Asuragen presents data on next generation sequencing of FFPE tumor samples at Molecular Medicine Tri-Conference 2013
Asuragen Inc., a leading molecular diagnostic company, today presented data on SuraSeq™, its proprietary enrichment method for targeted next-generation sequencing (NGS), including recently published data in the Journal of Molecular Diagnostics, at the Molecular Medicine Tri-Conference in San Francisco. In addition to the published data, new data generated by Asuragen indicates that SuraSeq™ can assess up to three times the number of residual clinical FFPE DNA samples than other commercial cancer panels and methods, offering high depth, targeted NGS of oncogenes across a broad range of FFPE biopsies and improved analytical sensitivity compared to “gold standard” methods, such as Sanger sequencing.
“There remains a paucity of published data for the application of targeted NGS to real-world cancer specimens, such as FFPE tumor biopsies. Our publication describes novel enrichment methods and quality control checks of nanogram quantities of FFPE and FNA DNA that were sequenced on complementary NGS platforms to provide accurate and sensitive detection of “druggable” mutations,” commented Gary Latham, Ph.D., Vice President, Research and Technology Development at Asuragen.
Implementation of next-generation sequencing into routine clinical practice requires compatibility with common tumor specimens, such as FFPE and fine-needle aspiration (FNA) biopsies, and validated processes for controls, samples, platforms, and data analysis pipelines. Asuragen’s study in the Journal of Molecular Diagnostics describes the validation of a two-step PCR enrichment workflow (SuraSeq™ 500) that interrogates 540 known cancer-relevant variants from 16 oncogenes across distinct NGS chemistries (Illumina GAIIx and Ion Torrent PGM). The study included a rigorous characterization of the sequencing “noise” associated with FFPE samples, and the development of a novel bioinformatics pipeline to resolve this background to reveal low-level mutations. NGS variant calls from 38 residual clinical colorectal cancer FFPE specimens and 10 thyroid FNA specimens demonstrated an accuracy of 96.1% compared with Sanger sequencing, and 99.6% compared to Asuragen’s Signature® KRAS mutation assay. Importantly, the publication also demonstrates the value of an orthogonal NGS platform in confirming cancer mutations identified from the primary NGS assay: Five “driver” mutations in the FFPE tumor cohort that were co- identified by the two independent NGS systems failed to be detected by Sanger sequencing, including variants that were confirmed using highly sensitive Signature mutation assays. SuraSeq™ offers high depth, targeted NGS of oncogenes across a broad range of FFPE biopsies and improved analytical sensitivity compared to last-generation, “gold standard” methods, such as Sanger sequencing, and can enable unprecedented versatility for mutation screening and confirmation to advance existing and emerging clinical applications. The SuraSeq™ technology is available through Asuragen’s Translational Diagnostics laboratory, including three panels ranging from 250 to greater than 7,500 mutations of clinically relevant cancer genes (SuraSeq™ 200, 500, 7500).
About SuraSeqTM NGS Services
The use of genomic profiling to discover novel, disease-associated mutations has enormous potential to improve clinical decision-making. Asuragen specializes in targeted next-generation sequencing for sensitive detection of clinically actionable mutations from limiting DNA quantities. SuraSeq™ NGS Services are optimized to provide high resolution mutation profiling from challenging clinical biopsies through a combination of quantitative sample characterization and qualification, novel enrichment designs that specifically accommodate poor quality DNA, and innovative bioinformatics algorithms that call low abundance mutations with high sensitivity and positive predictive value.
Asuragen is a molecular diagnostics company with a pioneering position in miRNA using genomics to drive better patient management through best-in-class clinical testing solutions. The Company uses a breadth of technologies and talent to discover, develop and commercialize diagnostic products and clinical testing services with efficiency and flexibility both internally and for our companion diagnostic partners. Today, Asuragen’s products, services and technologies drive countless patient management decisions across oncology, genetic disease and other molecular testing modalities. In the future, we envision the Company’s development of miRNA-based clinical diagnostics will help transform medicine by improving clinical outcomes and health economics. For more information, visit www.asuragen.com.