Oncology

Your Partner in Advanced Genomics & Genetic Testing




  • Chromosome Analysis (4-6 Days)

    • Complete band-for-band analysis
    • Specialized elongation techniques
    • High quality chromosomes

    Fluorescent in situ Hybridization (24 - 48 Hrs)

    •   FISH PROBE LIST

    •   FISH PANELS FOR LEUKEMIAS & LYMPHOMAS

        Cancer-Specific panels designed


      • *Panel recommended for pediatric patients, Adults patients with B-Cell ALL only FISH for BCR/ABL1 and MLL (KMT2A) are recommended
        Disease(s): Acute lymphoblastic (lymphocytic) leukemia, B-Cell
        Probes:
         TEL/AML1 (ETV6/RUNX1) t(12;21)(p13;q11.2)
         BCR/ABL1 Plus t(9;22)(q34;q11.2)
         CEP4, CEP10, CEP17 Hyper- or Hypodiploidy
         MLL (KMT2A) 11q23 rearrangements
         CDKN2A(p16) /CEP9 -9/9p deletion
        Clinical Significance:
        B- Cell precursor ALL is primarily a disease of childhood with 75% of patients under the age of 6 with both blood and bone marrow involvement.
        Extramedullary involvement is typically of the central nervous system, lymph nodes, spleen, liver and testes.
        The morphology of cells is mainly FAB L1 or L2, where only a small percentage of patients have a mature B-cell immunophenotype.
        Cytogenetics still provides the main standard for classification.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
          24-48 hrs
        CPT Codes:
          2015: 88377x5
      • Disease(s): Acute lymphoblastic (lymphocytic) leukemia, T-Cell
        Probes:
         BCR/ABL1 Plus t(9;22)(q34;q11.2)
         MLL (KMT2A) 11q23 rearrangements
         CDKN2A(p16) /CEP9 -9/9p deletion
         TCR alpha/delta 14q11 rearrangements
        Clinical Significance:
        T-cell ALL accounts for approximately 15% of childhood and 25% of adult ALL patients and has a high risk for malignancy in both groups. Genes involved in various stages of thymocyte development are rearranged or deregulated, resulting in a multistep process for pathogenesis, consistent with multiple genetic changes seen in leukemic cells.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x4
      • Disease(s): Acute myeloid leukemia
        Probes:
         ETO/AML1 (RUNX1T1/RUNX1) t(8;21)(q22;q22) (M2)
         PML/RARα t(15;17)(q22;q21.2) (M3)
         MLL (KMT2A) 11q23 rearrangements (M0-M7)
         MYH11/CBFβ inv(16)(p13q22), t(16;16) (M4)
         EVI1 (MECOM) inv(3)(q21q26) (M1, 2, 4, 6, 7)
        Clinical Significance:
        Acute myelogenous leukemia (AML), the most common type of leukemia in adults with incidence greatly increasing after age 55-60, constitutes 70% of acute leukemias. AML is characterized by an excess accumulation of immature myeloblasts in bone marrow, leading to a lack of differentiated granulocytes, monocytes, thrombocytes and erythrocytes. Classification of AML into major subgroups from morphological, cytochemical and immunophenotype criteria has resulted in the following FAB subtypes, M0-M71,2: minimally differentiated AML (M0); without maturation (M1); with maturation (M2); acute promyelocytic leukemia, hypergranular (M3) or micro- and hypogranular (M3v); acute myelomonocytic leukemia (M4), including M4Eo with eosinophilia; acute monoblastic leukemia (M5a) and monocytic leukemia (M5b); acute erythroleukemia (M6) and acute megaloblastic leukemia (M7). A more recent WHO classification defines four subgroups: 1) AML with recurrent genetic abnormalities (i.e. as revealed by karyotype or tested for by FISH, above); 2) AML with multilineage dysplasia; 3) therapy-related AML (t-AML) and myelodysplastic syndromes (t-MDS); 4) not otherwise categorized.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x5
      • Disease(s): Chronic Lymphocytic Leukemia
        Probes:
         MYB/CEP6 -6, 6q deletion
         ATM/p53 11q and 17p deletion
         CEP12 +12
         D13S319/13qter -13/13q deletion
         CCND1/IGH t(11;14)(q13;q32)
         IGH/BCL2 t(14;18)(q32;q22.1) Reflex Only
