Comprehensive Genomic Profiling of Breast Cancer by Massively Parallel Sequencing Reveals New Routes to Targeted Therapies
Jeffrey Ross, Christine Sheehan, Alex Parker, Mirna Jarosz, Sean Downing, Roman Yelensky, Doron Lipson, Philip Stephens, Gary Palmer, Maureen Cronin. Albany Medical College, Albany, NY; Foundation Medicine Inc., Cambridge, MA
Background: The recent introduction of massively parallel (next-generation) DNA sequencing to clinical samples has enabled the discovery of novel and unanticipated genomic-derived drug targets of therapy for patients with refractory metastatic breast cancer.
Design: After DNA was extracted from 4 formalin-fixed paraffin embedded sections cut at 10 microns from 15 cases of primary invasive breast carcinomas, the exons of 145 cancer-related genes were fully sequenced by next-generation technology using the Illumina HiSeq 2000 (Illumina Inc. San Diego, CA) to at an average sequencing depth of 253X. Tumoral DNA was evaluated for point mutations, insertions, deletions, copy number alterations and translocations.
Results: 15/16 (94%) of the tumors revealed 33 total somatic genomic alterations (mean 2.2 alterations per tumor) with a range of 0 to 4 alterations per sample. Standard of care alterations consisted of 3(19%) tumors with HER2 copy number increases. The NGS HER2 copy number measurements by NGS in the HER2 amplified cases averaged 80% of the counted HER2 copies on FISH assessment of the same tumor block. Genes co-amplified with HER2 included RARA. 10/16 (63%) of tumors harbored at least one alteration that potentially could have led to clinical trials of novel targeted therapies including copy number increases for IGF-1R in 2 (13%) tumors [IGF-1R inhibitors], MDM2 in 1 (6%) tumor [nutlins], CCND1 in 3 (19%) tumors [CDK inhibitors], CCNE1 in 1 (6%) tumor [CDK inhibitors] CDK4 in 1 (6%) tumor (CDK inhibitors), and FGF1R in 1 (6%) tumor (FGF1R inhibitors). 5 (31%) of tumors had 1 or more PIK3CA mutations [PIK3CA and mTOR inhibitors]. 6/16 (38%) of tumors had alterations classically associated with adverse clinical outcome including TP53 and PTEN mutations and HER2 copy number increases.
Conclusions: Deep massively parallel DNA sequencing of clinical breast cancer samples uncovers an unexpectedly high frequency of genomic alterations that could influence therapy selection for the disease. Deep sequencing of genomic DNA can provide a broad cancer-related gene survey at a depth of coverage that provides sensitive detection for all classes of genomic alterations, and when applied to breast cancer patients can reveal actionable genomic abnormalities that inform treatment decisions.
Tuesday, March 20, 2012 8:15 AM
Platform Session: Section B, Tuesday Morning