Molecular Diagnostics

Molecular Diagnostics

Antony Shrimpton, PhD, Director
Phone: 315 464-6807
Email: shrimpta@upstate.edu

Constance Stein, PhD, Assistant Director
Phone: 315 464-4716

Celeste Lamberson, MS, MT(ASCP), Molecular Diagnostics Coordinator
Phone: 315 464-6806
Email: lambersc@upstate.edu

The Molecular Diagnostics Laboratory offers a growing menu of molecular testing for inherited diseases, genetic risk factors associated with complex, multifactorial disorders, and acquired hematological disorders. The Director and Assistant Director are members of the American College of Medical Genetics and hold American Board of Medical Genetics Certificate of Qualification in Clinical Molecular Genetics. We are a referral laboratory for other hospitals and clinics throughout New York State.

Laboratory Contact Information

The laboratory is staffed Monday - Friday from 8:00AM - 6:00PM
Phone: 315-464-6806
Fax: 315-464-6827

Specimen Shipping Address

Upstate Medical University
Clinical Pathology - Rm 3814 SUH
750 East Adams St
Syracuse, NY 13210

 

 

Genetic Tests Available

Cystic Fibrosis Direct Mutation Analysis

Test Includes: Direct detection of 41 CF mutations, including the 25 CF mutations recommended by the American College of Medical Genetics for routine CF screening. Approximately 90% of CF chromosomes found in CF patients in Upstate New York will be detected.
Indications: Prenatal Population screening to identify CF carriers
Diagnosis of CF in symptomatic individuals
Carrier detection in asymptomatic family members of CF patients
Prenatal detection of CF mutations in families with a history of CF
Sample Requirements: Carrier or Diagnostic: Peripheral Blood - 5 ml EDTA anticoagulated.
Prenatal: 2 confluent T-25 flasks of cultured amniocytes.
A maternal blood sample is also required for maternal cell contamination studies.
Shipping Requirements: Transport at room temperature.
Peripheral blood must be received within 48 hours of collection.
Cultured amniocytes must be shipped via overnight courier.
Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Genetic Test for Cystic Fibrosis PDF document
  • Comments: When completing the requisition, please include patient's racial background (risk of CF varies with race), the relationship of the patient to any family members with a history of CF (include identity of CF mutations if known), and the purpose (diagnostic or carrier) for testing.
    Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83900 x 1
    83896 x 40
    83912 x 1

    Factor V Gene Mutation Analysis

    Test Includes: Direct molecular detection of the R506Q (Factor V Leiden) point mutation. If Leiden positive, reflex testing for the D2194G point mutation in the Factor V gene will be perfomred.
    Indications: Factor V Leiden and D2194G are genetic risk factors for venous thromboembolism
    Sample Requirements: Peripheral Blood - 5ml EDTA anticoagulated.
    Shipping Requirements: Transport at room temperature.
    Peripheral blood must be received within 48 hours of collection.
    Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Genetic Test for Factor V (Leiden and D2194G)and Prothrombin 20210G>A PDF document
  • Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83896 x 2
    83898 x 1
    83903 x 1
    83912 x 1

    Fragile X Detection

    Test Includes: Direct molecular detection and methylation status of the CGG trinucleotide repeat region within the FMR-1 gene on the X chromosome.
    Indications: Expansions of the CGG repeat region within the FMR-1 gene are associated with Fragile X syndrome, premature ovarian failure, and a late onset neurodegenerative disorder with cerebellar ataxia and intention tremor (FXTAS).
    Sample Requirements: Peripheral Blood - 5-10ml EDTA anticoagulated
    Prenatal: Will only be performed when the mother is a confirmed premutation carrier. Requires four T-25 confluent flasks of cultured amniocytes.
    Shipping Requirements: Transport at room temperature.
    Peripheral blood must be received within 48 hours of collection.
    Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Molecular Test for Fragile X Syndrome PDF document
  • Comments: Normal CGG repeat range is 6 to ~50 repeats.
    Premutation expansions range from 60 to ~200 repeats. The DNA is not methylated and mental capacity is normal. Female Premutation carriers are at risk for premature ovarian failure. Male and female premutation carriers are at risk for FXTAS.
    Full mutation expansions are greater than 200 repeats and the DNA of the repeat region is methylated. All males with a full mutation have impaired mental capacity. 30 - 50% of females with a full mutation show some degree of mental impairment.
    Please indicate on the requisition whether the patient is at risk for a premutation or full mutation
    Turnaround Time: Approximately 4 weeks
    CPT Codes: Full mutation analysis
    83891 x 1
    83892 x 2
    83894 x 2
    83896 x 1
    83898 x 1
    83912 x 2
    Additional codes for Premutation
    83892 x 1
    83894 x 1
    83896 x 1
    83897 x 1

