Department of Pathology

Division of Molecular Pathology | James Molecular Laboratory

Developmental and Metabolic Genetic Disorders
  • Test Code:  C9orf72
  • Test Name:  C9orf72 Hexanucleotide Repeat Analysis (ALS/FTD)
  • CPTCode:  81479
  • Test Description:  Hexanucleotide repeat expansions in the first intron of the C9orf72 gene (NM_001256054 [GRCh37/hg19]) are primarily associated with familial (autosomal dominant) and sporadic amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and combined ALS-FTD.
    C9orf72 alleles with less than 20 hexanucleotide repeats are typically classified as normal whereas disease-associated expansions typically have 30 or more hexanucleotide repeats. Due to limited genotype-phenotype information, repeat sizes in the intermediate range (20-29) have uncertain disease-association.
    Our diagnostic strategy uses long-range repeat-primed PCR amplification in combination with capillary electrophoretic sizing to determine the number of hexanucleotide repeats in the C9orf72 gene. This methodology permits discrete quantification of up to 145 C9orf72 hexanucleotide repeats; alleles with greater than 145 hexanucleotide repeats are also detected by this assay but exceed the resolution of capillary electrophoresis and are reported as >145. This assay is limited to C9orf72 hexanucleotide repeat analysis, other sequence or copy number variants will not be detected.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 2 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  HUNTB
  • Test Name:  Huntington's Disease
  • CPTCode:  81271
  • Test Description:  Huntington’s disease (HD) is an autosomal dominantly inherited disease caused by a mutational expansion of a polymorphic repetitive trinucleotide sequence (CAG)n located in the 5’ region of the HTT gene. The number of CAG repeats in normal individuals ranges from 11 to about 27 copies. There is an intermediate range of 28 to 35 repeats that is not associated with the disease phenotype, but maybe unstable and expand in further generations. In HD, the range of repeat lengths expands to greater than 35 repeats and is unstable. A gene with 36-39 repeats may result in incomplete penetrance or later onset of symptoms. In this assay, the number of repeats is established by PCR analysis, followed by fragment sizing through capillary gel electrophoresis at sufficient resolution to allow separation of alleles with one repeat difference. A second confirmation PCR test, utilizing a different set of primers, is performed on all samples showing expansions. CAG expansions account for >99% of cases of HD and therefore a result of >40 repeats is >99% sensitive. Pre- and post-test genetic counseling is required.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  MYOTON
  • Test Name:  Myotonic Dystrophy (DM1/DMPK) Comprehensive Analysis
  • CPTCode:  81234, 81239 (if needed)
  • Test Description:  Myotonic dystrophy type I (DM1) is an autosomal dominant neuromuscular disorder that is caused by a mutational expansion of a repetitive trinucleotide sequence (CTG)n located in the 3’ untranslated region of the myotonin-protein kinase gene (DMPK). The number of CTG repeats in normal individuals ranges from five to approximately 34 copies. Individuals with 35 to 49 CTG repeats (premutation alleles) have not been reported to develop DM1, but the number of repeats may increase when transmitted in the next generation. When the repeat size exceeds 50 CTGs (in some patients up to several thousands), the allele becomes unstable and results in the DM1 phenotype. Our diagnostic strategy consists of a long-range PCR with two distinct PCR reactions, using gene-specific and repeat-specific primers, to detect and then to characterize expanded/abnormal alleles if present. The smaller repeat sizes (< 100 CTGs) associated with normal or mildly affected cases is established by PCR analysis, followed by fragment sizing through capillary gel electrophoresis at sufficient resolution to allow separation of alleles with one repeat difference. Large expansions (>100 CTGs) are confirmed by a distinctive ladder using the repeat-specific primers. This combination of these two PCR reactions can detect and characterize all DM1 mutations.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 2 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  SMNSEQ
  • Test Name:  SMN1/SMN2 DNA Sequencing/Compound Heterozygote
  • CPTCode:  81336
  • Test Description:  The standard molecular diagnostic test for spinal muscular atrophy (SMA) is copy number assessment of SMN1 and SMN2 (see separate test code). In that assay, the absence of both copies of the SMN1 gene is a very reliable and sensitive indicator of SMA. However, about 5% of affected patients have other types of mutations in the SMN1 gene that will not be detected solely by copy number analysis. In these cases, most affected patients will be compound heterozygous for a hypomorphic or inactivating allele that is in –trans with an SMN1 deleted allele.
    To detect SMN1 variants (nonsense mutations, missense mutations, splice site mutation insertions, and small deletions), PCR-based Sanger sequencing of exons 1 through 7 of SMN1/SMN2 is performed. Upon detection of a variant, the specimen reflexes to long-range allele-specific DNA sequencing to determine the gene of origin, SMN1 or SMN2.
    This test is appropriate for a patient with a SMA-like phenotype who possesses a single copy of SMN1. It can be added on after the initial diagnostic testing has been performed or to complement a diagnostic screen performed in another laboratory.
    Important limitations of this assay include: 1) Due to technical limitations the gene of origin for variants in exon 1 cannot be confirmed; 2) DNA sequencing does not detect large deletions or insertions; 3) Mutations in patients exhibiting mosaicism or chromosomal rearrangements may not be detectable using sequencing technology; 4) Rare variants of unknown significance may be detected
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 2 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  SMAMUT
  • Test Name:  Spinal Muscular Atrophy, SMN1 Diagnostic
  • CPTCode:  81329
  • Test Description:  The survival motor neuron 1 (SMN1) gene has been shown to be homozygously deleted in approximately 95% of the autosomal recessively inherited spinal muscular atrophy (SMA) cases (0 SMN1 copies). The majority of the other 5% of affected patients are compound heterozygotes possessing a single SMN1 deletion (1 SMN1 copy) and a smaller intragenic type of mutation within the SMN1 gene. Loss of SMN1 is essential to the pathogenesis of the disease, while the disease severity is primarily correlated with the number of copies of SMN2. Most type I patients have two copies of SMN2 (and occasionally one copy). Three gene copies are common in SMA type II patients, whereas type III patients often have 3 or 4 copies of SMN2. The copy number of SMN1 and SMN2 are determined by coamplification of SMN1, SMN2, and internal copy number standards, and the ratios are quantitated. End-point detection of amplification of fluorescently tagged PCR products is done by running the samples through a capillary gel electrophoresis. The test has a sensitivity of approximately 95% and nearly 100% specificity.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 2 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  SMADSG
  • Test Name:  Spinal Muscular Atrophy, SMN1 Carrier Testing
  • CPTCode:  81329
