Molecular Genetics Tests

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Methodology Test Name Test Description Print View
Molecular ABL1 Kinase Domain Mutation Analysis RT-PCR and sequencing of the BCR-ABL1 fusion transcript for qualitative detection of mutations associated with imatinib resistance View
Molecular AML Reflex Panel Routine cytogenetics with automatic addition of the NeoTYPE™ AML Prognostic Profile when cytogenetics results show intermediate risk including normal cytogenetics, +6, +8, -Y, or del(12p). The AML Prognostic Profile includes concurrent analysis of select exons of the following genes: CEBPA, DNMT3A, FLT3, IDH1, IDH2, NPM1, RUNX1, and WT1. View
Molecular B-Cell & T-Cell Gene Rearrangement PCR for detection of clonal IgH, Ig kappa, and T cell receptor gene gamma gene rearragements. View
Molecular B-Cell Gene Rearrangement Detection of clonal IgH and Ig kappa gene rearragements by PCR of IgH framework regions 1, 2, 3 and joining regions, Ig kappa FR3 and Jk regions. View
Molecular BCL1 Translocation, t(11;14) Real-time PCR for quantitative detection of t(11;14) BCL1/IgH rearrangements. Analytical sensitivity is approximately 1 tumor cell in 1000 normal cells. Positive results are reported as a ratio between quantities of (11;14) DNA and a normal control gene. This translocation is also known as CCND1/IgH or BCL1/JH. View
Molecular BCL2 Translocation, t(14;18) PCR and fragment analysis for quantitative detection of IGH-BCL2 translocations associated with 70-80% of follicular lymphoma and approximately 20% of diffuse large B-cell lymphoma. Translocations involving the major (MBR), minor (MCR), and 3' MBR sub-cluster regions of BCL2 are analyzed. Positive results quantify the ratio of mutant BCL2 to internal control DNA. Testing may be performed on plasma to increase sensitivity. View
Molecular BCR-ABL1 Translocation, t(9;22) – quantitative Real-time RT-PCR for detection of t(9;22) BCR-ABL1 fusion transcripts that result in p190 (E1) or p210 (E13, E14) fusion proteins. Analytical sensitivity is 1 tumor cell in 100,000 normal cells. Log reduction score is reported. View
Molecular BRAF Mutation Analysis

Bi-directional sequencing of exon 15 of the BRAF gene, which includes qualitative detection of V600 mutations E, K, D, and others, plus other significant exon 15 mutations. For solid tumors, tumor enrichment is performed before extraction.

See more details about BRAF Mutation Analysis in Melanoma.

