Genomic Health will present results from its first biomarker study using next-generation sequencing at the San Antonio Breast Cancer Symposium in December, company officials said this week.
CEO Kim Popovits said during a call to discuss the company's third-quarter earnings this week that the study was one of 16 abstracts accepted for presentation at the annual conference.
The company said in August that it had completed the 130-patient transcriptome sequencing breast cancer study of formalin-fixed, paraffin-embedded tissue (CSN 8/9/2011).
A key goal of the study was to assess sequencing technology on FFPE tissue. Popovits said this week that the company believes the project "to be the first clinical outcomes study using fixed paraffin-embedded tissue with this new technology."
She said that the company has so far completed two "early clinical research studies" using paraffin-embedded tissue in more than 200 patients.
"We've developed the capability to do both mutation analysis and whole-transcriptome profiling, and we're now applying these capabilities in full clinical development," she said, though she did not elaborate.
The company believes that mutation analysis alone will not be sufficient in helping physicians guide cancer therapy and envisions RNA-seq as a crucial component of genomic medicine.
"We believe that in the future, physicians and patients will require a comprehensive genomic analysis — including specific mutations as well as gene expression — to better inform treatment decisions," Popovits said during the call.
She added that Genomic Health aims "to be the first company to provide a platform that combines whole-transcriptome profiling and mutation analysis for large clinical studies using fixed paraffin-embedded tissue to translate genomic data into actionable clinical tests."
The company plans to provide further detail on these activities "early in 2012," she said.
Genomic Health began implementing next-gen sequencing as part of its discovery pipeline just over two years ago and plans to eventually move its molecular diagnostic platform from quantitative RT-PCR to next-gen sequencing.
Brad Cole, Genomic Health's chief operating officer, said this week that "100 percent of the 'R'" in the company's R&D budget is currently dedicated to next-gen sequencing-based projects, "and more than half of the 'D'" beyond its existing PCR-based projects in breast and prostate cancer.
Next-gen sequencing "is a significant portion of our R&D line," Cole said, but did not provide further details.
The company spent a total of $9.6 million on R&D in the third quarter, a 17 percent increase over $8.9 million in the year-ago period.
The company reported total third-quarter revenues of $52.1 million, a 12 percent jump over $46.3 million in the comparable period of 2010.
Net income decreased 16 percent to $3.2 million from $3.7 million.
As of Sept. 30, Genomic Health held cash and cash equivalents of $38.3 million. Cash, cash equivalents, and investments in marketable securities totaled $87.4 million.