  • Test Description:  The SMN1 gene has been shown to be homozygously deleted in approximately 95% of the autosomal recessively inherited spinal muscular atrophy (SMA) cases. Carrier status is established by the accurate determination of the SMN1 copy number. Non-carriers have 2 and occasionally more copies of SMN1, whereas carriers have a single copy of the SMN1 gene. The SMN1 copy number is determined by a quantitative multiplex PCR (qPCR) assay, which co-amplifies multiple genomic loci to determine gene copy number. The copy number of SMN1 is determined by coamplification of SMN1, SMN2, and the internal standards, and the ratios are quantitated. End-point detection of amplification of fluorescently tagged PCR products is done by running the samples through a capillary gel electrophoresis. The clinical sensitivity of the carrier test is about 90%. Causes for the reduced clinical sensitivity are due to the occurrence of carriers who have two copies of the SMN1 gene on one chromosome and a homozygous deletion on the other (2+0 carriers). In certain ethnic backgrounds, the g.27134T>G SNP (rs143838139) has been shown to modify the residual risk of being a 2+0 carrier. Beginning on 7/8/2020, detection of this risk modifying SNP will be included for patients with 2 copies of SMN1. The SMN1 gene has been shown to have a de-novo mutation rate of about 2%. The dosage analysis does not test for SMN1 point mutations which occur in about 5% of affected individuals. The SMN2 copy number is correlated with the severity of the affected state and does not provide information regarding the carrier state.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 2 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
Hematology and Thrombotic Risk Assays
  • Test Code:  FACVMB
  • Test Name:  Factor V Leiden
  • CPTCode:  81241
  • Test Description:  Resistance to activated protein C has been observed in 30-40% of patients with idiopathic venous thromboembolism (VTE). The most common cause of resistance to activated protein C is variation in the Factor V gene which replaces the arginine at codon 506 with glutamine (common names, Factor V Leiden, G1691A, R506Q, c.1601G>A, p.Arg534Gln). This change creates a Factor V variant which cannot be properly inactivated by protein C. The Factor V Leiden has an incidence of approximately 5% in the general population. Heterozygotes Factor V Leiden carriers have an approximate 5-fold increased risk for VTE, while the risk among homozygous carriers is increased 80- to 100-fold. This assay screens for Factor V Leiden by PCR followed by restriction enzyme digestion.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  FACVMB
  • Test Name:  Factor V Leiden
  • CPTCode:  81241
  • Test Description:  Multiple variations in the genes in the coagulation cascade can lead to increased risk of venous thromboembolism (VTE). Resistance to activated protein C has been observed in 30-40% of patients with idiopathic VTE. The most common cause is a variation in the Factor V gene which replaces the arginine at codon 506 with glutamine (G1691A, R506Q, c.1601G>A, p.Arg534Gln). This Factor V Leiden variant cannot full activate protein C and is present in approximately 5% of the general population. Heterozygotes Factor V Leiden carriers have an approximate 5-fold increased risk for VTE, while the risk among homozygous carriers is increased 80- to 100-fold. The G20210A (c.*97G>A) variation in the prothrombin (F2) gene has been shown to be associated with an increased risk of idiopathic venous thromboembolism (VTE). This mutation leads to increased prothrombin synthesis due to altered post-transcriptional mRNA processing. Carriers of G20210A have higher plasma prothrombin levels and a 2- to 3-fold increased risk of VTE. The prothrombin G20210A has an incidence of approximately 2% in the general population. This panel offers testing for both Factor V Leiden and F5 G20210A. Both assays screens for these variants by PCR followed by restriction enzyme digestion.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  HHCH
  • Test Name:  Hereditary Hemochromatosis
  • CPTCode:  81256
  • Test Description:  Hereditary hemochromatosis (HH) is an autosomal recessive iron-overload, which affects men more than women, associated with mutations in the HFE gene. Most cases are due to a homozygous single base mutation (c.845G>A) resulting in the substitution of tyrosine for cysteine at codon 282 (p.Cys282Tyr). Studies indicate that at least 85% of HH patients carry two copies of the mutation. A second low-penetrant mutation, p.His63Asp, also occurs in the HFE gene. Approximately 3-5% of affected patients will be compound heterozygotes, possessing one copy of the p.Cys282Tyr and one copy of the p.His63Asp mutation. This assay screens for both HH-associated mutations by PCR followed by restriction enzyme digestion.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  MTHFRB
  • Test Name:  Methylene Tetrahydrofolate Reductase, Thermolabile Polymorphism
  • CPTCode:  81291
  • Test Description:  Increased levels of homocysteine have been identified as a risk factor for both arterial and venous thromboembolic disease. Elevated levels of homocysteine can result from genetic or nutritional disturbances. A polymorphism (677C>T, c.665C>T, p.Ala222Val) in the gene encoding for 5,10-methylenetetrahydrofolate reductase (MTHFR) gives rise to a thermolabile form of the enzyme that is associated with increased levels of homocysteine when inherited as a homozygous trait. The polymorphism alters a conserved amino acid. The incidence of the homozygous state among Caucasians is approximately 9%, making it a commonly-occuring genetic risk factor for premature atherosclerotic vascular disease and thromboembolic disease. The heterozygous state has an incidence of approximately 42% among Caucasians and is associated with near-normal levels of homocysteine, therefore the heterozygous state does not appear to be a significant risk for vascular disease. This assay screens for this MTHFR polymorphism using PCR followed by restriction enzyme digestion.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  PRMUTB
  • Test Name:  Prothrombin Variant
  • CPTCode:  81240
  • Test Description:  The G20210A (c.*97G>A) variation in the prothrombin gene (F2) has been shown to be associated with an increased risk of idiopathic venous thromboembolism (VTE). This mutation leads to increased prothrombin synthesis due to altered post-transcriptional mRNA processing. Carriers of G20210A have higher plasma prothrombin levels and a 2- to 3-fold increased risk of VTE. The prothrombin G20210A has an incidence of approximately 2% in the general population. This assay screens for the G20210A prothrombin variation by PCR followed by restriction enzyme digestion.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 1 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
Fluorescent in situ hybridization (FISH) Tests
  • 1p19q (CNS tumors)
  • 3p/3q (Renal Cancer)
  • ALK (NSCLC or Lymphoma)
  • BCL2
  • BCL6
  • CCND1 (Cyclin D1)
  • DDIT3 (CHOP)
  • EGFR (CNS)
  • EWSR1 (EWS)
  • HER2
  • High Grade Lymphoma
  • Lung Cancer Fish Panel
  • MALT1 (Lymphoma)
  • MAML2 (mucoepidermoid carcinoma)
  • MDM2
  • MET
  • MYC
  • NUTM1
  • RET
  • ROS1
  • SS18 (SYT1)
  • XY

** Click on a test to see details & components **

Cancer PCR/sequencing Tests
  • Test Code:  BCR190
  • Test Name:  BCR-ABL1, P190, quant RT-PCR (ALL)
  • CPTCode:  81207, G0452
  • Test Description:  This assay detects the e1a2 BCR-ABL1 fusion transcript associated with Philadelphia chromosome (Ph) positive lymphoblastic leukemia/lymphoma (ALL). Transcripts are detected in reverse transcription real-time PCR method followed by capillary electrophoretic transcript typing and reported as a ratio of BCR-ABL1 to ABL1 transcript. Assay sensitivity is 4-5 logs producing a highly sensitivity quantitative assay suitable for therapy response monitoring in Ph+ ALL. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with relevant clinicopathologic findings and other laboratory testing, when available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3-10 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  BCR210
