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Genomic Health Announces Positive Results of First Clinical Outcomes Study for Biomarker Discovery Using Next Generation Sequencing at the 2011 CTRC-AACR San Antonio Breast Cancer Symposium
Date:12/8/2011

stics."

Based on these data, Genomic Health is accelerating its efforts to provide a comprehensive genomic platform for clinical research and development combining both whole transcriptome profiling and mutation analysis next year.  Accordingly, the company is accelerating its investment in information technology infrastructure to support the flow and storage of vast amounts of patient genomic data.

"Next generation sequencing allows researchers to process and analyze large volumes of data in a fraction of the time currently required by conventional gene expression profiling technologies," said Jose Esteban, MD, Providence Saint Joseph Medical Center, Burbank, Calif., a co-investigator of the study.  "New methodology used in this study applies NGS-based whole transcriptome profiling to very low amounts of RNA from FFPE tissue that had been archived for up to 12 years, to provide vast amounts of data, with data quality sufficient for broad biomarker discovery from regions outside the previously identified protein-coding sections of the genome." 

Genomic Health scientists carried out whole transcriptome RNA-Seq on FFPE tumor RNA from a cohort of 136 breast cancer patients with tumor tissue obtained at the time of diagnosis and established clinical outcomes for disease recurrence.  These tumors were originally analyzed by RT-PCR in the biomarker discovery phase of the development of the 21-gene Oncotype DX assay.  Sequencing was carried out using the Illumina® HiSeq 2000 instrument and generated over 40 terrabytes of data for analysis.  The data analysis methods used in this biomarker discovery study were the result of a two year effort to optimize methods for RNA-Seq data normalization and other statistical parameters.  

RNA-Seq results were successfully generated for all patients using RNA inputs of just 100 nanograms.  Bar-coded RNAs were sequenced with two samples per flow cell lane, y
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SOURCE Genomic Health, Inc.
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