Molecular Pathology Laboratory

You are here

Molecular Pathology Laboratory

The primary mission of the Molecular Pathology Laboratory at NewYork-Presbyterian/Weill Cornell Medical Center is to provide the best clinical molecular diagnostic services for the clinicians and pathologists providing care to patients at NewYork-Presbyterian.  Since its inception, this laboratory has been developing and performing state-of-the-art molecular-based tests to aid in the diagnosis and management of infectious disease, genetic disorders, solid tumor malignancies and monitoring transplant, working closely with clinicians, pathologists and health care professionals. The Laboratory is directed by Hanna Rennert, PhD, FACMG, with ten staff members (a PhD technical specialist, supervisor and laboratory technologists). The laboratory is CLIA-certified and accredited by New York State Department of Health and the College of American Pathologists.


The Molecular Pathology Laboratory

CANCER GENE MUTATION PANEL-50 FACT SHEET

CANCER GENE MUTATION PANEL-50 FAQ

Test Menu

Oncology test menu:

  • EGFR mutation analysis by real-time PCR of a targeted mutation panel for 21 mutations in exons 18-21 using the therascreen EGFR RGQ PCR method (Qiagen), for determining mutation status in tumors from patients with lung cancer for appropriate predictive prognosis and treatment.
  • BRAF mutation analysis (exon 15 V600E) by Sanger sequencing, for determining mutation status in tumors from patients with thyroid cancer, colorectal cancer, melanoma, brain tumors or lung cancer for appropriate predictive prognosis and treatment.
  • KRAS mutation analysis (exon 2 codons 12 and 13 mutations) by Sanger Sequencing, for determining whether a tumor harboring a mutation is useful in selecting appropriate treatments for individual patients with lung cancer and metastatic colorectal cancer.
  • Microsatellite instability (MSI) analysis by fluorescent multiplex PCR and capillary electrophoresis fragment size analysis, for assessing the status of the mismatch repair (MMR) protein in tumors from patients with colorectal cancer for detecting Lynch syndrome for appropriate predictive prognosis and treatment and for detecting Lynch Syndrome.
  • Cancer Gene Mutation Panel for the identification of mutations in 50 cancer-related genes using targeted next generation sequencing (NGS) and the Ion AmpliSeq Cancer Hot Spot Panel v2 by Ion Torrent (Life technologies), The panel facilitates the  detection of actionable and targetable mutations in lung, colorectal, thyroid, brain and skin cancer (melanoma)for appropriate diagnosis, prognosis and selection of therapy. The panel will also identify relevant genes that may have implications for enrollment of the patient in clinical trials.  The genes interrogated in the panel are listed below:


ABL1AKT1ALKAPCATM
BRAFCDH1CDKN2ACSF1RCTNNB1
EGFR ERBB2 ERBB4EZH2FBXW7
FGFR1FGFR2FGFR3FLT3GNA11
GNASGNAQHNF1AHRASIDH1
IDH2JAK2JAK3KDRKIT
KRASMETMLH1MPLNPM1
NOTCH1NRASPDGFRA PIK3CA PTEN
PTPN11RB1RETSMAD4SMARCB1
SMOSRCSTK11TP53VHL

Genetic Test Menu

  • Thrombophilia mutation analysis by PCR and allele-specific hybridization using e-Sensor (GenMark), for detecting Factor V Leiden (F5 c.1601G>A, p.Arg534Gln), Prothrombin mutation (F2 c.*97G>A) and MTHFR polymorphisms (c.665C>T, p.Ala222Val; c.1286A>C, p.Glu429Ala), for identifying patients at risk of thrombosis for the determination of appropriate treatment. 
  • Cystic Fibrosis (CF) testing by Invader InPlex assay using PCR and FRET detection (Hologic/Third Wave Technologies), for the identification of 44 mutations in diagnostic patients and for carrier screening.  The test is complaint with the ACMG 2001 and 2004 Cystic Fibrosis screening recommendations.

Monitoring Engraftment Test

  • Bone Marrow engraftment (BME) analysis by fluorescent multiplex PCR and capillary electrophoresis fragment size analysis, for determining BME status in patients with hematopoietic malignancies after allogeneic bone marrow for appropriate predictive prognosis and treatment.

Infectious Disease Test Menu

  • Human immunodeficiency virus 1 (HIV-1) viral load by quantitative real-time PCR using the Roche Cobas Ampliprep/Taqman HIV-1 v.2.0 assay (quantitative range 20-10,000,000 copies/mL), for monitoring HIV disease and response to antiretroviral therapy.
  • Human immunodeficiency virus 1 (HIV-1) drug resistance (NRTI, NNRTI and PI mutations) testing by Sanger sequencing using the ViroSeq HIV-1 Genotyping System v.2.0 (Abbott Diagnostics), for monitoring drug resistance to antiretroviral therapy
  • Hepatitis C viral (HCV) load by quantitative real-time PCR using the Roche Cobas Ampliprep/Taqman HCV v.2.0 assay (quantitative range 15-100,000,000 IU/mL), for confirming active infection and for monitoring response to antiretroviral therapy.
  • Hepatitis B viral load by quantitative real-time PCR using Roche Cobas Ampliprep/Taqman HBV assay (quantitative range 20-170,000,000 IU/mL), for confirming active infection and for monitoring response to therapy.
  • Cytomegalovirus (CMV) by quantitative real-time PCR using the Qiagen CMV Taqman reagents and the ABI7900HT system (quantitative range 200-500,000 copies/mL), for identifying patients at risk for CMV disease and monitoring of antiviral therapy in transplant patients.
  • Epstein-Barr virus (EBV) by quantitative real-time PCR using the Qiagen EBV Taqman reagents and the ABI7900HT system (quantitative range 200-400,000 copies/mL), for identifying patients at risk for EBV disease and monitoring of antiviral therapy in transplant patients.
  • Human herpes virus 6 (HHV-6) by quantitative real-time PCR using the Biomerieux/Argene HHV-6 Taqman reagents and the ABI7900HT system (quantitative range 200-300,000 copies/mL), for identifying patients at risk for HHV-6 disease and monitoring of antiviral therapy in transplant patients.
  • BK virus (BKV) by quantitative real-time PCR using the Qiagen BKV Taqman reagents and Qiagen Rotor-Gene Q instrument (quantitative range 200-18,600,000 copies/mL), for identifying patients at risk for BKV-related renal disease and monitoring of antiviral therapy in transplant patients.

MOLECULAR GENETIC FELLOWSHIP

General Contact

Molecular Pathology Laboratory
The Department of Pathology & Laboratory Medicine 
Weill Cornell Medical College - NewYork-Presbyterian Hospital
525 East 68th Street, F5
New York, NY 10065

Phyllis Ruggiero, Manager
tel: 212-746-2994

BACK TO TOP