Molecular Genetics

Molecular genetics is a state of the art technology used to identify and improve the accuracy of diagnosis in patients with genetic and neoplastic conditions. Molecular diagnostics focus on gene and protein activity patterns within a cell. Retrieving these molecular signatures can help clinicians in selecting targeted therapies for individual patients. We offer comprehensive services ranging from single gene testing to combination test panels.

MOLECULAR
  • Quantitative BCR-ABL p210/p190
    Real-time RT-PCR for quantitative detection of t(9;22) BCR-ABL1 fusion transcripts that result in major p210 (E13, E14) or minor p190 (E1) fusion proteins with option to add p230 detection (micro or atypical variant). p230 testing may be ordered as a stand-alone test. For p210 and p190, analytical sensitivity is 1 tumor cell in 100,000 normal cells, log reduction score and percent abnormal are reported, and longitudinal data will appear as a NeoTRACK Result on the report. For p230, results are reported as percent abnormal.
  • ABL1 Kinase Domain Mutation
    Detects ABL1 kinase domain mutations in patients with BCR-ABL1-positive chronic myelogenous leukemia (CML) or acute lymphoblastic leukemia (ALL). RNA is isolated, reverse transcribed to complementary DNA (cDNA), and the DNA sequence of targeted regions of ABL (exons 4, 6-7) is determined using next-generation sequencing (NGS) technology. Analysis includes detection of the common T315I mutation.
  • MPN Molecular Panel (JAK2 V617F, CALR, MPL, JAK2 Exon 12 Mutation Analysis)
    Includes analysis of JAK2 V617F, JAK2 Exon 12-14, CALR exon 9, and MPL exon 10. Testing is performed on plasma for increased sensitivity whenever possible. Tests may also be ordered individually.
  • JAK2 V617F Mutation Analysis
    Detects the V617F mutation. V617F testing may be ordered as part of the MPN Molecular Panel.
  • JAK2 Exon 12-13
    RT-PCR and bi-directional sequencing to detect non-V617F mutations in exons 12-14 and most of exon 15, corresponding to the majority of the JAK2 pseudokinase domain. Exon deletion mutations are detectable. Testing is performed on plasma for increased sensitivity whenever possible. V617F analysis is recommended before or concurrently with this test. Exon 12-14 Mutation Analysis may be ordered separately, with concurrent V617F testing as part of the MPN Molecular Panel.
  • CALR Mutation Analysis
    Bi-directional sequencing of exon 9 of the CALR (calreticulin) gene with fragment length analysis for enhanced detection of low levels of insertion/deletion mutations. This test may be ordered separately or as part of the MPN Molecular Panel.
  • MPL Mutation Analysis
    Bi-directional sequencing of exon 10 of the MPL gene to detect all possible mutations at the W515 and S505 codons, and other mutations throughout the exon. Testing is performed on plasma for increased sensitivity whenever possible. This test may be ordered separately or as part of the MPN Molecular Panel.
  • T-Cell Clonality Assessment
    Available as global test only. Markers are VB1, VB2, VB3, VB4, VB5.1, VB5.2, VB5.3, VB7.1, VB7.2, VB8, VB9, VB11, VB12, VB13.1, VB13.2, VB13.6, VB14, VB16, VB17, VB18, VB20, VB21.3, VB22, and VB23 (24 markers). Two additional T-cell markers are used to identify the population of interest and the markers vary from case to case.
  • B-Cell Clonality Assessment
    Detection of clonal IgH gene rearrangements by PCR of IgH framework regions 1, 2, 3 and joining regions. In addition, Ig Kappa gene rearrangement analysis is performed using specific oligonucleotides recognizing the Vk, intragenic and Jk regions.
  • IgVH Hypermutation Analysis
    RT-PCR and bi-directional sequencing of the variable region of the immunoglobulin heavy chain for detection of mutation from germline sequence. The mutated VH gene family is identified in positive reports (>3% sequence deviation). Mutation may not be detectable in specimens containing < 10% clonal B-cells.
  • FLT3/NPM1 Mutation Analysis
    Detection of internal tandem duplication and exon 20 tyrosine kinase domain (TKD) mutations using bi-directional sequencing. Positive results identify specific TKD mutations or report ITD results quantitatively as percent abnormal ITD peak. Testing may be performed on plasma to increase sensitivity.
    PCR and fragment analysis of exon 12 of the NPM1 gene to detect small insertion mutations specific to AML. Positive results are reported quantitatively as percent abnormal DNA. Testing may be performed on plasma to increase sensitivity.
