Genomic Health Reports Use of Illumina NGS Technology on Archived Tumors for Biomarker Discovery

Genomic Health reports that it has completed a survey of the whole human transcriptome using Illumina’s next-generation DNA sequencing technology to test hypotheses for biomarker discovery in archived tumor and normal breast tissue samples.

“These results demonstrate the use of next-generation sequencing of formalin-fixed tissue to accelerate testing of hypotheses for biomarker discovery,” according to Joffre Baker, CSO at Genomic Health. “Our long-term goal for this and future studies is to validate the findings with large, well-designed clinical trials in an effort to connect either gene mutations or expression profiles to clinical outcomes and provide additional personalized information to physicians and patients.”

Genomic Health scientists were comparing gene-expression profiles between 12 normal and 12 tumor formalin-fixed breast specimens, all of which were 10–13 years old. Each sample, on average, yielded 19 million base pairs of DNA with approximately 85% mapping to unique sites in the human genome.

Further evaluation showed that 3,584 coding genes were differentially expressed between tumor and normal specimens. The association of each of these with the risk of breast cancer recurrence was sought by consulting published gene-expression results from approximately 3,000 patients with breast cancer tumors for which there was a record of clinical outcome.

The analysis showed that sets of transcripts over-expressed in tumors compared with normal tissues produced only a modest enrichment for prognostic significance. Further evaluation of these transcripts by gene-set analysis produced a group that is highly enriched for prognostic genes, according to Genomic Health.

In addition, an algorithm was developed to detect and quantify transcripts from noncoding regions of the genome. More than 1,000 differentially expressed noncoding sequences were thus identified. RT-PCR assays were designed for a number of the noncoding transcripts and were used to screen a 136-patient cohort of breast cancer specimens. Several of these noncoding RNAs proved to be associated with breast cancer recurrence risk.

Genomic Health is a molecular diagnostics company developing and commercializing clinical laboratory services that analyze the underlying biology of cancer. It commercializes the Oncotype DX® Breast Cancer test, has been shown to predict the likelihood of chemotherapy benefit as well as recurrence in early-stage ER-positive breast cancer. Genomic Health also provides the Oncotype DX Colon Cancer test, a multigene-expression test developed for the assessment of risk of recurrence in patients with stage II disease.

Total product revenue for 2009 was $146.6 million, a 34.87% increase from 2008 product revenues of $108.7 million. Total revenue for 2009 increased to $149.5 million compared with $110.6 million in 2008. Third quarter 2010 product revenue increased by 18% from the same period in 2009. Genomic Health says that as of September 30, 2010, more than 10,000 physicians in over 55 countries had ordered more than 175,000 Oncotype DX tests.