Next Generation Sequencing From Paraffin Tissue, Enhancing Understanding of Tumor Biology
Genomic Health Announces Results from Two Studies Demonstrating Innovations in Next Generation Sequencing From Paraffin Tissue, Enhancing Understanding of Tumor Biology
Results Presented at the 14th Annual Advances in Genome Biology and Technology Meeting Reveal Novel Method for RNA-Sequencing and Mutation Identification
REDWOOD CITY, Calif., Feb. 25, 2013 Genomic Health today announced the results of two studies demonstrating that DNA strand-of-origin information can help further refine the identification of prognostic biomarkers, and that tumor specific gene mutations can be effectively examined using archival fixed paraffin embedded tumor (FPET) tissue, enabling an improved and more practical process of tumor analysis. These new findings were presented at the 14th Annual Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Fla.
"Our continued research efforts demonstrate the biological and technical capabilities of our advanced next generation sequencing (NGS) methods for biomarker discovery and validation," said Steven Shak, M.D., chief medical officer and executive vice president for research and development at Genomic Health. "These findings will accelerate the development of future tests based on our ongoing clinical research that combines both whole transcriptome profiling and mutation analysis."
Novel Next Generation Sequencing and Bioinformatics Methods Enhance Biomarker Discovery
•Building on study results published in PLoS One -- where Genomic Health scientists carried out whole transcriptome RNA-Seq on FPET RNA from a cohort of 136 breast cancer patients -- this analysis evaluated the impact of DNA strand-of-origin information on the identification of prognostic biomarkers.
During DNA transcription, only one of the two double-stranded DNA molecules is used as a template for an RNA transcript and protein production. Analytic approaches that do not consider the strand-of-origin of RNA sequencing data can be limited in their accuracy in assigning reads to human genes. Therefore, to perform this study, Genomic Health scientists developed a proprietary NGS and bioinformatics approach to produce a more definite specification of the strand-of-origin of the RNA transcript. The application of this method enabled more precise detection of expressed genes that were significantly associated with breast cancer recurrence, and permitted the identification of 228 additional candidate genes associated recurrence risk in breast cancer.
Enabling Detection of Tumor Specific Mutations Using FPET to Improve Precision of Cancer Diagnosis
•Reliable differentiation between inherited variations in DNA (germline mutations) and tumor specific variations in DNA (somatic mutations) plays a key role in determining the accuracy and precision of cancer genome sequencing. However, optimally, determination of germline mutations requires the presence of the blood samples in addition to the FPET specimen. This new study showed that by utilizing Genomic Health's proprietary NGS methods to analyze archival FPET specimens, the company can now reliably detect germline variants and tumor specific mutations when the patient's blood sample is not available.
As part of this study, 190 frequently mutated cancer genes were sequenced using the Illumina HiSeq™ 2000 System from FPET blocks, analyzing both the patient's tumor tissue and adjacent non-tumor tissue. Similar sequence analysis was performed on patient-matched blood samples. Readily-available adjacent non-tumor tissue in the FPET specimen was a sufficient alternate source of germline variants to enable the accurate detection of cancer-specific somatic mutations in the tumor.
"Individual patients have an abundance of unique somatic mutations which underscores the heterogeneity of cancer and the importance of gaining better understanding of individual tumor biology for more accurate diagnosis," said Samuel Levy, Ph.D., Genomic Health's chief scientific officer. "By applying this technique to work with patients' archival FPET tissue to identify and account for germline variants, we can learn more from the FPET tumor tissue saved from landmark clinical studies when matched blood samples are not available."