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Fox Chase Case Study Demonstrates NGS Panel's Ability to Accurately Diagnose Cancer

NEW YORK (GenomeWeb) – A case study from the Fox Chase Cancer Center has illustrated the ability of the center's 50-gene next-generation sequencing cancer panel to correctly diagnose tricky cases and impact patients' treatment.

Researchers from Fox Chase published the details of the patient case in the Journal of the National Comprehensive Cancer Network this month.

In the paper, the researchers described a 72-year-old woman who had been diagnosed with triple negative breast cancer at the age of 70. She had undergone surgery and radiation and was receiving checkups every three months.

In March 2014, however, she developed a cough severe enough that she went to the hospital. A CT scan identified a large lung mass. Physicians biopsied the mass, and its morphology and immunohistochemical profile led pathologists to believe it was a primary tumor. A subsequent MRI also found two small brain metastases and the woman was diagnosed with stage IV lung cancer. Although she had never smoked, she grew up being exposed to second-hand smoke. The patient received radiation therapy for her brain metastases and chemotherapy.

However, physicians also used the center's 50-gene next-generation sequencing-based test, CancerCode, on DNA from the lung biopsy. The panel identified three somatic mutations in ERRB2, TP53, and SMARCB1. Because of the ERBB2 mutation, the physicians also requested screening of the original breast cancer biopsy. Sequencing identified the same three mutations in the original breast tumor, which provided "strong genetic evidence that the tumor in the lung was actually a metastasis from the breast primary, because the two tumors shared the identical genetic mutational profile," the authors wrote.

Immunohistochemistry of the lung tumor found that it was HER2 positive and physicians subsequently switched her therapy to include trastuzumab and pertuzumab, monoclonal antibodies that target HER2, along with the general chemotherapy agent carboplatin. The patient has achieved an ongoing partial response, the authors reported.

The authors hypothesized that although the original breast tumor was in fact HER2 negative, the driver mutation in HER2 existed in the original tumor, but was a minor clone. The HER2 positive clone was then likely "selected for metastatic spread" and became the dominant clone.

"Genetic mutational profiling using NGS, although not yet standard in patients with breast cancer or in patients with unknown primary tumors, may be extremely valuable in not only finding targetable genetic mutations but also potentially yielding relevant diagnostic information when a unique genetic mutational profile is detected," the authors wrote.

In addition, screening for biomarkers such as HER2, as well as including an NGS panel for select patients, "reflects a personalized medicine approach, which allows one to find new therapeutic targets and identify the subset of patients who may derive benefit from targeted therapies that can dramatically impact their care."