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 FISH probes) and a high resolution comparative genomic hybridization + single nucleotide polymorphisms (aCGH+SNP) array for detection of loss, gain, or copy number loss of heterozygosity in cancer related 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, metaphase and multicolor FISH studies (using more than 100 FISH probes)
  • Array CGH (comparative genomic hybridization)+ single nucleotide polymorphisms (SNPs), Agilent Cancer Platform

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

The technologies we offer are integral diagnostic and prognostic tools in hematological malignancies and oncology and include a full range of services for clinicians and researchers within the Mount Sinai Health System. 

We provide services with fast turnaround times for chromosome analysis (G-banding and multicolor metaphase analysis), fluorescence in situ hybridization (FISH) assays, and array comparative genomic hybridization + single nucleotide polymorphisms (aCGH+SNPs) with more than 15,000 clinical tests each year. In order to achieve fast turnaround times, we explore and adapt to new technologies in both the laboratory setting as well as through our Information Technology resources. The SoftCTG module from Soft Computer Corp allows our laboratory to integrate all aspects of our work and allows for a paperless environment. Our team includes medical technologists, all licensed by the New York State Department of Education. 

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 Research Clinical Consortium. Our laboratory is accredited by the New York State Department of Health and College of American Pathologists.

Our clinical services involve techniques that identify cancer cells that 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 fusing 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+SNPs.

  • Cell Culture: This process involves the controlled growth of cells in vitro.
  • Routine G-banded chromosome analysis: We perform chromosome analysis using samples such as bone marrow, unstimulated peripheral blood, and fresh tumor tissue.
  • 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: Array CGH+SNPs use isolated DNA which is competitively hybridized to the reference DNA to detect loss, gain, or cnLOH in cancer related genes.

Collection information is located on the requisition form.

 

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

  • Hematological malignancies
    • Chronic Myelogenous Leukemia (CML): BCR-ABL1
    • Ph Negative Myeloproliferative Neoplasm (Ph- MPN): D5S23-EGR1, D7Z1-D7S522, D8Z2, CEP9-CDK2A, ATM, RB1, D20S108, D5S23-CSF1R, CDKN2C-CKS1B
    • Hyper Eosinophilic syndrome (HES): FIP1L1, PDGFRB
    • Myelodysplastic Syndrome (MDS): EGR1, CEP7, D7S522,CEP8, RB1, KMT2A, ETV6, D20S108
    • Myelodysplastic Syndrome (MDS)/ Acute Myelogenous Leukemia (AML): MECOM-RPN1
    • Acute Myelogenous Leukemia (AML): BCR-ABL1, RUNX1-RUNXT1,PML-RARA, CBFB, KMT2A, TP53, D17Z1
    • Therapy-related AML: EGR1-D5S23, CEP7-D7S522, KMT2A, D21S341
    • Pediatric - Acute Lymphoblastic Leukemia (ALL): BCR-ABL1, ETV6-RUNXT1, TCF3-PBX1, CDKN2A-CEP9, KMT2A, CEP4, CEP10, CEP17
    • Adult - Acute Lymphoblastic Leukemia (ALL): BCR-ABL1, CEP7-D7S522, CDKN2A-CEP9, KMT2A, IGH
    • T-Cell Acute Lymphoblastic Leukemia (T-ALL): CEP9-CDKN2A, JAK2, BCR-ABL1, KMT2A, ETV6-RUNX1, RB1/MYB
    • Ph-Like Acute Lymphoblastic Leukemia (Ph-Like ALL): PDGFRB, JAK2, IGH, CEP9-CDKN2A, BCR-ABL1,  D5S23- CSF1R 
    • Chronic Lymphocytic Leukemia (CLL): CEP12, D13S319/LAMP1, IGH, ATM, TP53
    • Multiple Myeloma: CCND1-IGH, FGFR3-IGH, MAF-IGH, TP53, D13S319/LAMP1, CDKN2C-CKS1B, IGH, IGH-MAFb
    • Non-Hodgkin’s Lymphoma (NHL): IGH-BCL2, D8Z2-MYC-IGH, CCND1-IGH,
    • BIRC3-MALT1, BCL6, ALK
    • Non-Hodgkin’s Lymphoma Aggressive (Triple Hit Lymphoma): BCL6, MYC, D8Z2-MYC-IGH, IGH-BCL2
    • Chimerism and Minimal residual disease in stem cell transplantations: XX/XY
  • Solid Tumors
    • Breast Cancer: ERBB2-CEP17
    • Bladder Cancer: Urovysion: CEP3,CEP7,CDKN2A(9p21) and CEP17
    • Neuroblastoma: D2Z1 / MYCN
    • Sarcoma
      • Ewing: EWSR1
      • Synovia: D18Z1 / SS18
      • Alveolar Rhabdosarcoma: FOXO1
      • Myxoid Liposarcoma: FUS, DDIT3
      • Nodular fasciitis: USP6
      • Well Differentiated/Dedifferentiated Liposarcoma- MDM2/D12Z3
  • Oligodendroglioma: 1p36, 1q25; 19p13, 19q13
  • Lung Cancer: ALK, ROS1
    • Cholangiocarcinoma: Urovysion: CEP3, CEP7, CDKN2A(9p21) and CEP17
    • Spitzoid Neoplasm: MYB, RREB1, D6Z1, CEP9, CDKN2A, CCND1

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

Our research includes investigations into the role of chromosomal aberrations in the pathogenesis of myeloproliferative neoplasms.

Director

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 the multistep pathogenesis of CML, involvement of 9p in Polycythemia Vera, and the use of FISH for clinical diagnostics and gene mapping in hematological malignancies.

Laboratory Supervisors

Mariya Bezugly, NYSDOE

Issa Leonard, NYSDOE- and ASCP-certified

Joseph Tripodi, NYSDOE- and ASCP-certified


QC Manager

Valentina Mizhiritskaya, NYSDOE- and ASCP-certified

Tumor CytoGenomics Specialists

Amy Kong, NYSDOE- and ASCP-certified

Meri Razavi, NYSDOE- and ASCP-certified

 

Clinical Laboratory Technologists (all certified by the NYSDOE)

Daiva Ahire Jayson Bastien, PhD

Kimberly Call

Ewa Danisewicz

Mariya French

Edgard Gallardo

Murielle Houssou

Joanna Kierzkowski

Lauren Moskowitz

Evelina Niedbala

Paulina Norko

Ewa Radozycka

Sarina Sherpa

Michael Yurich

Sharon Zirkiev

 

Administrative Assistant

Ethel Sistrunk