  • FLT3 Mutation Analysis
    Detection of internal tandem duplication and exon 20 tyrosine kinase domain (TKD) mutations using bi-directional sequencing. Positive results identify specific TKD mutations or report ITD results quantitatively as percent abnormal ITD peak. Testing may be performed on plasma to increase sensitivity.
  • NPM1 Mutation Analysis
    PCR and fragment analysis of exon 12 of the NPM1 gene to detect small insertion mutations specific to AML. Positive results are reported quantitatively as percent abnormal DNA. Testing may be performed on plasma to increase sensitivity.
  • cKIT (D816V) Mutation Analysis
    Bi-directional sequencing of KIT exons 8, 9, 11, 13 and 17 for detection of activating mutations including the common mutation D816V. For solid tumors, tumor enrichment is performed before extraction. In hematological disease, testing may be performed on plasma to increase sensitivity.
  • PML/RARA Quantitative
    Real-time RT-PCR for quantitative detection of the t(15;17) PML-RARA fusion transcript. Both long and short isoforms of the fusion transcript are detected. Positive results identify the isoform and quantify it as a ratio with the amount of transcript from a normal control gene. Analytical sensitivity is 1 tumor cell in 100,000 normal cells.
  • CEBPA Mutation Analysis
    Bi-directional sequencing of the relevant coding region and fragment analysis for detection of sequence variant and internal tandem duplication mutations. The SNP genotype at rs34529039 is reported. Testing is performed on plasma for increased sensitivity whenever possible.
  • MLL-PTD Mutation Analysis
    Detects the MLL partial tandem duplication (PTD) between exons 2 and 8 in the MLL gene.
NEXT-GEN SEQUENCING
  • AML Favorable: Risk Profile
    This test is performed by sequencing of select exons of the genes FLT3 and KIT. Test orders include summary interpretation of all results together. Individual genes from a validated list of myeloid genes can be added-on.
  • AML Prognostic Profile
    This test is performed by sequencing the entire coding regions of the genes listed. ASXL1, BCOR, BRAF, CEBPA, CSF3R, DNMT3A, ETV6, EZH2, FLT3, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KMT2A (MLL), KRAS, NPM1, NRAS, PDGFRA, PHF6, PTPN11, RUNX1, SETBP1, STAG2, TET2, TP53 and WT1. FLT3 is performed by multiple methods. Individual genes from a validated list of myeloid genes can be added-on. Test orders include summary interpretation of all results together.
  • MDS/CMML Profile
    This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. ASXL1, BCOR, BCORL1, BRAF, CBL, CEBPA, CUX1, DNMT3A, ETV6, EZH2, FLT3, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KRAS, NPM1, NRAS, PDGFRA, PTEN, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TET2, TP53, U2AF1, and ZRSR2. FLT3 is performed by multiple methods. Individual genes from a validated list of myeloid genes can be added-on. Test orders include summary interpretation of all results together.
  • MPN Profile
    This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. ABL1, ASXL1, BRAF, CALR, CEBPA, CSF3R, EZH2, FLT3, HRAS, IDH1, IDH2, JAK2 including V617F and Exons 12+14, KIT, KRAS, MPL, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SRSF2, TET2, and U2AF1. CALR and FLT3 are performed by multiple methods. Individual genes from a validated list of myeloid genes can be added-on. Test orders include summary interpretation of all results together.
  • Myeloid Profile
    This test is performed by the sequencing the entire coding regions of the genes listed. ABL1, ASXL1, ATRX, BCOR, BCORL1, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CEBPA, CSF3R, CUX1, DNMT3A, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, IKZF1, JAK2 including V617F and Exons 12+14, JAK3, KDM6A, KIT, KRAS, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PTEN, PTPN11, RAD21, RUNX1, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2. CALR and FLT3 are performed by multiple methods. Test orders include summary interpretation of all results together.
  • JMML Profile
    This test is performed by sequencing the entire coding regions of the genes listed. BRAF, CBL, CEBPA, FLT3, HRAS, JAK2 including V617F and Exons 12+14, JAK3, KIT, KRAS, NPM1, NRAS, PDGFRA, PTEN, PTPN11, and SETBP1. FLT3 is performed by multiple methods. Individual genes from a validated list of myeloid genes can be added-on. Test orders include summary interpretation of all results together.
  • Lymphoma Profile
    This test is performed by multiple methods to detect mutations in the following genes BCL1, BCL2, BRAF, CARD11, CD79B, EZH2, MYD88 and NRAS. The test is performed by sequencing the entire coding regions of the genes listed unless otherwise noted. BCL1/ IgH translocation t(11;14) is performed by real-time PCR and BCL2 t(14;18) is performed by fragment length analysis. Test orders include summary interpretation of all results together.