Tumor CytoGenomics

Our laboratory provides state-of-the-art services in the detection of acquired chromosomal abnormalities associated with hematological malignancies and solid tumors. We offer all available cytogenetic techniques to identify the type and nature of complex structural abnormalities present in malignant (cancerous) cells. We also offer fluorescence in situ hybridization testing using disease-specific panels (more than 100 probes) and a high resolution array comparative genomic hybridization (CGH) for detection of loss or gain of 92 percent of cancer genes.

We offer a full range of services for clinicians and researchers from Mount Sinai and beyond, including the following assays:

  • Cell culture
  • Routine G-banded chromosome analysis
  • Interphase and metaphase FISH studies (using more than 100 FISH probes)
  • Array CGH (agilent cancer platform)+single nucleotide polymorphisms

Our mission is to enhance the quality of clinical and molecular cytogenomic service through the development and implementation of state-of-art technologies for patient care, education, and clinical research.

The technologies we offer are integral diagnostic and prognostic tools in hematology and oncology and include a full range of services for clinicians and researchers from Mount Sinai and beyond. 

We provide services with fast turnaround times for chromosome analysis (G-banding and multicolor metaphase analysis) and fluorescence in situ hybridization (FISH) assays, using over 100 FISH probes, in more than 15,000 clinical tests each year. We use a GSL (genetic slide loader), which is a fully automated system for scanning and imaging metaphase cells from up to 124 slides. Our team includes medical technologists, all licensed by the New York State Department of Education (NYSDOE). 

We are a major collaborator in international, multicenter clinical trials such as Childhood Oncology Group and Alliance for Clinical Trials in Oncology. Most notably, we are the core Laboratory for the International Myeloproliferative Neoplasms MPN) Research Clinical Consortium. Our Laboratory is accredited by the New York State Department of Health and College of American Pathologists.

Cancer cells generally gain multiple types of chromosomal aberrations during tumor progression, including rearrangements, deletions, and duplications. Besides gain or loss of chromosomes, chromosomal rearrangements include a hybrid gene which is formed by fusion of portions of two different genes at the chromosomal breakpoints of two or more chromosomes; we can detect these rearrangements using the FISH technique. Sometimes, we see the same hybrid gene in multiple types of cancers, indicating that such genes might initiate malignant progression in a variety of tissues.

The Tumor CytoGenomics Laboratory conducts the following types of tests, including chromosome analysis, FISH assays (using more than 100 FISH probes), and array CGH.

  • Cell Culture: This process involves the controlled growing of cells in the laboratory.
  • Routine G-banded chromosome analysis: We perform these analyses using samples such as bone marrow, unstimulated peripheral blood, and tumors.
  • Interphase and metaphase FISH studies: These studies use chromosome enumeration probes, single copy or locus specific probes, translocation probes, and multi-color FISH probes.
  • Array CGH+SNP: These studies use isolated DNA which is competitively hybridized to the reference DNA to detect loss or gain of 98 percent of cancer genes.

Below is the list of disease-specific genes that we test  in our laboratory:

  • Hematological malignancies
    • Chronic Myelogenous Leukemia (CML): BCR-ABL1, BCR-ABL1-ASS
    • Ph Negative Myeloproliferative Neoplasam: PDGFRB, EGR1, CEP7/D7S522, CEP8, CEP9/CDK2A and B, ATM, RB1, D20S108
    • Hypereosinophilic syndrome: FIP1L1
    • Myelodysplastic Syndrome: EGR1, CEP7, D7S522,CEP8, RB1, KMT2A, ETV6, D20S108
    • Acute Myelogenous Leukemia (AML): BCR-ABL1, RUNX1-RUNXT1,,PML-RARA, CBFB, KMT2A
    • Therapy-related AML: EGR1,CEP7/D7S522, 21q22, KMT2A
    • Acute Lymhoblastic Leukemia (ALL) – Pediatric: BCR-ABL1, ETV6-RUNXT1, TCF3-PBX1, CDKN2 A and B at 9p21, KMT2A, CEP4, CEP10, CEP17
    • ALL – Adult: BCR-ABL1, CEP7/D7S522, CDKN2 A and B at 9p21, KMT2A
    • Chronic Lymphocytic Leukemia: CEP12, D13S319/LAMP1, IGH, ATM, P53
    • Multiple Myeloma: CCND1-IGH, FGFR3-IGH, MAF-IGH, 1q21,PBX1-TCF3, P53, ATM, 5q33, D13S319/LAMP1, ASS
    • Non Hodgkins Lymphoma: IGH-BCL2, MYC-IGH, CCND1-IGH, API2-MALT1, BCL6, ALK
    • Chimerism and Minimal residual disease in stem cell transplantations: XX/XY
  • Solid Tumors
    • Breast Cancer: ERBB2
    • Bladder Cancer: UrovysionR: CEP3,CEP7,9p21 and CEP17
    • Neuroblastoma: N-MYC
    • Sarcoma (Ewing: EWSR1, Synovia: SYT, Alveolar Rhabdosarcoma: FOXO1A, Malignant Liposarcomna: FUSNodular fasciitis: USP6
    • Oligodendroglioma: 1p36, 1q25; 19p13, 19q13
    • Lung Cancer: ALK, ROS1
    • Cholangiocarcinoma: UrovysionR: CEP3, CEP7, 9p21 and CEP17
    • Spitzoid Neoplasm: MYB,RREB1, D6Z1, CEP9, CDKN2,CCND1

The Tumor CytoGenomics Laboratory provides an important technical resource to investigators at the Mount Sinai Health System and other medical centers in New York City. Conventional cytogenetics and molecular cytoGeneomics are fundamental adjunct to a variety of other molecular and cellular techniques for the determination of chromosomal or gene rearrangements (cytoGenomics). 

Our research also includes probe development and investigations into the role of chromosomal aberrations in the pathogenesis of myeloproliferative neoplasms.

Vesna Najfeld, PhD, Director of the Tumor CytoGenomics Laboratory since 1980, is an international leader in cancer cytogenetics, specifically for chronic myeloproliferative disorders. She has been recognized for delineating a multistep pathogenesis of CML, involvement of 9p in Polycythemia vera, and the use of FISH for clinical diagnostics and gene mapping in hematological malignancies.

Linda Cannizzaro, PhD, Associate Director

Mariya Bezugly, Laboratory Supervisor, NYSDOE- and American Society for Clinical Pathology (ASCP)-certified

Joseph Tripodi, M.Sc. Laboratory Supervisor, NYSDOE- and ASCP-certified

Valentina Mizhiritskaya, QC Manager, NYSDOE- and ASCP-certified

Issa Leonard, Lab Coordinator, NYSDOE- and ASCP-certified

Medical Technologists (all certified by the NYSDOE)
Sarina Sherpa
Amy Kong
Daiva Ahire
Jody Yurich
Joanna Kierzkowski
Jayson Bastien, PhD
Ewa Radozycka
Edgar Gallardo
Lauren Moskowitz
Patricia Stan

Ethel Sistrunk, Administrative Assistant