        Clinical Significance:
        Chronic lymphocytic leukemia (CLL) and its nodal variant, small lymphocytic lymphoma (SLL) account for 7% of all B- and T/NK-cell lymphomas. Chromosome aberrations occur in more than 80% of CLL with successful stimulation (i.e. with a B-cell mitogen). The neoplastic cells of CLL have low spontaneous mitotic activity and therefore mitogens are necessary. Although standard karyotyping of cells from unstimulated cultures of peripheral blood or bone marrow, as well as cultures stimulated with a B-cell mitogen (interleukin, pokeweed, TNF-α, TPA or some combination) are recommended, FISH is recommended in addition to chromosome analysis.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x5 ( 88377x6 if reflex run)
      • Disease(s): Myelodysplastic Syndrome
        Probes:
         EGR1/5p15.31 -5/5q deletion
         D7S796/D7S486 -7/7q deletion
         CEP7/CEP8 -7/+8
         D20S108/MYBL2 -20/20q deletion/idic(20q)
         EVI1 (MECOM) inv(3)(q21q26) Reflex Only
         MLL (KMT2A) 11q23 rearrangements Reflex Only
         TEL/AML (ETV6/RUNX1) t(12;21)(p13;q11.2) Reflex Only
        Clinical Significance:
        MDS, has an increased incidence in older patients and is a heterogeneous group of clonal bone marrow disorders. They are characterized by the presence of dysplastic hematopoietic cells and cytopenia that can progress to an acute leukemia. 10-15% of patients with MDS have acquired the syndrome through therapy related (t-MDS) treatment following chemotherapy or radiation. Conditions that can mimic MDS include vitamin B12 or folate deficiencies, infections and congenital conditions. A normal karyotype occurs in about 30-60% of MDS patients. If a clonal abnormality is detected about 25% of them can further progress to AML. Chromosome abnormalities in primary MDS, in order of frequency, include -7/del(7), -5/del(5), +8, abnormal 17p, -Y, del(20q), and 11q23 rearrangements. Prognosis typically worsens if more than one abnormality is present.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x4 (88377x7 if reflex run)
      • Disease(s): Multiple Myeloma, Plasma Cell Proliferative Disorders
        Probes:
         IGH 14q32 rearrangements
         TP53/ATM 17p deletion
         D13S319/13qter -13/13q deletion
         CEP9/CEP15 +9 and +15
         FGFR3/IGH t(4;14)(p16.3;q32) IGH Reflex Only
         CCND1/IGH t(11;14)(q13;q32) IGH Reflex Only
         IGH/MAF t(14;16)(q32;q23) IGH Reflex Only
        Clinical Significance:
        Multiple myeloma (MM) is an incurable malignancy with a yearly incidence in the US of ~14,000 people and comprises ~2% of deaths from cancer. The median survival rate for MM is about 3 years. Clinical features include: bone pain; anemia; repeated infections (immunoinsufficiency); features of renal failure and hypercalcemia; abnormal bleeding, lytic bone lesions and destruction of bone tissue; occasional macroglossia; carpal tunnel syndrome; diarrhea due to amyloid disease; hyperviscosity syndrome with purpura, hemorrhage, visual failure, CNS symptoms, etc. MM and non-IgM MGUS (premalignant monoclonal gammopathy of undetermined significance) are neoplastic monoclonal proliferations of bone marrow plasma cells with phenotypic features of PB/long-lived plasma cells. MM is distinguished from MGUS by having >10% plasma cells (PC) in BM. Both MM and non-IgM MGUS show marked increase in prevalence with age, and more prevalent in African American than Caucasians by about 2 fold. The origin of plasma cells is from B-cell immunoblasts which in turn originate in germinal centers of lymph nodes or spleen. Plasma cells initially secrete IgM and later typically migrate to bone marrow to differentiate into long-lived plasma cells, responsible for the heterogeneous production of immoglobulins IgA, IgD, IgE and IgG.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x4 (88377x7 if reflex run)
      • Disease(s): Myeloproliferative Neoplasms
        Probes:
         PDGFRA/FILIP1/CHIC2 4q12 rearrangements (3 color)
         PDGFRB 5q33 rearrangements
         FGFR1 8p12 rearrangements
         BCR/ABL1 Plus t(9;22)(q34;q11.2)
        Clinical Significance:
        Myeloproliferative neoplasms (MPNs) are a group of diseases of the bone marrow in which excess cells are produced. All MPNs arise from precursors of the myeloid lineages in the bone marrow and all of which are related, many evolving into myelodysplastic syndrome and acute myeloid leukemia. This particular neoplasm, MPN, is classified in the hematologic neoplasms category and is further broken down into four main myeloproliferative diseases. These four are categorized by the presence of the Philadelphia chromosome. Essential thrombocytosis (ET), polycythemia vera (PV), and myelofibrosis (MF) are all Philadelphia chromosome negative, and chronic myelogenous leukemia (CML) is Philadelphia chromosome positive.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x4
      • Disease(s): B-Cell Lymphoma
        Probes:
         IGH/BCL2 t(14;18)(q32;q22.1)
         c-MYC 8q24 rearrangements
         BCL6 3q27 rearrangements
         CCND1/IGH t(11;14)(q13;q32) Reflex Only
         cMYC/IGH t(8;14)(q24;q32) Reflex Only
         MALT1 18q21 rearrangements Reflex Only
         CEP3/CEP7/CEP12 +3,+7, and +12 (Tissue Only)
        Clinical Significance:
        B-Cell lymphomas are “blood cancers” in the lymph glands. They develop more frequently in older adults and in immunocompromised individuals. B-Cell lymphomas include both Hodgkin’s and non-Hodgkin’s lymphomas and are typically divided into low and high grade. Prognosis and treatment depends on the specific type of lymphoma as well as the stage and grade. Common types include diffuse large B cell lymphoma, follicular lymphoma, marginal zone lymphoma, mucosa-associated lymphatic tissue lymphoma, small cell lymphocytic lymphoma, chronic lymphocytic leukemia, and mantle cell lymphoma. Chromosomal translocations involving the immunoglobulin heavy locus (IGH) is a classic cytogenetic abnormality for many B-Cell lymphomas. In these cases, the immunoglobulin heavy locus forms a fusion protein with another protein that has either pro-proliferative or anti-apoptotic abilities.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
         Formalin-Fixed Paraffin Embedded Tissue: Tissue sections 4-5 micron sections, 2 slides per probe, fixation time must be between 6-48 hours, include H&E slide with area of interest marked
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x3 (88377x6 if reflex run; 88377x1 if run for tissue)
      • Disease(s): T-Cell Lymphoma
        Probes:
         TCL1 14q32.1 rearrangements
         D7S796/D7S486 7q deletion/i(7q)
         CEP7/CEP8 -7 and +8
         CDKN2A(p16)/CEP9 -9/9p deletion (Tissue Only)
         MLL (KMT2A) 11q23 rearrangements (Tissue Only)
        Clinical Significance:
        Approximately 10% of non-Hodgkin lymphoma cases are due to T-Cell lymphomas. They are compromised of four classes; Extranodal T cell lymphoma, Cutaneous T-Cell lymphoma, Anaplastic large cell lymphoma, and anioimmunoblastic T-cell lymphoma based on cytologic grading. The survival rate of T cell lymphoma varies widely depending on the subtype. Treatment options also vary, but the standard lymphoma therapies including chemotherapy, radiation, stem cell transplantation, and surgery are effective.
        Specimen Requirements:
         Bone Marrow Aspirate (Preferred): 2-5ml, Green-top sodium-heparinized vacutainer
         Peripheral Blood: 5-10ml, Green-top sodium-heparinized vacutainer
         Formalin-Fixed Paraffin Embedded Tissue: Tissue sections 4-5 micron sections, 2 slides per probe, fixation time must be between 6-48 hours, include H&E slide with area of interest marked
        Storage and Transportation:
         Keep at room temperature.
        Turn Around Time (TAT):
         24-48 hrs
        CPT Codes:
         2015: 88377x3 (88377x2 if run on tissue)


