Pathologists and specialists in laboratory medicine at the Penn Center for Personalized Diagnostics (CPD) are performing genomic testing—including large-scale, massively parallel DNA sequencing and chromosomal analysis for identification of large structural rearrangements—to define genomic alterations in hematologic and solid tumor cancers for cancer patients at Penn Medicine.
Massively parallel DNA sequencing (sometimes known as next-generation sequencing or NGS) can recognize abnormalities in tumor cells that are not readily apparent to pathologists at a microscopic level. When applied to the DNA of an individual's cancer cells, the process can yield a complete profile of the tumor genome, including personal mutation signatures for distinct tumor subtypes, that is as distinct as a fingerprint.
In addition, the testing for genomic rearrangements can detect tumor susceptibility to some targeted therapies. Together these analyses are powerful detectors of signatures that can be used to identify individualized treatment options and to gauge the extent to which a patient will respond to treatment.
At the CPD, a joint initiative between the Department of Pathology and Laboratory Medicine and the Abramson Cancer Center at Penn Medicine, approximately 75% of patients tested have received genomic testing results that altered prognosis or empowered the treating oncologists to alter the patients' treatment therapy, or both.
The Penn CPD is a CAP/CLIA certified laboratory. The equipment and instrumentation at the CPD currently include an Illumina HiSeq 2500, two Illumina MiSeq sequencers and an ION® Personal Genome Machine, all of which are capable of detecting low-level mutation loads and are instrumental in the sequencing of genomic DNA in tumor specimens.
The CPD offers two cancer gene-sequencing panels (below), a custom hematologic malignancy panel, focused primarily on AML, MDS and CLL, and a more comprehensive solid tumor panel, containing 47 genes known to be mutated in a wide range of tumor types.
Case Study
Figure 1: Thoracic CT scan demonstrating stage IV non-small cell lung cancer in the right lung. A solid tumor cancer gene sequencing panel and cytogenetic analysis at the Penn Center for Personalized Diagnostics identified an EML4-ALK mutation in this patient.
Mr. M, a 43-year-old policeman, was referred to the Abramson Cancer Center by his personal physician after a chest CT scan revealed a massive lesion in his right lung (Figure 1). The x-ray was preceded by several months of declining health attended by weight loss, severe headache, back pain and chronic low-grade fever.
A sputum analysis and fine needle aspiration biopsy at the Abramson Cancer Center confirmed the presence of stage IV non-small cell lung cancer (NSCLC). Soon thereafter, a full-body MRI found lesions at Mr. M's spine and brain, as well.
Mr. M was young and had never smoked, characteristics more likely to be associated with the presence of mutations in targetable genes, including the epidermal growth factor receptor (EGFR), and the tyrosine kinase mutation EML4-ALK, both potent oncogenic drivers linked to lung tumorigenesis.
EGRF mutations are identified in 15% to 20% of lung adenocarcinomas and ALK gene rearrangements are found in 3% to 5% of NSCLCs. Both gene mutations are seen predominately in younger patients who never smoked, a unique subset of the NSCLC population, and are rarely seen in older individuals and those with a smoking history.
In recent years, very efficacious tyrosine kinase inhibitors have been developed to treat patients with EGFR and EML4-ALK mutations. However, because each agent is designed to target a specific mutation, it was critical to initiate a complete profile of Mr. M's tumor genome.
At the Penn Center for Personalized Diagnostics, a comprehensive solid tumor panel and cytogenetic analysis was subsequently performed on tissue derived from Mr. M's tumor. The report delivered to his oncologist two weeks later confirmed an EML4-ALK translocation (Figure 2).
Figure 2: Fluorescence in situ hybridization (FISH) image of positive ALK: adjacent red and green signals represent normal ALK, while separated red and green signals indicate ALK rearrangement.
Mr. M immediately began therapy with crizotinib, an oral, small molecule tyrosine kinase inhibitor that targets ALK. Crizotinib has been shown in clinical trials to offer sustained progression-free survival in NSCLC patients with brain metastases, and is associated with much lower rates of adverse effects than many other cancer therapies.
Mr. M responded well to treatment. A CT scan taken at eight weeks post-diagnosis demonstrated an 80% reduction in the dimension of his lung tumor (Figure 3), near eradication of brain metastases and a significant reduction of spinal lesions. At one year post-diagnosis, Mr. M has returned to work and his disease is stable.
Figure 3: CT scan of the same patient following 8 weeks of therapy with crizotinib, a tyrosine kinase inhibitor that targets ALK, showing an 80% reduction in the dimension of the lung tumor.
Faculty Team
A joint initiative between the Department of Pathology and Laboratory Medicine and the Abramson Cancer Center at Penn Medicine, the Center for Personalized Diagnostics (CPD) integrates molecular genetics, pathology informatics and genomic pathology to develop personalized diagnostic profiles for individuals with cancer.
Using customized computational methods, including large-scale, massively parallel DNA sequencing and chromosomal analysis, the CPD identifies personal mutation signatures for distinct tumor subtypes. This information may then be used to determine whether a tumor is susceptible to targeted therapies and to elucidate potential cancer treatment options.
The Penn Center for Personalized Diagnostics
Faculty and Staff
Kojo Elenitoba-Johnson, MD
Director, Center for Personalized Diagnostics
Jennifer Morrissette, PhD, FACMG
Clinical Director, Center for Personalized Diagnostics
Robert Babak Faryabi, PhD
Assistant Professor of Pathology and Laboratory Medicine
CPD Faculty Lead, Bioinformatics
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Center for Personalized Diagnostics
3020 Market Street, Suite 220A
Philadelphia, PA 19104
215-573-0675