  • Test Name:  BCR-ABL1, P210, quant RT-PCR (CML)
  • CPTCode:  81206, G0452
  • Test Description:  Detects the b2a2 and b3a2 BCR-ABL1 fusion transcripts associated with chronic myelogenous leukemia (CML). Transcripts are detected in a multiplex reverse transcription real-time PCR method followed by capillary electrophoretic transcript typing. Results are reported as a ratio of BCR-ABL1 to ABL1 transcript, normalized to the international scale (IS). Assay sensitivity is 4-5 logs producing a highly sensitivity quantitative assay suitable for therapy response monitoring in CML. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with relevant clinicopathologic findings and other laboratory testing, when available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3-10 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  BCR ABL t(9:22)
  • Test Name:   BCR ABL, t(9:22) - quantitative
  • CPTCode:   81479, G0452
  • Test Description:   Detects the b2a2, b3a2 and e1a2 BCR-ABL1 fusion transcripts associated with Philadelphia chromosome (Ph) positive lymphoblastic leukemia/lymphoma (ALL) and chronic myelogenous leukemia (CML). Transcripts are detected in a multiplex reverse transcription real-time PCR method followed by capillary electrophoretic transcript typing. For b2/b3a2 transcripts, results are reported as a ratio of BCR-ABL1 to ABL1 transcript, normalized to the international scale (IS). Assay sensitivity is 4-5 logs producing a highly sensitivity quantitative assay suitable for therapy response monitoring in CML and Ph+ ALL. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with relevant clinicopathologic findings and other laboratory testing, when available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3-10 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  BRAFM
  • Test Name:  BRAF Mutation Analysis, Exon 15 (V600)
  • CPTCode:  81210
  • Test Description:  Activating mutations in exon 15 of BRAF, particularly at codon 600, are common in tumors of many types. This assay utilizes DNA sequencing to evaluate for V600E and alternate pathogenic mutations in this exon. This assay is useful to identify V600E/K/R mutations in melanoma which may be responsive to BRAF-directed kinase inhibitors, detect V600E mutations characteristic of hairy cell leukemia, identify V600 mutations that have diagnostic and prognostic significance in papillary thyroid carcinoma, and to profile BRAF mutation status in carcinomas of colon, ovary and endometrium.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Cerebrospinal fluid and cytology fluid: secure screw-cap tube
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
    • Ship fresh tissue on dry ice after snap-freezing
  • Test Code:  BTKPLCG2
  • Test Name:  BTK and PLCG2, Comprehensive Mutation Profiling
  • CPTCode:  81233, 81320, G0452
  • Test Description:  Chronic lymphocytic leukemia (CLL) and other B-cell malignancies often have abnormal activation of targetable growth regulatory kinases such as the Bruton’s tyrosine kinase (BTK). BTK inhibitors have been shown to be highly efficacious in CLL and some B-cell lymphomas. However, subsets of treated patients become resistant due to acquisition of particular BTK and PLCG2 mutations. Testing for these mutations can assist in understanding causes of therapy resistance and monitoring responses to BTK inhibitors. The assay will detect all pathogenic mutations in the coding region of both genes but is validated for coverage of the BTK C481S hotspot mutation to at least 1% allele frequency in the purified cells. Other resistance hotspots covered include PLCG2 L845F, R665W, and S707Y. This assay includes a pathologist interpretation in the report that correlates molecular findings with hematologic findings and available clinical and other laboratory data. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with relevant clinicopathologic findings and other laboratory testing, when available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 5-10 ml preferred, 5 ml minimum (sample sufficient to yield a minimum of 5 x 10E4 enriched B cells is required for testing); green-top (heparin) or yellow-top (ACD) tubes are acceptable.
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack. DO NOT FREEZE
  • Test Code:  BTKR
  • Test Name:  BTK Resistance Mutation (C481S)
  • CPTCode:  81233
  • Test Description:  Bruton tyrosine kinase (BTK) inhibitors, such as ibrutinib, are widely used in the treatment of chronic lymphocytic leukemia (CLL) and other B-cell lymphoproliferative disorders. Prolonged treatment with BTK inhibitors can result in the emergence of mutations in BTK, particularly C481S, that are associated with disease progression and trigger a change in therapy. Clinical studies performed at OSU demonstrate that even low levels of BTK C481S can herald eventual disease progression and consideration of therapy switch. This assay sensitively detects the C481S mutation in BTK (c.1442G>C or c.1441T>A) using mutation-specific digital droplet PCR.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum; Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube or slides with at least two identifiers; provide CBC data or pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  CALR
  • Test Name:  Calreticulin mutation analysis
  • CPTCode:  81219
  • Test Description:  Insertion-deletion frameshift mutations in exon 9 of the calreticulin gene (CALR) are identified in approximately 25% of patients with myeloproliferative neoplasms (MPN) and are essentially mutually exclusive with JAK2, MPL and CSF3R pathogenic mutations. Among MPN subtypes, CALR mutations are associated with essential thromobocythemia/thrombocytosis (ET), seen in 60-70% of cases that lack JAK2 V617F, and primary myelofibrosis (PMF), seen in 80-90% of JAK2 mutation-negative cases. PMF cases with mutated CALR have a lower risk of thrombosis and longer overall survival than patients with JAK2 V617F or lack both mutations.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube or slides with at least two identifiers; provide CBC data or pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  CEBPA
  • Test Name:  CEBPA Mutation Analysis
  • CPTCode:  81218
  • Test Description:  The CCAAT/enhancer binding factor alpha (CEBPA) gene is mutated in 7-10% of acute myeloid leukemia (AML). Biallelic CEBPA mutation, in the absence of FLT3 mutation, has been associated with favorable prognosis in AML. This assay detects missense and insertion/deletion mutations anywhere in the coding region of CEBPA In blood and bone marrow samples using capillary gel sizing and Sanger sequencing. The presence of single versus double or biallelic mutations is reported.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3-10 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  COLNGS
  • Test Name:  Colon Cancer Mutation Panel (COLMOL)
  • CPTCode:  81445, G0452
  • Test Description:  Colorectal cancer (CRC) and other GI malignancies frequently show activating mutations in the RAS pathway or other interacting growth regulatory genes. Activating KRAS mutations are found in up to 90% of carcinomas of the pancreas/bile duct and 50% of colorectal carcinomas and have been clearly shown to predict lack of response to EGFR immunotherapeutic agents, such as cetuximab. However, other relatively frequently mutated genes such as AKT1, APC, BRAF, CDH1, CTNNB1, FBXW7, MET, MLH1, NRAS, PIK3CA, PTEN, PTPN11, RB1 and SMAD4, STK11 and TP53 may also have predictive effects in CRC. This assay detects pathogenic variants in the commonly-mutated areas of 48 genes involved implicated in CRC or neoplasms in the differential. This panel includes extended analysis of KRAS and NRAS (exons 2-4) as recommended by the newest National Comprehensive Cancer Center (NCCN) guidelines. The interpretive comment, provided by a board-certified molecular pathologist, provides guidance on mutation significance. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 10 uncoated/non-plus sections preferred (10 uM thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with two identifiers; provide pathology report if sending from outside OSU
