Comprehensive Genotype Determined for Individual Cancer Cases

A multiplexed polymerase chain reaction (PCR) assay, known as SNaPshot, which is a clinical genotyping test, is based on a commercial platform and it was integrated into routine practice as Clinical Laboratory Improvement Amendments (CLIA)-certified tests.

Scientists at Massachusetts General Hospital (Boston, MA, USA) evaluated 589 samples taken from individuals with NSCLC using SNaPshot from March 2009 to May 2010. Genotyping was carried out on DNA derived from formalin-fixed paraffin-embedded (FFPE) tumor specimens using SNaPshot, a targeted mutational analysis assay designed by the group. The SNaPshot platform consists of multiplexed PCR and single-base extension reactions that generate fluorescent-labeled probes designed to discern hot-spot mutation sites.

Out of the samples taken 546 had sufficient tissue to be tested. Turnaround time varied from one to 8.9 weeks, the longer time usually resulted from samples being retested. In 282 (51%) of the samples one or more mutations or rearrangements were discovered, with the most prevalent being: 13% in the epidermal growth factor receptor (EGRF); 5% in the anaplastic lymphoma tyrosine kinase receptor (ALK); 24% in the Kirsten rat sarcoma viral oncogene homolog (KRAS); 4% in the phosphoinositide-3-kinase, catalytic, alpha polypeptide (PIK3CA) and 5% in the tumor protein p53 (TP53) genes.

Out of the 353 participants, the 170 who had advanced disease with stage IIIb, IV or recurrent, had genetic mutations or rearrangements in v-raf murine sarcoma viral oncogene homolog B1 (BRAF), Human Epidermal growth factor Receptor 2 (HER2), ALK, PIK3CA, EGRF, and KRAS genes. These patients were classified as "potentially targetable" as they could join clinical trials analyzing medications targeting these genetic changes. The SNaPshot genetic screening was based on the platform from Applied Biosystems (Carlsbad, CA, USA).

Lecia Sequist, MD, MPH, the senior author of the study said, "To our knowledge we are the first center to offer this broad multiplexed genetic screening to all non-small-cell lung cancer patients. Broad genotyping is going to become part of everyday care for lung cancer patients - the field is clearly moving in this direction. Our study is exciting because it demonstrates that indeed it is possible today to integrate testing for multiple genetic biomarkers into a busy clinic and steer patients toward personalized therapies.” SNaPshot can be performed in the majority of existing clinical molecular diagnostic laboratories affiliated to hospitals and other institutions, using equipment already available. The study was published on November 9 2011, in the cancer journal Annals of Oncology.

Related Links:
Massachusetts General Hospital
Applied Biosystems