    Hereditary Hemochromatosis Detection

    Test Includes: Direct molecular detection of the C282Y and H63D point mutations of the HFE gene.
    Indications: Molecular testing is an aid in the diagnosis of Hereditary Hemochromatosis
    Sample Requirements: Peripheral Blood - 5ml EDTA anticoagulated.
    Shipping Requirements: Transport at room temperature.
    Peripheral blood must be received within 48 hours of collection.
    Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Genetic Test for Hereditary Hemochromatosis PDF document
  • Comments: When present on both chromosomes (homozygous), the C282Y mutation is strongly associated with an increased risk for Hemochromatosis.
    Individuals with one copy of C282Y and one copy of the H63D mutation are also at increased risk of Hemochromatosis. However, the penetrance of Hereditary Hemochromatosis in C282Y/H63D compound heterozygotes has been estimated to be only about 1%
    Individuals with one copy of C282Y in the absence of H63D may be at increased risk for Hemochromatosis.
    Individuals with one or two copies of H63D but not carrying the C282Y mutation are most likely not at increased risk for Hemochromatosis.
    Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83892 x 2
    83898 x 2
    83894 x 1
    83912 x 1

    MTHFR (Methyltetrahydrofolate reductase)

    Test Includes: Direct molecular detection of the point mutation 677C>T in the MTHFR gene.
    Indications: The 677C>T mutation in the MTHFR gene has been reported to be associated with hyperhomocysteinemia.
    Sample Requirements: Peripheral Blood - 5 ml EDTA anticoagulated.
    Shipping Requirements: Transport at room temperature.
    Peripheral blood must be received within 48 hours of collection.
    Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Molecular Test for MTHFR 677C>T PDF document
  • Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83892 x 1
    83894 x 1
    83898 x 1
    83912 x 1

    Prothrombin 20210G>A Detection

    Test Includes: Direct molecular detection of the point mutation 20210G>A in the Prothrombin gene.
    Indications: Prothrombin 20210G>A is a genetic risk factor for venous thromboembolism.
    Sample Requirements: Peripheral Blood - 5 ml EDTA anticoagulated.
    Shipping Requirements: Transport at room temperature.
    Peripheral blood must be received within 48 hours of collection.
    Required Paperwork:
  • DNA Based Genetic Testing PDF document
  • Authorization for the Genetic Test for Fa ctor V (Leiden and D2194G)and Prothrombin 20210G>A PDF document
  • Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83896 x 2
    83898 x 1
    83903 x 1
    83912 x 1

    Hematology Oncology Tests Available

    B-cell Clonality

    Test Includes: Detection of monoclonal population of B-lymphocytes.
    Indications: In conjunction with immunophenotyping, this assay provides information to aid in the diagnosis and classification of lymphoid lymphoma and leukemia
    Sample Requirements: Peripheral Blood - minimum of 10 ml of EDTA anticoagulated blood (for patients with a relatively normal absolute lymphocyte count).
    For patients with significantly reduced absolute lymphocyte counts, please call the lab before obtaining the sample.
    Bone marrow - minimum of 1 ml of EDTA anticoagulated BM.
    Fresh Tissue - 3-5mm representative sample (immediately place on ice and transport to the lab).
    Fixed paraffin embedded tissue - please send block.
    Shipping Requirements: Peripheral Blood and Bone marrow - Transport at room temperature for receipt in the lab within 24 hrs. of collection.
    Fresh tissue - transport on wet ice for receipt in the lab within 2 hours of collection.
    Required Paperwork:
  • Molecular Oncology Requisition PDF document
  • Comments: Clone must constitute at least 10% of the sample in order to be detected.
    Tissue fixatives other than formalin are not accepted. When sending fixed tissue, please include a copy of the surgical report and a representative slide.
    Turnaround Time: 3-5 days
    CPT Codes: 83891 x 1
    83900 x 1
    83901 x 3
    83894 x 1
    83912 x 1

    Clonality (via rearrangement of the TCR-gamma chain target)