  • PML-RARA

    Formalin-Fixed, Paraffin Embedded FISH/Soft Tissue/Lymphoma/MISC FISH (3-5 Days)

    • Disease(s): Non-small Cell Lung Carcinoma
      Probes:
       ALK 2p23
       ROS1 6q22
       RET 10q11
       MET 7q31/CEP7
       EGFR 7p11/CEP 7
      Clinical Significance:
      85-90% of lung cancers are non-small cell lung cancer. Within those NSCLC,
      3-5% of them have a rearrangement of the ALK gene that responds to
      treatment with XALKORI® (crizotinib). 1-2% of NSCLC show a
      rearrangement in the ROS1 gene, which also is responsive to XALKORI®
      (crizotinib). Patients with EGFR mutations usually are responsive to
      treatment with an EGFR-directed kinase inhibitors treatment.
      Specimen Requirements:
      Formalin-Fixed Paraffin Embedded Tissue: Tissue sections 4-5 micron
      sections, 2 slides per probe, fixation time must be between 6-48 hours,
      include H&E slide with area of interest marked
      Storage and Transportation:
       Keep at room temperature.
      Turn Around Time (TAT):
       3-5 days
      CPT Codes:
       2015: 88377x5
    • Brain Cancer: Oligodendroglioma 1p-/19q
    • Breast Cancer: Her2/neu (PathVysion)17q11.2 –12, TOP2A, ZNF217
      Amplification
    • Bladder Cancer: Urine bladder cancer (UroVysion)
    • Disease(s): Prostate Cancer
      Probes:
       PTEN 10q23/CEP 10
      Clinical Significance
      Most common detected cancer in males, affecting 1 in 6 men in the United
      States. Prostate cancer is thought to begin in males between the ages 20’s
      or 30’s and diagnosed within their 60’s due to its slow progression . PTEN is
      a common tumor suppressor gene that is inactivated in cancers, such as
      prostate cancer. PTEN abnormalities show greater risk of metastasis and a
      poorer prognosis.
      Specimen Requirements:
      Formalin-Fixed Paraffin Embedded Tissue: Tissue sections 4-5 micron sections,
      2 slides per probe, fixation time must be between 6-48 hours, include H&E slide
      with area of interest marked
      Storage and Transportation:
       Keep at room temperature.
      Turn Around Time (TAT):
       3-5 days
      CPT Codes:
       2015: 88377x1
    • Synovial Sarcoma: SYT (SS18) 18q11.2
    • Ewing sarcoma: EWSR1 22q12
    • Disease(s): Melanoma
      Probes:
       RREB1 6p25
       CCND1 11q13
       MYB/CEP6 6q23
       c-Myc 8q24
       CDKN2A(p16)/CEP9 9p21 (Spitzoid Melanoma Only)
      Clinical Significance:
      Melanoma is a type of skin cancer which forms melanocytes (pigment-containing cells) in the skin. It can originate in any part of the body that contains these particular cells. The primary cause of melanoma is ultraviolet light exposure. Treatment of this disease includes surgical removal of the tumor, if discovered early, or chemotherapy and immunotherapy. Radiation -therapy is useful for melanomas that have relapsed or have spread. Melanoma is less common than other skin cancers, however it is more deadly if not found in the early stages.
      Specimen Requirements:
      Formalin-Fixed Paraffin Embedded Tissue: Tissue sections 4-5 micron sections, 2 slides per probe, fixation time must be between 6-48 hours, include H&E slide with area of interest marked
      Storage and Transportation:
       Keep at room temperature.
      Turn Around Time (TAT):
       3-5 days
      CPT Codes:
       2015: 88377x5
    • Colorectal, Cervical, Endometrial, & Ovarian Cancer: MET, PTEN
    • Gastric/Esophageal Tumor: Her2, MET, PTEN
    • Thyroid Cancer: MET, PPAR Gamma, RET
    • Other: CCND1/IGH t(11; 14); BCL2/IGH t(14;18); MALT1 18q21; MDM2 12q15; MYC 8q24

  • Her2 neu

CytoSNP-850K BeadChip (7-10 Days)

  • Provides the most comprehensive coverage of cytoge-nomic-relevant genes for cancer mutations
  • Increased performance and detection sensitivity
  • Over 850,000 single nucleotide polymorphisms (SNPs) screened with 15x redundancy

Inherited Cancer Sequencing Panel : Breast, Colorectal, & Lynch Syndrome

  • BRCA1, BRCA2 Sequencing and Deletion Duplication Analysis
  • BRCA1, BRCA2, PALB2 Sequencing and Deletion Duplication Analysis
  • High Risk Breast Cancer Panel: APC, ATM, BRCA1, BRCA2, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, PALB2, PMS2, PTEN, STK11, TP53
  • Breast and Ovarian Cancer Panel: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, FANCC, MLH1, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RADS1C, RADS1D, STK11, TP53
  • Lynch Syndrome Panel: EPCAM, MLH1, MSH2, MSH6, PMS2
  • Polyposis Panel: APC, MUTYH
  • Comprehensive Colorectal Cancer Panel: APC, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2