    • Transport FNA in RPMI media to the lab within 3 days of collection and store 4C until ready to transport
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  EGFRM
  • Test Name:  EGFR Mutation Analysis (exons 19/21)
  • CPTCode:  81235
  • Test Description:  Activating mutations in the epidermal growth factor receptor (EGFR) are present in approximately 10% of non-small cell lung carcinomas. These mutations are associated with response to EGFR-directed kinase inhibitors, such as erlotinib and gefitinib. The most common responsive EGFR mutations are insertions/deletions in exon 19 and a point mutation in exon 21 producing the L858R missense substitution. This assay selectively detects mutations in these two sites within EGFR, using PCR-based fragment analysis with restriction digestion.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 8 uncoated/non-plus sections preferred (10 micron thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Ship glass slides or paraffin block in secure carriers with padding
    • Ship frozen tissue on dry ice after snap-freezing
  • Test Code:  XRAS
  • Test Name:  Extended RAS mutation panel
  • CPTCode:  81275, 81276, 81210, 81311, G0452
  • Test Description:  Colorectal cancer (CRC) and other GI malignancies frequently show activating mutations in the RAS/BRAF pathway or other interacting growth regulatory genes. Activating RAS mutations are found in up to 90% of carcinomas of the pancreas/bile duct and 65% of colorectal carcinomas and have been clearly shown to predict lack of response to EGFR immunotherapeutic agents, such as cetuximab. This panel includes extended analysis of KRAS (exons 2-4, codon 12, 13, 61, 117 and 146), NRAS (exons 2 and 3, codons 12, 13 and 61) and BRAF (exon 15, codons 600 and 601) as recommended by the newest National Comprehensive Cancer Center (NCCN) guidelines. The interpretive comment, provided by a board-certified molecular pathologist, provides guidance on mutation significance. Thyroid FNA or thyroid tumor tissue sections can also be tested for diagnostic/prognostic indications. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • FFPE: 1 block or 1 H&E and 8 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 4 slides minimum)
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
  • Test Code:  FLT3B, FLT3BM
  • Test Name:  FLT3, ITD and TK Mutation Analysis
  • CPTCode:  81245, 81246
  • Test Description:  Two acquired activating mutations in the FLT3 tyrosine kinase gene are commonly associated with acute myelogenous leukemia (AML). An internal tandem gene duplication (ITD, also known as FLT3-LM) has been identified in about 20-30% of the patients. The second type of mutation is a missense variation at aspartic acid residue (codon 835) (TKD) and occurs in about 7% of the cases. Identification of these mutations is clinically important since patients harboring one or both of these mutations generally have a worse prognosis and a higher rate of relapse. This assay screens for the ITD and TKD variations by PCR and capillary electrophoresis (ITD) and PCR followed by restriction enzyme digestion and then capillary electrophoresis (TKD). The assay has an estimated sensitivity of detection of 1 in 20 cells.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack or at RT. DO NOT FREEZE
  • Test Code:  HCNGS
  • Test Name:  Hematologic Neoplasm Mutation Panel
  • CPTCode:  81450, G0452
  • Test Description:  This next-generation sequencing (NGS) panel assesses for mutations in genomic DNA from blood, bone marrow aspirate or tissue that are useful for the diagnosis, therapy selection and followup monitoring of a variety of hematologic neoplasms. Separate sets of 50 genes designed for myeloid neoplasms (MDS, myeloproliferative neoplasms and AML), CLL/low-grade B-cell lymphoma and ALL/high-grade B-cell lymphoma/T-cell lymphoma are available. *Provider must specify clinical indication when ordering* to allow appropriate panel to be selected. Chromosomal translocation/fusion transcripts are NOT assessed. Decalcified bone marrow biopsies are NOT acceptable for testing.
    With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist providing guidance on mutation significance, integrating genetic test results with other laboratory testing, and review of morphologic/histologic material, if available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 4mL preferred, 0.5mL minimum
    • Bone marrow aspirate: purple (EDTA); 2mL preferred, 0.5mL minimum
    • Non-decalcified, formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum)
  • Handling:
    • Label tube with two identifiers
    • Transport to lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice. DO NOT FREEZE
    • Provide pathology report or CBC/hematology values if sending from outside OSU Medical Center
  • Molecular Components: Listed below are gene lists for four hematologic NGS panel pools allowing for targeted selection of gene sets associated with particular diagnoses.
    • Myeloid Neoplasm Mutation Panel Gene List: ABL1, ANKRD26, ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CSF3R, DDX41, DNMT3A, ELANE, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KMT2A, KRAS, MAP2K1, MPL, MYD88, NOTCH1, NPM1, NRAS, PHF6, PIK3CA, PTEN, PTPN11, RAD21, RUNX1, SF3B1, SETBP1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, TERC, TERT, TET2, TP53, UBA1, U2AF1, WT1, ZRSR2
    • CLL/ Low Grade B-cell Lymphoma Mutation Panel Gene List: ASXL1, B2M, BCL2, BCOR, BCORL1, BIRC3, BRAF, BTK, CARD11, CD79B, CREBBP, CXCR4, DDX41, DNMT3A, ELANE, EZH2, ETV6, FBXW7, GATA2, GNA13, KLF2, KIT, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PIK3CD, PIK3CG, PIM1, PLCG2, POT1, PTEN, PTPRD, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, STAT6, TERC, TERT, TET2, TP53, U2AF1, XPO1, ZRSR2
    • T-cell/Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, GNA13, ID3, IDH2, JAK1, JAK3, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PRKCB, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT5B, STAT6, TCF3, TET2, TP53, XPO1
    • Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, FOXO1, GNA13, ID3, IDH2, IRF8, JAK1, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT6, TCF3, TET2, TNFRSF14, TP53, XPO1
  • Test Code:  IDH12
  • Test Name:  IDH1 and IDH2 mutations
  • CPTCode:  81120, 81121
  • Test Description:  Isocitrate dehydrogenase 1 and -2 (IDH1 and IDH2) are involved in cell metabolism and epigenetic gene regulation and are frequently mutated in human cancers. In acute myeloid leukemia (AML), IDH mutation may predict for response to IDH-targeted therapies and be an adverse prognostic factor in some subclasses of otherwise favorable-risk disease. In brain tumors, IDH-mutant gliomas have been associated with a better prognosis than cases that lack IDH mutations. Among the differential diagnosis of CNS tumors, IDH mutation may assist in the diagnosis and classification of glial tumors This pyrosequencing test using genomic DNA detects all mutations at codon 132 (exon 4) of IDH1 and codons 140 and 172 (exon 4) of IDH2 in blood, bone marrow, and formalin-fixed paraffin-embedded tissue (FFPE).