    Test Includes: Clonality detection in leukemia and lymphoma based on T-cell receptor gamma chain gene rearrangement.
    Indications: In conjunction with immunophenotyping, this assay provides information to aid in the diagnosis and classification of leukemia and lymphoma. Detection of clonality is not restricted to clones of T-lymphocyte lineage
    Sample Requirements: Peripheral Blood - minimum of 10 ml of EDTA anticoagulated blood (for patients with a relatively normal white blood count).
    For patients with significantly reduced white blood counts, please call the lab before obtaining the sample.
    Bone marrow - minimum of 1 ml of EDTA anticoagulated BM.
    Fresh Tissue - 3-5mm representative sample (immediately place on ice and transport to the lab).
    Fixed paraffin embedded tissue - please send block.
    Shipping Requirements: Peripheral Blood and Bone marrow - Transport at room temperature for receipt in the lab within 24 hrs. of collection.
    Fresh tissue - transport on wet ice for receipt in the lab within 2 hours of collection.
    Required Paperwork:
  • Molecular Oncology Requisition PDF document
  • Comments: Clone must constitute at least 10% of the sample in order to be detected.
    Rearrangement of the T-cell receptor gamma chain is a good marker for clonality but is not by itself indicative of T-lymphocyte lineage. Lineage of clones detected in this assay should be determined by morphology and cell surfacemarkers.
    Tissue fixatives other than formalin are not accepted. When sending fixed tissue, please include a copy of the surgical report and a representative slide.
    Turnaround Time: 3-5 days
    CPT Codes: 83891 x 1
    83900 x 1
    83901 x 1
    83898 x 1
    83894 x 1
    83912 x 1

    JAK2 (Janus Kinase 2) V617F Mutation Detection

    Test Includes: Direct molecular detection of an acquired JAK2 mutation, V617F.
    Indications: The V617F mutation within the JAK2 gene is associated with the chronic myeloproliferative disorders polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis with myeloid metaplasia (also called idiopathic myelofibrosis - IM). In conjunction with a negative BCR/ABL1 translocation result, V617F testing is useful for distinguishing these chronic myeloproliferative disorders from a reactive process.
    Sample Requirements: Peripheral Blood - 4 ml of EDTA anticoagulated blood.
    Bone marrow - minimum of 1 ml of EDTA anticoagulated BM.
    Shipping Requirements: Peripheral Blood and Bone marrow - Transport at room temperature for receipt in the lab within 24 hrs. of collection.
    Required Paperwork:
  • Molecular Oncology Requisition PDF document
  • Comments: V617F mutation must be present in at least 1% of the white blood cell fraction in order to be detected.
    Turnaround Time: 7-10 days
    CPT Codes: 83891 x 1
    83900 x 1
    83894 x 1
    83912 x 1

    FLT3 (FMS-related Tyrosine Kinase 3)

    Test Includes: Direct molecular detection of internal tandem duplications or other nucleotide insertions within the juxtamembrane domain or the first intracellular tyrosine kinase domain of the FLT3 gene that results in an increase in the length of the FLT3 protein (referred to as FLT3 length mutations). Point mutations involving codon D835 or I836 in the activation loop of the protein are also detected (referred to as FLT3-TKD mutations).
    Indications: FLT3 length mutations are found in about 25% of adult AML and 10-15% of pediatric AML cases, and are associated with a poor prognosis. The clinical significance of FLT3-TKD mutations is less clear
    Sample Requirements: Peripheral Blood - 4 ml of EDTA anticoagulated blood.
    Bone marrow - minimum of 1 ml of EDTA anticoagulated BM.
    Shipping Requirements: Peripheral Blood and Bone marrow - Transport at room temperature for receipt in the lab within 24 hrs. of collection.
    Required Paperwork:
  • Molecular Oncology Requisition PDF document
  • Comments: An FLT3 mutation must be present in at least 5% of the white blood cell fraction in order to be detected.
    Turnaround Time: 2-4 days
    CPT Codes: 83891 x 1
    83892 x 1
    83894 x 3
    83898 x 3
    83912 x 1

    Quantitative BCR/ABL1 p210 Analysis

    Test Includes: Quantification of the BCR/ABL1 fusion gene mRNA transcript that directs production of the aberrant 210 kdal protein associated with development of chronic myelogenous leukemia.
    Indications: Quantitative BCR/ABL1 p210 testing aids in the diagnosis of chronic myelogenous leukemia (CML) and assists in monitoring the presence of residual disease post treatment.
    Sample Requirements: Peripheral Blood - 6 ml of EDTA anticoagulated blood.
    Shipping Requirements: Transport sample at room temperature for receipt in the lab within 24 hrs. of collection.
    Required Paperwork:
  • Molecular Oncology Requisition PDF document
  • Comments: Results are expressed as both a normalized percent ratio of BCR/ABL1 fusion gene transcripts to ABL1 control gene transcripts and as a percent on the International Scale.
    Turnaround Time: 4-7 days
    CPT Codes: 83902 x 1
    83891 x 1
    83896 x 2
    83013 x 1
    83898 x 2
    83912 x 1