Abstract 69: Identification of rare and novel alleles in FFPE tumor samples using laser capture microdissection (LCM) and Ampliseq™ sequencing technologies

Abstract

Abstract Tumors are becoming recognized as genetically heterogeneous masses of cells with different clonal histories. Identifying the mutations present in these heterogeneous masses can lead to important insights into the future behavior of the tumor and possible intervention mechanisms. However, the rarity of pathogenic mutations in small subsets of cells can make identification of such alleles difficult. In this study, we demonstrate a complete workflow that facilitates the identification of rare and novel alleles from FFPE tumor sections. We collected small regions with different cellular morphologies from lung tumor samples using laser capture microdissection, extracted both DNA and RNA from these regions, and characterized mutations present and transcript abundances by using Ampliseq™ targeted sequencing. We show that LCM facilitates the detection of alleles that are not detectable in macrodissected tissue scrapes. We also show that different regions of a tumor have very different patterns of alleles detectable and have a great deal of genetic diversity. Finally, we show that RNA expression patterns are also clearly different in the different regions. Interestingly, dissected regions with similar gross tissue morphologies display differences in alleles present and RNA expression patterns. These results suggest the best way to analyze mutations present in a tumor is to microdissect different subregions of the tumor, and using Ampliseq™ panels to identify the alleles present in those subregions. Citation Format: Stephen Jackson, Paul Choppa, Kulvinda Kulvar, Kristin Schmidt. Identification of rare and novel alleles in FFPE tumor samples using laser capture microdissection (LCM) and Ampliseq™ sequencing technologies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 69. doi:10.1158/1538-7445.AM2015-69