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • FFPE: 1 block or 1 H&E and 8 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum)
  • Handling:
    • Label tube or slides with at least two identifiers; provide CBC data or pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  IGHBC
  • Test Name:  IGH/B-cell Gene Rearrangement, PCR
  • CPTCode:  81261, G0452
  • Test Description:  The immunoglobulin heavy chain (IGH) gene undergoes DNA rearrangement as B cells develop. The IGH PCR assay, which can be performed in blood, bone marrow, cytology samples or fresh or fixed tissues, can be used to diagnose B-cell lymphomas and leukemias or alternatively to support the presence of a reactive/polyclonal B-cell population. This assay uses multiplex PCR of the IGH locus for the FR1, FR2 and FR3 primer sets followed by fluorescent fragment analysis by capillary eletrophoresis. This protocol has an overall sensitivity of 90% for detection of a clonal B-cell population at the assay sensitivity limit but can be negative for rearrangement in up to 30% of B-cell neoplasms with a high rate of IGVH mutations (typically follicular lymphomas and myeloma). The assay can also be used to monitor sequential samples for the presence of persistent/recurrent B-cell lymphoma or leukemia. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Cerebrospinal fluid and cytology fluid: secure screw-cap tube
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
    • Ship fresh tissue on dry ice after snap-freezing
  • Test Code:  IGHM
  • Test Name:  IGH Somatic Hypermutation
  • CPTCode:  81263, 81261, G0452
  • Test Description:  This assay analyzes RNA extracted from blood or bone marrow leukocytes for the presence of clonal rearrangements of the immunoglobulin heavy chain gene (IGH). If a clonal B-cell population is present, the extent of somatic mutation of the IGH variable region (IgVH) is determined by Sanger sequencing. IgVH analysis is used in patients with chronic lymphocytic leukemia (CLL) to identify the adverse prognostic group in which the mutation rate is below 2% (“unmutated CLL”). Due to structural sequence changes, a small percentage of CLL cases may be unamplifiable by PCR from cDNA. In those cases, partial IGVH PCR amplification and sequencing from cDNA and DNA can be analyzed. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with relevant clinicopathologic findings and other laboratory testing, when available
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Cerebrospinal fluid and cytology fluid: secure screw-cap tube
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
    • Ship fresh tissue on dry ice after snap-freezing
  • Test Code:  JAK2
  • Test Name:  JAK2 V617 Mutation Analysis
  • CPTCode:  81270
  • Test Description:  Testing for the V617F mutation in JAK2 can assist in diagnosis and classification of myeloproliferative neoplasms and monitoring responses to therapy. The JAK2 V617F mutation is seen in 90% of polycythemia vera, 40-50% of essential thrombocythemia, primary myelofibrosis, occasional cases of myeloproliferative neoplasms of other types, and chronic myelomonocytic leukemia. This assay does not examine exon 12 mutations seen in some cases of polycythemia vera.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  KIT816
  • Test Name:  KIT D816V Mutation Detection
  • CPTCode:  81273
  • Test Description:  Genomic DNA is extracted and subjected to mutation-specific digital droplet polymerase chain reaction (ddPCR) to assess for the D816V hotspot mutation in the KIT gene (hg19, NM_000222:c.2447A>T; p.D816V), which is recurrent in mast cell neoplasms and certain subtypes of AML. Other mutations, including alternative mutations at codon 816, will not be detected by this assay. Target amplification is carried out in independent ddPCR reactions with fluorescently-labeled probes specific for the wild type and mutant sequences. Mutation levels are reported as a percent ratio of mutant to total events at endpoint. This assay can be used for diagnostic/disease subclassification purposes as well as for therapy selection and minimal residual disease detection in patients with mast cell neoplasms and/or certain subtypes of AML. The low reportable range is approximately 0.01% mutation-bearing alleles. Samples with events below the defined cutoff are reported as negative.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 5-10 unstained sections cut onto non-plus/uncoated glass slides (2 slides minimum) or shaves in centrifuge tube
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  PULNGS
  • Test Name:  Lung Cancer Mutation Panel (PULMOL)
  • CPTCode:  81445, G0452
  • Test Description:  Oncogenic mutations are common in non-small cell lung carcinoma (NSCLC), particularly adenocarcinoma. The identification of activating EGFR mutations that can be targeted by kinase inhibitors is critical to selecting frontline, maintenance and salvage therapy at diagnosis and relapse. AKT1, ALK, BRAF, ERBB2/HER2, FGFR1/2/3, MET and PIK3CA can also demonstrate activating mutations that may be targetable. Other mutations such as in KRAS and TP53 have strong prognostic significance and help provide therapeutic guidance. This 48-gene Ion Torrent next-generation sequencing panel assesses the commonly-mutated areas of these genes. Also assessed are CDKN2A, CTNNB1, ERBB4, FBX7, HRAS, MAP2K1, NOTCH1, NRAS, PTEN, PTPN11, SMAD4, SMARCB1, STK11 and VHL which can be mutated in NSCLC and help in classification. The panel components identify commonly dysregulated pathways and/or pathogenetic risk groups of lung cancer. ALK, ROS1 and RET translocations are not tested for in this panel, and can be ordered by separate FISH assays. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 10 uncoated/non-plus sections preferred (10 micron thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with two identifiers; provide pathology report if sending from outside OSU
    • Transport FNA in RPMI media to the lab within 3 days of collection and store 4C until ready to transport
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  HCNGS
  • Test Name:  Hematologic Neoplasm Mutation Panel
  • CPTCode:  81450, G0452
  • Test Description:  This next-generation sequencing (NGS) panel assesses for mutations in genomic DNA from blood, bone marrow aspirate or tissue that are useful for the diagnosis, therapy selection and followup monitoring of a variety of hematologic neoplasms. Separate sets of 50 genes designed for myeloid neoplasms (MDS, myeloproliferative neoplasms and AML), CLL/low-grade B-cell lymphoma and ALL/high-grade B-cell lymphoma/T-cell lymphoma are available. *Provider must specify clinical indication when ordering* to allow appropriate panel to be selected. Chromosomal translocation/fusion transcripts are NOT assessed. Decalcified bone marrow biopsies are NOT acceptable for testing.
    With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist providing guidance on mutation significance, integrating genetic test results with other laboratory testing, and review of morphologic/histologic material, if available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 4 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Non-decalcified. formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum)
  • Handling:
    • Label tube with two identifiers
    • Transport to lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice. DO NOT FREEZE
    • Provide pathology report or CBC/hematology values if sending from outside OSU Medical Center
  • Molecular Components: Listed below are gene lists for four hematologic NGS panel pools allowing for targeted selection of gene sets associated with particular diagnoses.
    • Myeloid Neoplasm Mutation Panel Gene List: ABL1, ANKRD26, ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CSF3R, DDX41, DNMT3A, ELANE, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KMT2A, KRAS, MAP2K1, MPL, MYD88, NOTCH1, NPM1, NRAS, PHF6, PIK3CA, PTEN, PTPN11, RAD21, RUNX1, SF3B1, SETBP1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, TERC, TERT, TET2, TP53, UBA1, U2AF1, WT1, ZRSR2
    • CLL/ Low Grade B-cell Lymphoma Mutation Panel Gene List: ASXL1, B2M, BCL2, BCOR, BCORL1, BIRC3, BRAF, BTK, CARD11, CD79B, CREBBP, CXCR4, DDX41, DNMT3A, ELANE, EZH2, ETV6, FBXW7, GATA2, GNA13, KLF2, KIT, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PIK3CD, PIK3CG, PIM1, PLCG2, POT1, PTEN, PTPRD, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, STAT6, TERC, TERT, TET2, TP53, U2AF1, XPO1, ZRSR2
    • T-cell/Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, GNA13, ID3, IDH2, JAK1, JAK3, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PRKCB, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT5B, STAT6, TCF3, TET2, TP53, XPO1
    • Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, FOXO1, GNA13, ID3, IDH2, IRF8, JAK1, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT6, TCF3, TET2, TNFRSF14, TP53, XPO1
  • Test Code:  MGMT
  • Test Name:  MGMT Promoter methylation, Tumor
  • CPTCode:  81287
  • Test Description:  MGMT promoter methylation can be used to assess silencing of expression of this DNA repair enzyme in tumors. In brain tumors, particularly glioblastoma, presence of MGMT methylation is a predictor of response to certain chemotherapy (e.g. the alkylating agent temozolomide). Such testing can identify a favorable prognostic group where single-agent temozolomide therapy may be warranted. MGMT promoter methylation may also have prognostic significance in other tumor types.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 10 uncoated/non-plus sections preferred (10 micron thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with two identifiers; provide pathology report if sending from outside OSU
    • Transport FNA in RPMI media to the lab within 3 days of collection and store 4C until ready to transport
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  MSI
  • Test Name:  Microsatellite Instability (MSI) Analysis, Tumor
  • CPTCode:  81301, G0452
  • Test Description:  The presence of variable expansions of DNA microsatellite sequences is termed microsatellite instability (MSI) and is a feature of many tumors. MSI can result from inherited germline defects in the mismatch repair (MMR) proteins and/or acquired MMR mutations or gene silencing during tumor development. Germline MMR mutation, characteristic of Lynch syndrome or hereditary non-polyposis colorectal cancer (HNPCC), produces early-onset colon, endometrial and sebaceous tumors.
