Introduction: There is an urgent need for deep targeted sequencing for detection of varieties of somatic aberrations, including single nucleotide variants (SNV), insertions/deletions (indels), loss of heterozygosity (LOH), and copy number variants (CNV) in heterogeneous FFPE cancer patient specimens. We have developed a Next Generation Sequencing (NGS)-based assay for deep sequencing of a number of selected oncogenes and tumor suppressor genes for testing of clinical breast cancer samples. The panel includes those genes, which are commonly mutated in cancers (e.g. breast and ovarian cancer), based on The Cancer Genome Atlas studies and are potentially indicative of responses to experimental compounds undergoing clinical trials. Importantly, the assay can be used in FFPE samples which pose challenges because of high variability in quality and often suboptimal quantities.

Methods: To minimize FFPE sample input requirement, we optimized multiple assay steps. DNA was extracted from macrodissected FFPE tissue, and randomly fragmented. The DNA library was constructed and subject to target capture and enrichment before being sequenced on the Illumina MiSeq® systems. To analytically qualify the assays, we tested well-characterized cell lines and reference HapMap cell lines. Furthermore, to confirm the performance of the NGS results in clinical FFPE samples, we compared the results generated using orthogonal methodologies, e.g. SNVs using a custom Ion AmpliSeq™ panel (Life Technologies) on Ion Personal Genome Machine® (PGM), or CNVs using real-time PCR assays or custom Nanostring nCounter® CNV assays (NanoString Technologies). To establish the lower limit of detection, we used mixed DNA samples from FFPE cell lines and from HapMap DNA and further tested Horizon FFPE reference DNA containing mutations at defined allele frequencies.

Results: For FFPE DNA extraction, we selected Cobas® FFPE kit (Roche), and Maxwell® CSC DNA FFPE kit (Promega) for higher yield and better purity. For library construction, we chose a KAPA streamlined library preparation kit. For target capture, we used custom xGEN® DNA probes (Integrated DNA Technologies) for improved flexibility in assay optimization, reduced reagent cost, and minimizing batch-to-batch variability. We were able to detect SNVs for >99% of exons selected down to a 5% sensitivity level using about 100 ng FFPE DNA input. Indels, CNV and LOH could also be detected reliably.

Conclusions: We developed a targeted NGS assay that could be used in clinical trials and meets the dual challenge of limited DNA amounts and/or variable quality often associated with FFPE clinical specimens and the detection of low level mutations. Considering the recent recognition of Illumina NGS platform by FDA, this approach can represent a path forward to assist in cancer patient assessment, clinical trial recruitment and care.

Citation Format: Wenge Shi, Christine Chin, Tingdong Tang, Loretta Hipolito, Preethi Srinivasan, Derek Chiang, David Peng, Emmanuelle Di Tomaso, Shabnam Tangri, Jelveh Lameh, Reinhold Pollner. Development of a clinical targeted next generation sequencing test for challenging formalin-fixed paraffin-embedded (FFPE) cancer samples. [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 1892. doi:10.1158/1538-7445.AM2014-1892