Mutations were detected in 9/22 samples (41%). One sample contained 3 mutations while the majority of mutated cases had 1-2 mutations identified. A total of 12 mutations were identified: TP53 (4), SMAD4 (2), ERBB4 (2) (S341L and D228N), PTEN (2)(K267RfsTer9 and C136Y), FBXW7 (1) and KRAS (1). Conclusions: Overseas collaboration for next generation sequencing of gastric cancer samples is feasible. Quality control is a common challenge and may improve with larger sized biopsies or tissue blocks. Frequency of mutations is lower than expected. ERBB4 mutations identified are not known to be pathogenic. The PTEN mutations observed are considered pathogenic and this may be a feasible target for therapy. A fusion panel and amplification profiling may be more effective in identifying potential targets for therapeutic trials. Limitations: Small sample size. Panel limited to mutations. Citation Format: Mary D. Chamberlin, Francine B. De Abreu, Torrey L. Gallagher. Next-generation sequencing of gastric cancer samples from Rwanda: a feasibility study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4376. doi:10.1158/1538-7445.AM2017-4376