    This MSI assay, which examines 7 mononucleotide microsatellite sequences in tumor DNA from a patient, can be used in association with immunohistochemical detection of MMR proteins in a HNPCC screening algorithms. The pattern in the tumor is compared to normal DNA reference and classified as having high microsatellite instability (MSI-H, 2+ markers), low/equivocal microsatellite instability (MSI-L, 1 marker) or being microsatellite stable (MSS). Detection of MSI can be followed by other testing (BRAF V600E mutation status and/or MLH1 promoter methylation analysis) to help differentiate germline from somatic causes. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 8 uncoated/non-plus sections preferred (10 uM thickness), 2 slides minimum or 1 paraffin block
    • Tissue/block must contain adequate amounts of tumor
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  MLHEND
  • Test Name:  MLH1 Promoter Methylation, Tumor
  • CPTCode:  81288, G0452
  • Test Description:  MLH1 promoter methylation can be used to assess silencing of expression of this DNA repair enzyme in tumors. Testing for MLH1 promoter methylation is indicated in MLH1-negative and/or microsatellite unstable colorectal tumors and other tumors characteristic of Lynch syndrome/HNPCC (e.g. endometrial and sebaceous skin tumors).This assay is utilized for HNPCC protocols after finding absent MLH1 immunohistochemical (IHC) expression and prior to MLH1 gene sequencing. The presence of MLH1 methylation is almost always indicative of a somatic cause for MLH1 protein loss, with no further workup indicated in most cases. An unmethylated MLH1 gene along with MLH1 IHC loss would indicate the need for germline MLH1 sequencing. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 10 uncoated/non-plus sections preferred (10 micron thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with two identifiers; provide pathology report if sending from outside OSU
    • Transport FNA in RPMI media to the lab within 3 days of collection and store 4C until ready to transport
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  MPL
  • Test Name:  MPL Mutation Detection
  • CPTCode:  81338 (Z02IF)
  • Test Description:  Testing for the codon 505 and 515 mutations in MPL can assist in diagnosis and classification of myeloproliferative neoplasms and monitoring responses to therapy. Activating mutations in the MPL gene are associated with approximately 5%-8% of primary myelofibrosis (PMF) cases and 1%-4% of essential thrombocythemia (ET) cases. This assay, which uses PCR-based pyrosequencing, has a limit of detection of approximately 5% mutant-bearing alleles and does not examine for the rare MPL mutations outside of these codons.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  MPN
  • Test Name:  Myeloproliferative Neoplasm Mutation Panel (JAK2, CALR, MPL)
  • CPTCode:  81270 (JAK2), 81219 (CALR), 81338 (MPL)
  • Test Description:  Myeloproliferative neoplasms (MPNs) are usualy driven by activation of the JAK2-STAT signaling pathway, which is most typically achieved by driver mutations in JAK2, MPL, and CALR. Among MPNs, the JAK2 V617F mutation is found in almost all patients with PV and in 50–60% of those with ET or PMF. Frameshift mutations in exon 9 of CALR are reported in 20-35% of patients with ET and PMF and hotspot mutations in codon 505 and 515 of the MPL gene are found in approximately 5% of patients with ET and PMF.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  MYD88
  • Test Name:  MYD88 Mutational Analysis (L265P, V217F)
  • CPTCode:  81305
  • Test Description:  Genomic DNA is extracted and subjected to mutation-specific digital droplet polymerase chain reaction (ddPCR) to assess for the two mutations in MYD88  (L265P and V217F) that are seen in low-grade B-cell lymphoproliferative disorders (B-LPD). The L265P mutation (currently designated as MYD88 p.Leu273Pro, c.818T>C, NP_002459) is highly associated with lymphoplasmacytic lymphoma (LPL)/Waldenstrom macroglobulinemia (WM).  The V217F (MYD88 p.Val217Phe, c.649G>T, NM_002468) is most commonly associated with CLL. Other MYD88 mutations (such as those seen in  large B-cell lymphoma) will not be detected by this assay. Target amplification is carried out in independent ddPCR reactions with fluorescently-labeled probes specific for the wild type and mutant sequences. Mutation levels are reported as a percent ratio of mutant to total events at endpoint. This assay can be used to monitor for residual disease in patients with fully predominant L265P or V217F MYD88 mutation at diagnosis. The low reportable range is approximately 0.1% mutation-bearing alleles. Samples with events below the defined cutoff are reported as negative.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
    • Fluid (e.g. cerebrospinal fluid): secure screw-cap tube
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  HCNGS
  • Test Name:  Hematologic Neoplasm Mutation Panel
  • CPTCode:  81450, G0452
  • Test Description:  This next-generation sequencing (NGS) panel assesses for mutations in genomic DNA from blood, bone marrow aspirate or tissue that are useful for the diagnosis, therapy selection and followup monitoring of a variety of hematologic neoplasms. Separate sets of 50 genes designed for myeloid neoplasms (MDS, myeloproliferative neoplasms and AML), CLL/low-grade B-cell lymphoma and ALL/high-grade B-cell lymphoma/T-cell lymphoma are available. *Provider must specify clinical indication when ordering* to allow appropriate panel to be selected. Chromosomal translocation/fusion transcripts are NOT assessed. Decalcified bone marrow biopsies are NOT acceptable for testing.
    With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist providing guidance on mutation significance, integrating genetic test results with other laboratory testing, and review of morphologic/histologic material, if available.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 4 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Non-decalcified. formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum)
  • Handling:
    • Label tube with two identifiers
    • Transport to lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice. DO NOT FREEZE
    • Provide pathology report or CBC/hematology values if sending from outside OSU Medical Center
  • Molecular Components: Listed below are gene lists for four hematologic NGS panel pools allowing for targeted selection of gene sets associated with particular diagnoses.
