Abstract 3883: Multiplexed formats for detection of SNPs for cell line authentication and cancer related mutations

Abstract

Abstract Rapid and accurate identification of SNPs and mutations are useful in ensuring that the correctly identified cell lines are being used in cancer research studies and for accurate identification of SNPs and indels in cancer cells. In this study we report on a method that uses nucleic acid isolation methods, multiplexed PCR to amplify up to 48 regions within the human genome followed by an oligonucleotide ligation assay that can detect SNPs, mutations and indels. The protocol takes about 4 hrs to complete and uses panels optimized for human cell identification and detection of mutations in EGFR and KRAS genes. We typed the NCI-60 panel and several cell lines from the ATCC using two panels. One is a panel of SNPs that has been tested with samples from over 46 human populations to identify a set of SNPs that would discriminate globally. This SNP set has 48 markers with high heterozygosity (>0.4) and low Fst values (<0.06) across multiple human populations. The panel has a high power of discrimination. (Hum Genet; 127 (3) 315-324; 2010) comparable to that obtained with STR kits. A panel of 31 samples from closely related individuals within families was typed to test the power of discrimination. In another study, we applied this system to a cancer mutation study, in which an assay for detecting 29 EGFR and 5 KRAS gene mutations was developed. These mutations are frequently found in human cancers. DNA preparations from 48 ATCC and 60 NCI tumor cell lines were genotyped by this assay. These SNPs and mutations were further confirmed by the Sanger sequencing chemistry, showing 100% concordance between two technologies. The information generated from this study will be definitely useful when these cell lines are used as models for cancer study and cancer drug screening. In conclusion, we have developed a sensitive, highly accurate, high throughput genotyping system. Studies have demonstrated its effectiveness for successful SNP/InDel detection and mutation screening. This system has been successfully used for oncogen mutation studies in cancer cell lines. Overall, the system can become a valuable tool for molecular and clinical diagnostics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3883. doi:10.1158/1538-7445.AM2011-3883