Abstract 1520: Development of low-cost high throughput screening pipeline for detecting germline cancer causing mutations in Hispanic populations

Abstract

Cancer is a leading cause of non-communicable morbidity and mortality worldwide. Hispanics are the largest and fastest growing ethnic group in the U.S. and the largest population group in the Americas. Due to health care disparities, this population remains understudied and under-screened for cancer causing gene mutations. While many genes that predispose individuals for different cancers have been discovered, the prevalence of mutations in these genes remains largely undetermined in many populations. Developing customized screening panels and screening for novel variants for large population samples can be expensive and time consuming. We have developed a low-cost, high-throughput pipeline and method to screen 480 customizable amplicons (∼20 genes, ∼144Kbp) for up to 384 samples per run. By combining a bioinformatics pipeline for design and analysis with Fluidigm microfluidics PCR and Illumina MiSeq, we can quickly screen multiple cancer panels at a high depth of coverage, at a low cost per sample. The amplicon design pipeline provides ability to develop amplicon primer sets and pooling strategies. Libraries of 384 barcoded samples are run in a single MiSeq lane. Sequencing data is analyzed by an automated pipeline, which aligns using BWA-MEM, calls variants using VarScan 2, and annotates variants using multiple datasets using Annovar. We have applied these pipelines and methods to identify mutation in known cancer genes, such as APC, MSH2, MLH1, BRCA1, and BRCA2, in several hundred Hispanic individuals with familial and early-onset colon and breast cancer. While many of the mutations have been previously reported, we have identified several novel mutations that appear to have Amerindian origin. Moreover, a few are shared among many individuals in isolated geographic locations, suggesting founder effects are common in some of these populations. Over 50% of the patients screened to date have no mutations in our cancer panels; we plan to use these samples to screen for novel genes using whole exome or genome sequencing in the next phase of our study. In conclusion, we have developed a low-cost, high-throughput pipeline for screening customizable panels for known and novel mutations. Our study is an initial step to assess prevalence of known cancer causing genes and identify novel genes/mutations that contribute to different cancers in the Hispanic community. These discoveries provide a foundation for early detection, prevention, and treatment of familial cancers in Hispanic populations. Citation Format: Paul Lott, Ruta Sahasrabudhe, Anna Marie Tuazon, John Williamson, Ana Estrada, Mabel Bohorquez, Rodrigo Prieto, Angel Criollo, Alejandro Velez, Jorge Castro, Gilbert Mateus, María Magdalena Echeverry, Luis Carvajal-Carmona. Development of low-cost high throughput screening pipeline for detecting germline cancer causing mutations in Hispanic populations. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1520. doi:10.1158/1538-7445.AM2014-1520