Abstract
Abstract DNA extraction from formalin-fixed, paraffin-embedded (FFPE) tumor tissues typically results in low quantities of poor-quality, damaged DNA, which present challenges for sequencing. Here we present a fast, streamlined sample-to-answer workflow using probe design software and sample preparation methods optimized to overcome these challenges. DesignStudio® allows for the targeting of up to 1,536 user-defined genomic regions and supports amplicon sizes (150- and 175-bp) ideal for characterizing genomic hot-spot regions or sequencing of whole exons with FFPE DNA. The TruSeq® Custom Amplicon (TSCA) workflow delivers high target enrichment specificity (>80% of reads on target), robust target multiplexing (up to 1,536 amplicons per reaction), and scalable sample indexing (up to 96 libraries) that supports simultaneous sequencing using the MiSeq. We have optimized the DNA extraction and hybridization processes to achieve higher DNA yields and more uniform target representation, respectively. In addition, the improved TSCA assay and software analysis tools significantly reduce false-positive variant calls. In conclusion, we have developed an integrated solution for highly accurate and reproducible detection of somatic variants implicated in cancer biology. Citation Format: Elizabeth Upsall, Katherine Chang, Ian Lewis, April Tian, Anita Iyer, Richard Shen, Charles Lin. Rapid, highly multiplexed somatic mutation analysis of FFPE tissues by deep amplicon sequencing on MiSeq®. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4154. doi:10.1158/1538-7445.AM2013-4154
Published Version
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call