Molecular Pathology Services | NYU Langone Health

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Anatomic Pathology Services Molecular Pathology Services

Molecular Pathology Services

Directed by Matija Snuderl, MD, molecular pathology in NYU Langone’s Department of Pathology is an emergent and rapidly growing area focused on the use of standard and next-generation molecular diagnostics. Molecular pathology plays a critical role in establishing a diagnosis, prognosis, and prediction of response to therapy, and provides the basis of precision medicine.

Spanning both anatomic and clinical disciplines, state-of-the-art molecular pathology tests increase the specificity of disease diagnoses for identification and classification, clarify the prognosis and predictions for the potential behavior of disease, and determine the best therapeutic approaches and responses.

Molecular Pathology Services and Tests

The department has added a number of tests to its portfolio and has identified several others on the basis of clinical need to develop a broad scope of molecular pathology testing.

NYU Langone Genome PACT

NYU Langone Genome PACT (Profiling of Actionable Cancer Targets) is a qualitative in vitro diagnostic test that uses targeted DNA next-generation sequencing tumor tissue matched with normal specimens from patients with malignant neoplasms to detect tumor gene alterations in exons and selected promoter of 607 genes. The genome PACT is intended to provide information on somatic mutations including point mutations and small insertions and deletions for diagnostic and treatment decisions. Detected mutations are matched with available standard of care therapy or clinical trial providing critical information for the best management.

NYU Langone Oncomine

NYU Langone Oncomine is a targeted panel for detection of mutations, copy number gains, and gene fusions in 50 cancer genes. It is highly sensitive and targets relevant aberrations from DNA or RNA in a single workflow, targeting the most important genes in lung, breast, genitourinary, gastrointestinal, and brain cancers and melanomas that have approved targeted therapies and are relevant in clinical trials. Oncomine is particularly useful in small and limited samples for rapid and robust detection of actionable events.

NYU Langone FUSION-SEQer

NYU Langone FUSION-SEQer is a next-generation RNA sequencing fusion panel for solid tumors, analyzing 86 genes for detection of known and novel gene fusion events including diagnostic and targetable aberrations for precision oncology. Gene fusions are caused by chromosomal rearrangements and encode for fusion proteins that can act as drivers for initiation and progression of many cancers. Because of their specificity to cancer cells, they are excellent targets for therapeutics and personalized medicine. Gene fusions can also be used as diagnostic and prognostic markers as well as to monitor response to molecular therapies. FUSION-SEQer utilizes Anchored Multiplex PCR (AMP) chemistry and can capture both 5′ and 3′ fusions, including novel fusions that would be missed by opposing primer-based methodologies.

NYU Langone Whole-Genome DNA Methylation Analysis

DNA methylation has emerged as a powerful tool for molecular classification of brain tumors. Recent studies have identified that DNA methylation can be used for molecular subclassification of virtually all brain tumors. Methylation of CpG dinucleotides is a key epigenetic regulator of gene function during development and disease. The cancer DNA methylome is a combination of both somatically acquired DNA methylation changes and characteristics reflecting the cell of origin. The latter property allows, for example, tracing of the primary site of highly dedifferentiated metastases of cancers of unknown origin.

DNA methylation profiles have been widely used to subclassify central nervous system (CNS) tumors that were previously considered homogeneous diseases. These efforts have led to the identification of clinically and biologically distinct subgroups of medulloblastoma, ependymoma, diffuse glioma/glioblastoma, and atypical teratoid/rhabdoid tumor (ATRT). Furthermore, methylation data were used to dissect what was previously designated as CNS primitive neuroectodermal tumor (CNS PNET) into a variety of new molecularly defined entities. Several of these tumor subtypes are already included in the 2016 revision of the of the World Health Organization classification of CNS tumors, reflecting a progression toward integrated histo-molecular diagnosis.

Most importantly, utilization of a uniform approach via a single molecular test for classification of all brain tumors represents a cost-efficient and unbiased approach to provide molecular subclassification of brain tumors. NYU Langone collaborated on the development of the DNA methylation classifier (Capper et al., Nature, 2018) and was the first Clinical Laboratory Improvement Amendments (CLIA) laboratory to receive regulatory approval for this clinical testing. NYU Langone is currently expanding the use of DNA methylation for other cancer types.

Prosigna

The U.S. Food and Drug Administration (FDA) approved 50 gene RNA expression profiling of invasive breast cancer using PAM-50 prediction score. Prosigna provides critical information for predicting risk of recurrence and personalized medicine in breast oncology and helps providers and patients with critical choices regarding chemotherapy.

1p19q Loss of Heterozygosity

Testing for 1p19q status is one of the most critical biomarkers in neuropathology for diagnosis of oligodendroglioma and predicting chemosensitivity.

NYU MGMT Pyro

Glioblastoma is the most common malignant brain tumor of adults and requires aggressive therapy. Promoter hypermethylation of MGMT gene predicts response to chemotherapy and radiation. Rapid pyrosequencing assay performed by NYU Langone enables real-time decision-making regarding standard of care or clinical trial enrollment for this malignant disease.

NYU MSI PCR

Microsatellite instability is a hallmark of some tumors with aberrant mismatch repair and is a biomarker for response to immunotherapy. The FDA granted its first tissue/site-agnostic approval for immunotherapy in patients for adult and pediatric patients with unresectable or metastatic, microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) solid tumors in 2017. This testing is therefore critical when MSI high status is suspected and is critical for therapy.

Molecular Hematopathology Tests

We offer the following molecular hematopathology tests:

  • T- and B-cell clonality: immunoglobulin gene rearrangement, T-cell receptor gene rearrangement
  • myeloproliferative neoplasms: JAK2 V617F mutation, calreticulin mutations (CALR), quantitative PCR for BCR/ABL1 p210 transcript (international scale)
  • acute myeloid leukemia: FLT3-ITD, FLT3-TKD (D835) mutations, PML/RARA fusions t(15;17), RUNX1/RUNX1T1 fusion t(8;21)
  • acute lymphoblastic leukemia: BCR/ABL1 p190 qualitative
  • lymphoma: IGH/CCND1 t(11;14)(CYCLIN D1) fusion, IGH/BCL2 t(14;18) fusion, EBV, HTLV1, HHV8

Turnaround Time

Turnaround times are determined by specific arrangement, depending on the type of test.

Molecular Pathologists

Matija Snuderl, MD
Director, Molecular Pathology Services
Associate Professor, Department of Pathology

George Jour, MD
Director, Molecular Pathology Fellowship
Associate Director, Molecular Pathology Services
Clinical Assistant Professor, Departments of Pathology and Dermatology

Tatyana Gindin, MD, PhD
Associate Director, Molecular Pathology Services
Clinical Associate Professor, Department of Pathology

Xiaojun Feng, DRRERNAT
Assistant Director, Molecular Pathology Services
Research Assistant Professor, Department of Pathology

Deborah F. DeLair, MD, PhD
Director, Obstetrical and Gynecologic Pathology
Associate Professor, Department of Pathology

Paolo Cotzia, MD
Assistant Director, Pathology Operations, Center for Biospecimen Research and Development
Clinical Assistant Professor, Department of Pathology

Kyung E. Park, MD
Clinical Assistant Professor, Department of Pathology

Nicholas Ward, MD
Clinical Assistant Professor, Department of Pathology

Aristotelis Tsirigos, PhD
Professor, Department of Pathology

Contact Us

The molecular pathology laboratory is located in Manhattan at 240 East 38th Street. For inquiries relating to cytopathology services at NYU Langone, please email Dr. Snuderl, director of molecular pathology, at matija.snuderl@nyulangone.org.