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Molecular CARD11 Mutation Analysis Bi-directional sequencing of exons 5 and 6 of the CARD11 gene. Testing is available separately or as part of the NeoTYPE™ Lymphoma Profile. View
Molecular CD79B Mutation Analysis Bi-directional sequencing of exon 5 of the CD79B gene which includes detection of the common Y196 mutations. Testing is available separately or as part of the NeoTYPE™ Lymphoma Profile. View
Molecular 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. This test can be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular Chimerism / DNA Fingerprinting Analysis STR (short tandem repeat) analysis by PCR and capillary electrophoresis (fragment analysis) is used to define sample identity and to identify mixtures of two or more genotypes within a single sample. Fifteen autosomal markers and one gender-based marker are analyzed. This test is commonly used to assess engraftment after allogeneic stem cell transplant. Stem cell engraftment results are reported as full, partial, or split chimerism along with percentage of donor chimerism within the recipient sample. This assay detects minor cell populations down to 2-5% chimerism. View
Molecular c-KIT Mutation Analysis Bi-directional sequencing of KIT exons 8, 9, 11, 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. View
Molecular CLL Molecular Prognostic Panel Concurrent analysis of critical regions of the IgVH and SF3B1 genes by RT-PCR and bi-directional sequencing, and NOTCH1 by sequencing and fragment analysis. In IgVH analysis, the mutated VH gene family is identified in positive reports (which have >3% deviation from normal sequence). IgVH mutation may not be detectable in specimens containing <10% clonal B-cells. SF3B1 analysis covers exons 14-17, where at least 90% of the reported mutations are detected. This test detects SF3B1 mutations present at 10-15% or more in a wild-type background. View
Molecular DNMT3A Mutation Analysis Bi-directional sequencing of exon 26, a mutation hotspot region containing R882 and other mutations. In hematological disease, testing may be performed on plamsa to increase sensitivity. For solid tumors, tumor enrichment is performed before extraction.  This test can be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular EGFR Mutation Analysis Bi-directional sequencing of exons 18-21 of the EGFR gene for detection of EGFR-activating mutations and TKI resistance mutations in these exons. Tumor enrichment is performed before extraction.  View
Molecular ETV6-RUNX1 (TEL-AML1) Translocation, t(12;21) Real-time RT-PCR for quantitative detection of the t(12;21) ETV6-RUNX1 fusion transcript (formerly called TEL-AML1). Analytical sensitivity is 1 tumor cell in 100,000 normal cells. Positive results are reported as a percentage ratio between quantities of transcript of t(12;21) and the sum of t(12;21) plus a control gene. View
Molecular FLT3 Mutation Analysis Detection of internal tandem duplication and exon 20 tyrosine kinase domain (TKD) mutations using bidirectional 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. This test may be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular HRAS Mutation Analysis Bi-directional sequencing of HRAS exons 1 and 2 which includes sites of common activating mutations in codons 12, 13, and 61. View
Molecular IDH1 & IDH2 Mutation Analysis Bi-directional sequencing of the exon 4 mutation hotspot regions in both the IDH1 and IHD2 genes. IDH1 and IDH2 are analyzed concurrently. In hematological disease, testing may be performed on plamsa to increase sensitivity. For solid tumors, tumor enrichment is performed before extraction.  This test can be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular IgVH Mutation 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. View
Molecular inv(16), CBFB-MYH11 Translocation Real-time RT-PCR for quantitative detection of the inv(16) CBFB-MYH11 fusion transcript. Positive results are reported as ratio of the amount of fusion transcript with the amount of transcript from a normal control gene. This assay identifies type A fusions, which account for >90%. Analytical sensitivity is 1 tumor cell in 100,000 normal cells. View
Molecular JAK2 Exon 12-14 Mutation Analysis 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, by reflex after negative V617F testing, or as part of the MPN Reflex Panel. View
Molecular JAK2 V617F Mutation Analysis Detects the V617F mutation. The rare mutation V617I is also detected. Testing is performed on plasma for increased sensitivity whenever possible. V617F testing may be ordered separately, concurrently with full exon 12-14 sequencing, with reflex to exon 12-14 sequencing, or as part of the MPN Reflex Panel. View
Molecular KIT / PDGFRa Molecular Reflex Panel (GIST) This is a two-step reflex panel beginning with bi-directional sequencing of KIT exons 8, 9, 11, and 17. If negative, testing proceeds with bi-directional sequencing of exons 12 and 18 of the PDGFRA gene. Tumor enrichment is performed before extraction. Tests may also be ordered separately. View
Molecular KRAS & BRAF Mutation Analysis Concurrent analysis of KRAS and BRAF gene regions including KRAS exons 1 and 2 (with mutation detection in codons 12, 13, and 61) and BRAF exon 15 to detect V600 mutations and more. Tumor enrichment is performed before extraction.

This test is part of NeoGenomics’ comprehensive colorectal cancer testing.

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Molecular KRAS Mutation Analysis Bi-directional sequencing of exons 1 and 2 of the KRAS gene, which includes detection of mutations in codons 12, 13, and 61.  Tumor enrichment is performed before extraction. View
Molecular Microsatellite Instability Analysis (MSI) PCR and fragment analysis of paired normal and tumor tissue to determine microsatellite instability (MSI) at the standard five NCI-recommended loci. Positive results are reported as MSI-high (at least two markers are unstable) or MSI-low (one marker is unstable).

This test is part of NeoGenomics’ comprehensive colorectal cancer testing.

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Molecular 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 Reflex Panel. View
Molecular MPN Reflex Panel Sequential testing panel including analysis of JAK2 V617F, JAK2 Exon 12-14, and MPL exon 10. Testing proceeds by reflex through the three-step panel until a mutation is identified, when the result is considered informative and no further testing is performed. Testing is performed on plasma for increased sensitivity whenever possible. Tests may also be ordered separately. View
Molecular MYD88 Mutation Analysis Bi-directional sequencing of exon 5 of the MYD88 gene which includes detection of the common L265P mutation. Testing is available separately or as part of the NeoTYPE™ Lymphoma Profile. View
Molecular NeoARRAY™ SNP/Cytogenetic Profile

The NeoARRAY SNP/Cytogenetic Profile is available for hematological and solid tumor indications. With the best genome-wide coverage available, this test employs an enhanced SNP microarray with over 2.6 million SNP and non-polymorphic markers for detection of copy number variants (deletions, duplications, and amplifications) and loss of heterozygosity or uniparental disomy (LOH or UPD) in any chromosome. Sensitivity and specificity for detection of copy number variants >400 kb is >99%. Testing may not reliably detect abnormalities present in less than 20% of the cells tested. Balanced rearrangements, including translocations and inversions, are not detectable by this method.

