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Genomic Health Announces Results of Biomarker Discovery Program Using Next-Generation Sequencing

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Last week, Genomic Health, Inc. announced that its scientists had successfully used Illumina next-generation sequencing technology to survey expression of the whole human transcriptome and test hypotheses for biomarker discovery in archived tumor and normal breast tissue samples.

The study compared gene expression profiles between twelve normal and twelve tumor formalin-fixed (FFPE) breast specimens — all of which were 10-13 years old. Several thousand coding transcripts were identified as differentially expressed in tumor versus normal, non-cancerous breast tissue. Although association analysis with published patient gene expression data for which there was a record of clinical outcome showed only a modest enrichment for prognostic significance, further evaluation by gene set analysis produced a set that is highly enriched for prognostic genes.

An algorithm was developed to detect and quantify transcripts from non-coding regions of the genome. More than 1,000 differentially expressed non-coding sequences were identified. Several of these non-coding RNAs were used to screen a 136 patient cohort of breast cancer specimens and proved to be associated with breast cancer recurrence risk.

The study findings were presented at the 12th Annual Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida, USA.

Joffre Baker, Chief Scientific Officer at Genomic Health, said:

These results demonstrate the use of next-generation sequencing of formalin-fixed tissue to accelerate testing of hypotheses for biomarker discovery. 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 beyond that already available through the use of Oncotype DX.

Source: Genomic Health