    • Myeloid Neoplasm Mutation Panel Gene List: ABL1, ANKRD26, ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CEBPA, CSF3R, DDX41, DNMT3A, ELANE, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, JAK2, KIT, KMT2A, KRAS, MAP2K1, MPL, MYD88, NOTCH1, NPM1, NRAS, PHF6, PIK3CA, PTEN, PTPN11, RAD21, RUNX1, SF3B1, SETBP1, SH2B3, SMC1A, SMC3, SRSF2, STAG2, TERC, TERT, TET2, TP53, UBA1, U2AF1, WT1, ZRSR2
    • CLL/ Low Grade B-cell Lymphoma Mutation Panel Gene List: ASXL1, B2M, BCL2, BCOR, BCORL1, BIRC3, BRAF, BTK, CARD11, CD79B, CREBBP, CXCR4, DDX41, DNMT3A, ELANE, EZH2, ETV6, FBXW7, GATA2, GNA13, KLF2, KIT, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PIK3CD, PIK3CG, PIM1, PLCG2, POT1, PTEN, PTPRD, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, STAT6, TERC, TERT, TET2, TP53, U2AF1, XPO1, ZRSR2
    • T-cell/Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, GNA13, ID3, IDH2, JAK1, JAK3, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PRKCB, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT5B, STAT6, TCF3, TET2, TP53, XPO1
    • Aggressive B-cell Neoplasm Gene List: B2M, BCL2, BCOR, BIRC3, BRAF, BTK, CARD11, CCND3, CD28, CD79B, CREBBP, CXCR4, DNMT3A, EZH2, FOXO1, GNA13, ID3, IDH2, IRF8, JAK1, KLF2, KMT2A, KRAS, MAP2K1, MEF2B, MYD88, NOTCH1, NOTCH2, NRAS, PIK3CA, PHF6, PIM1, PLCG1, PLCG2, PTEN, PTPRD, RHOA, RPS15, SAMHD1, SETD2, SF3B1, SH2B3, SOCS1, STAT3, STAT6, TCF3, TET2, TNFRSF14, TP53, XPO1
  • Test Code:  NPM1
  • Test Name:  NPM1 Mutation Analysis
  • CPTCode:  81310
  • Test Description:  This ultra-sensitive PCR-based assay assesses for the most common oncogenic nucleophosmin 1 gene (NPM1) mutations seen in AML and other myeloid neoplasms. Genomic DNA is assessed using digital droplet PCR with a sensitivity of 0.1% mutant allele fraction, and is thus suitable for minimal residual disease monitoring during or following therapy. Only types A, B and D duplications in exon 12 are assessed. A report documenting the specific NPM1 mutation is thus required before testing.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3mL preferred, 0.5mL minimum
    • Bone marrow aspirate: purple (EDTA); 2mL preferred, 0.5mL minimum
  • Handling:
    • Label tube with at least two identifiers
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
    • Provide sequencing report characterizing NPM1 mutation type, if sending from outside OSU Medical Center
  • Test Code:  NRAS
  • Test Name:  NRAS Mutation Analysis
  • CPTCode:  81311
  • Test Description:  NRAS is a GTPase that when activated by point mutation produces dysregulated growth signaling and oncogenesis. Mutations in NRAS at codons 12, 13 or 61 are found in 10-15% melanomas, acute myeloid leukemias and follicular thyroid neoplasms and less commonly in other tumor types. This assay is commonly used in association with the BRAF, V600 mutation assay to subtype malignant melanoma to aid in therapy selection.
  • Specimen Description:
    • FFPE: 1 block or 1 H&E and 8 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 4 slides minimum)
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
  • Test Code:  NTRKF
  • Test Name:  NTRK Fusion Panel
  • CPTCode:  81194
  • Test Description:  NTRK gene fusions, which activate the tyrosine kinase domain of this family of growth signaling receptors, are found in solid tumors. Fusions involving NTRK1, NTRK2 and NTRK3 are all associated with response to kinase inhibitors. This RNA-based assay can be used to sensitivity detect any kinase-activating NTRK fusions in solid tumors in paraffin-embedded, formalin-fixed tissues. A wide variety of NTRK fusion partners have been identified in this assay. If a fusion is detected, the report will specify which NTRK gene and domain(s) are involved, which fusion partner is present and whether the fusion has been previously associated with solid tumors.
  • Specimen Description:
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
  • Handling:
    • Label tube or slides with at least two identifiers.
    • Provide pathology report if sending from outside OSU (preliminary report OK if case ID is on report).
  • Test Code:  PFNGS
  • Test Name:  Pancreatic fluid, mutation analysis
  • CPTCode:  81445, G0452
  • Test Description:  This 50-gene next-generation sequencing (NGS) panel detects disease-associated mutations that are associated with diagnosis and disease progression in pancreatic neoplasms. It is suitable for testing pancreatic cyst fluid. Among the genes in this panel, mutations in KRAS are commonly detected in intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neplasms (MCNs) but the presence of GNAS mutations is largely specific for IPMNs. AKT1, BRAF, NRAS, PIK3CA and PTEN mutations are seen less commonly in MCNs. In contrast, VHL mutations and/or deletions are characteristic of serous cystadenomas and CTNNB1 mutations in the absence of other genetic alterations may be observed in solid-pseudopapillary neoplasms. Additionally, IPMNs with high-grade dysplasia and invasive adenocarcinomas are reported to develop mutations in the TP53, SMAD4, and CDKN2A tumor suppressors.
    Several studies have shown that the detection of KRAS and GNAS variants improves the identification and classification of mucinous neoplasms compared to cytopathology and/or serum or carcinoembryonic antigen (CEA) alone. The presence of KRAS or GNAS mutations are 80-100% specific for mucinous pancreatic tumors as compared to benign lesions. With a combination of cytology, CEA and mutation profiling, sensitivity of pancreatic fluid analysis for detection of a mucinous neoplasm is greater than 90%. This test provides an interpretive comment by a board-certified molecular pathologist providing guidance on mutation significance.
  • Specimen Description:
    • Pancreatic cyst fluid in a sterile, container with a secure lid. Preferred volume: 1 ml, minimum volume 300 ul
  • Handling:
    • Label container with two patient identifiers; provide cytology report or source of fluid if sending from outside OSU medical center
    • Store at 4C until ready to transport
    • Transport fresh samples to the lab within 2 days of draw
    • Ship on wet ice pack or freeze on dry ice
  • Test Code:  APLQ
  • Test Name:  PML-RARA, quantitative PCR
  • CPTCode:  81315
  • Test Description:  This assay detects the PML/RARA fusion transcript associated with the t(15;17) chromosomal translocation and acute promyelocytic leukemia (APL or AML-M3). Real-time/quantitative reverse transcription PCR (RQ-PCR) of blood or bone marrow aspirate is recommended at diagnosis and at regular intervals to monitor response to therapy and remission status in APL. This assay reports normalized copy number (NCN) as a percentage of the PML-RARA transcript compared to ABL1 normalizing transcript. The transcript type is also indicated as short form (bcr3) or long/variant form (bcr1/bcr2).
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM at 4C until ready to transport
    • Ship blood/BM on wet ice pack. DO NOT FREEZE
  • Test Code:  STPNGS
  • Test Name:  Solid Tumor Mutation Panel
  • CPTCode:  81445, G0452
  • Test Description:  This 48-gene mutation next-generation sequencing (NGS) assay is particularly useful in determining the molecular pathogenesis/subtype and predictive/targetable mutations in melanoma, thyroid neoplasia and gastrointestinal stromal tumor (GIST). The interpretive comment, provided by a board-certified molecular pathologist, provides tumor-specific interpretations on mutation significance and integrating genetic results with other laboratory testing and review of the histologic material if available.

    Melanoma: Relevant diagnostic or targetable mutation profiles included in this panel for acral/cutaneous melanoma include BRAF, CTNNB1 (beta-catenin), KIT, KRAS, NRAS and PTEN, with GNAQ and GNA11 mutations present in nearly all uveal melanomas. Germline and somatic mutations in the tumor suppressor p16/CDKN2A play an important role in pathogenesis and progression of cutaneous melanoma, as do TP53 mutations. Recently, other potential novel driver mutations have been identified in the so called “pan-negative” melanomas i.e. which don’t harbor mutations in the above driver genes. Of the genes in this panel, these include ALK, AKT1, ERBB4 and KDR. Melanomas harboring activating ERBB4 mutations had been shown to be exquisitely sensitive to the tyrosine kinase inhibitor lapatinib.