Clients may request NeoARRAY on POC as the sole test, or they may order POC cytogenetics with reflex to NeoARRAY if the POC culture fails or if cytogenetic results are normal. For reflex orders, if there is no cell attachment or growth after 14 days in culture, a cytogenetics failure report will be issued and NeoARRAY will be performed. If there is limited cell attachment after 14 days in culture, NeoGenomics will contact the client for instructions. When array testing is not performed, a fee will be charged for DNA extraction (which is performed upon specimen receipt).

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Molecular NOTCH1 Mutation Analysis Bi-directional sequencing of exons 26, 27, and 34 is performed for detection of sequence variant mutations.  Fragment analysis is also performed for enhanced detection of insertion/deletion mutations. Testing can be performed on plasma when adequate leukemic cells are not available. This test may be ordered separately, as part of the NeoTYPE™ CLL Prognostic Profile, or as part of the CLL Molecular Prognostic Panel. View
Molecular 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. This test may be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular NRAS Mutation Analysis Bi-directional sequencing of NRAS exons 1 and 2 which includes sites of common activating mutations in codons 12, 13, and 61. View
Molecular PDGFRa Mutation Analysis Bi-directional sequencing of exons 12 and 18 of the PDGFRA (platelet-derived growth factor alpha) gene. These exons are mutation hotspots that account for the majority of PDGFRA mutations detected in gastrointestinal stromal tumors (GISTs) including the common TKI-resistance mutation D842V. Solid tumor enrichment is performed before extraction. This test may be ordered separately or as part of the KIT/PDGFRa Molecular Reflex Panel (GIST). View
Molecular PIK3CA Mutation Analysis Bi-directional sequencing of PIK3CA exons 1, 9, and 20 which are the most commonly-mutated regions of the gene. View
Molecular PML-RARA Translocation, t(15;17) 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. View
Molecular PTEN Mutation Analysis Bi-directional sequencing of all exons (1-9) of the PTEN gene. For solid tumors, enrichment is performed before extraction. This assay does not detect large deletions. View
Molecular RUNX1 Mutation Analysis Bi-directional sequencing of exons 4-10 of the RUNX1 gene. This test may be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View
Molecular RUNX1-RUNX1T1 (AML1-ETO) Translocation, t(8;21) Real-time RT-PCR for quantitative detection of the t(8;21) RUNX1-RUNX1T1 fusion transcript (formerly called AML1-ETO). Analytical sensitivity is 1 tumor cell in 100,000 normal cells. Positive results are reported as a ratio between quantities of (8;21) transcript and a normal control gene. View
Molecular SF3B1 Mutation Analysis RT-PCR and bi-directional sequencing of exons 14-17 of the SF3B1 gene. More than 90% of reported mutations are detected in these exons. This test detects mutations present at 10-15% or more in a wild-type background. Test may be ordered separately or as part of the NeoTYPE™ CLL Profile. View
Molecular T-Cell Gene Rearrangement Detection of clonal T-cell receptor gamma gene rearrangements by PCR of variable and joining regions. View
Molecular TP53 Mutation Analysis Bi-directional sequencing of TP53 exons 4-9. View
Molecular TPMT Genotyping This PCR-based allele discrimination assay is performed on genomic DNA and detects the four most common abnormal alleles of the thiopurine methyltransferase (TPMT) gene, which are TPMT*2 (238G>C), TPMT*3A (460G>A + 719A>G), TPMT*3B (460G>A), and TPMT*3C (719A>G). The status of the abnormal alleles tested is reported as not detected, heterozygous, or homozygous. The TPMT enzyme activity associated with the genotype is reported as normal, intermediate, or low or no activity. The abnormal alleles tested in this assay account for >95% cases of low or undetectable TPMT enzyme activity. View
Molecular UGT1A1 Genotyping Lengths of the TA repeat polymorphism in the promoter region of the UTG1A1 gene are determined by fragment analysis using capillary electrophoresis. The alleles detected include the common normal allele *1 (with 6 TA repeats) and the common abnormal allele *28 (7 repeats). The patient’s genotype is reported along with the associated high, intermediate, or low risk for toxicity from the drug irinotecan (Camptosar®). View
Molecular WT1 Mutation Analysis Bi-directional sequencing of exons 7 and 9 is performed for detection of sequence variant mutations.  Fragment analysis of exon 7 is also performed for enhanced detection of heterozygous insertion/deletion mutations. The SNP genotype at rs16754 is reported.  Testing is performed on plasma for increased sensitivity whenever possible.   This test may be ordered separately or as part of the NeoTYPE™ AML Prognostic Profile. View