    Thyroid neoplasms: Approximately 25% of medullary thyroid carcinoma (MTC) arise in patients with germline mutations in the RET gene representing multiple endocrine neoplasia type 2 (MEN2) syndrome, whereas the remaining MTC are sporadic with somatic mutations in RET seen in the majority of cases. The RET M918T mutation correlates with poor prognosis, higher prevalence of distant metastases, and may predict response to some RET inhibitors such as cabozantinib and vandetanib. Presumed disease-associated mutations seen in other MTC cases including missense variants and rarely deletions in HRAS, STK11, KRAS, MLH1, KIT, and MET. Relevant diagnostic or targetable mutation profiles for thyroid follicular neoplasms including BRAF, HRAS, KRAS and NRAS genes.

    GIST: Relevant diagnostic or targetable mutation profiles for GIST include KIT including missense, insertion (ins), and/or deletions (del) involving exons 11, 9, 13, and 17. GISTs with unmutated KIT often have activating mutations involving platelet-derived growth factor receptor-alpha (PDGFRA). Most of those mutations render tumor sensitive to the tyrosine kinase inhibitor imatinib. Uncommon but potentially targetable GIST-associated mutations covered by this panel include BRAF V600E mutation (mutually exclusive with KIT/PDGFRA mutations) and PIK3CA H1047L. Secondary resistance in GISTs treated with imatinib are often associated with other acquired KIT and PDGFR mutations, such as KIT V654A and T670I; some of which predict for response to other therapies.
  • Specimen Description:
    • Non-decalcified formalin-fixed paraffin-embedded tissues (FFPE): 1 H&E-stained slide and up to 10 uncoated/non-plus sections preferred (10 micron thickness), 2 slides minimum or 1 paraffin block
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with two identifiers; provide pathology report if sending from outside OSU
    • Transport FNA in RPMI media to the lab within 3 days of collection and store 4C until ready to transport
    • Ship glass slides or paraffin block in secure carriers with padding
  • Test Code:  GBTCR
  • Test Name:  T-cell clonality panel
  • CPTCode:  81340, 81342, G0452
  • Test Description: PCR (polymerase chain reaction) is performed for T-cell receptor gamma (TCRG) and beta (TCRB) sequences on genomic DNA extracted from this sample. For TCRG, two different TCRG-VJ PCR amplifications using the BIOMED-2 tubes 1 and 2 are performed and products analyzed by fluorescence capillary electrophoresis, with 3 PCR reactions (VDJ in Tubes A, B and DJ in Tube C) performed for TCRB. A control gene amplification is performed to assess adequacy of DNA. The analytic sensitivity for detection of a clonal T-cell population in a mixed sample is 1-15% depending on the number of reactive T cells present. The clinical sensitivity for detection of a T-cell neoplasm at diagnosis approaches 99%, when both results from both assays are combined. The presence of a clonal T-cell rearrangement by PCR, particularly in skin, blood or BM samples, is not directly equated with the presence of a T-cell lymphoproliferative disorders so correlation with morphology and other laboratory testing is necessary.
    With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
  • Test Code:  TCRB
  • Test Name:  T-cell receptor beta gene rearrangement, PCR
  • CPTCode:  81340, G0452
  • Test Description:  T-cell receptor (TCR) gene rearrangement studies by PCR can be used to assess for the presence of a clonal or oligoclonal proliferation of T-cells. The assay, which can be performed in blood, bone marrow, cytology samples or fresh or fixed tissues, can be used to diagnose T-cell neoplasms or alternatively to support the presence of a reactive/polyclonal T-cell population. This assay uses multiplex PCR of the TCRB locus using the Biomed-2 consensus primers followed by fluorescent fragment analysis by capillary eletrophoresis. This protocol has a sensitivity of at least 90% for detection of a clonal T-cell population at the assay sensitivity limit. The assay can also be used to monitor multiple tissue sites or sequential samples for the presence of systemic or persistent clonal T-cell population. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
    • Formalin-fixed, paraffin embedded tissue (FFPE): 1 block or 1 H&E and 10 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 2 slides minimum) or shaves in centrifuge tube
    • Fine needle aspirate: cells in culture medium such as RPMI
    • Cerebrospinal fluid and cytology fluid: secure screw-cap tube
    • Frozen tissue: snap-frozen in cryogenic vial or OCT block
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
    • Store blood/BM/fluid at 4C until ready to transport
    • Ship blood/BM/fluid on wet ice pack. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding
    • Ship fresh tissue on dry ice after snap-freezing
  • Test Code:  TCRG
  • Test Name:  T-cell receptor gamma gene rearrangement, PCR
  • CPTCode:  81342, GO452
  • Test Description:  T-cell receptor (TCR) gene rearrangement studies by PCR can be used to assess for the presence of a clonal or oligoclonal proliferation of T-cells. The assay, which can be performed in blood, bone marrow, cytology samples or fresh or fixed tissues, can be used to diagnose T-cell neoplasms or alternatively to support the presence of a reactive/polyclonal T-cell population. This assay uses multiplex PCR of the TCRG locus using the Biomed-2 consensus primers followed by fluorescent fragment analysis by capillary eletrophoresis. This protocol has a sensitivity of at least 90% for detection of a clonal T-cell population at the assay sensitivity limit. The assay can also be used to monitor multiple tissue sites or sequential samples for the presence of systemic or persistent clonal T-cell population. With this test code, the ordering clinician is provided with an interpretation by a board-certified molecular pathologist integrating genetic results with review of the histologic material submitted.
  • Specimen Description:
    • FFPE: 1 block or 1 H&E and 8 unstained sections cut onto non-plus/uncoated glass slides (10 micron thickness, 4 slides minimum)
    • Peripheral blood: purple (EDTA); 3 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube or slides with at least two identifiers; provide pathology report if sending from outside OSU
    • Transport fresh samples to the lab within 2 days of draw
  • Test Code:  UBA1
  • Test Name:  UBA1 M41T Mutation Detection
  • CPTCode:  81479
  • Test Description:  Genomic DNA is extracted and subjected to mutation-specific digital droplet polymerase chain reaction (ddPCR) to assess for the M41T hotspot mutation in the UBA1 gene (hg19, NM_003334.3:c.122T>C p.M41T), which is highly associated with the VEXAS syndrome, an adult-onset autoinflammatory disease in males associated with hematologic manifestations particularly myelodysplastic syndrome. Other mutations, including alternative mutations at codon 41, will not be detected by this assay. Target amplification is carried out in independent ddPCR reactions with fluorescently-labeled probes specific for the wild type and mutant sequences. Mutation levels are reported as a percent ratio of mutant to total events at endpoint. This assay can be used to establish a diagnosis and/or monitor known UBA1 p.M41T-mutated cases for therapeutic response and potential relapse. The low reportable range is approximately 0.1% mutation-bearing alleles. Samples with events below the defined cutoff are reported as negative.
  • Specimen Description:
    • Peripheral blood: purple (EDTA) or yellow (ACD); 3-5 ml preferred, 0.5 ml minimum
    • Bone marrow aspirate: purple (EDTA); 2 mL preferred, 0.5 ml minimum
  • Handling:
    • Label tube with two identifiers
    • Transport to the lab within 2 days of draw
    • Store blood at 4C until ready to transport
    • Ship blood on wet ice pack or at RT. DO NOT FREEZE
    • Ship glass slides or paraffin block in secure carriers with padding