Iowa Cancer Mutation Profiling and Interpretation
| Label Mnemonic: | ECMP |
| Epic code: | LAB8948 |
| Order form: | Molecular Oncology Requisition |
| Supply order: | Supply Order Form |
| Billing: | Billing Policies |
| CPT code: | 81445 |
Specimen(s):
Formalin Fixed, Paraffin Embedded Tissue Block or 10 unstained 4-8
micron thick sections on non-plus slides and an H&E slide of the
tissue, Blood or Bone Marrow Aspirate
Collection Medium:
|
| Pink top tube 6 mL (K2-EDTA) |
Minimum:
Specimen requires 20% or greater tumor cell content.
Collect 3 mL blood -OR- bone marrow in a pink EDTA top tube. Requires dedicated tube for molecular only.
Collect 3 mL blood -OR- bone marrow in a pink EDTA top tube. Requires dedicated tube for molecular only.
Rejection Criteria:
Specimens fixed in B5 fixative or decalcified will not be accepted.
Tumor specimens containing less than 20% tumor cells may be
unacceptable.
Testing Schedule:
Twice Weekly
Turn Around Time:
10-14 days
Comments:
The Iowa Cancer Mutation Profiling test is a massively parallel next
generation DNA sequencing-based assay that targets cancer-related
genes.
Genes with full exonic coverage included in the Iowa Cancer Mutation Profile for the detection of substitutions, small insertions and deletions (indels): APC, ARID1A, ATM, ATR, ATRX, AURKA, BAP1, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CHEK1, CIC, CREBBP, CRKL, DAXX, DDX3X, DICER, DNMT3A, DOT1L, EED, EPHA3, ERRFI1, FAM175A, FANCA, FANCC, FANCD2, FANCI, FANCL, FBXW7, FLT1, FUBP1, GATA3, IGF2, KMT2D, MAPK3, MCL1, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, NF2, NFKBIA, NOTCH1, NOTCH2, NOTCH3, PALB2, PARP1, PHF6, PIK3R1, PIK3R2, PMS2, POLD1, POLE, PTCH1, PTEN, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RB1, RNF43, SDHA, SDHB, SDHC, SDHD, SETD2, SIRT2, SLIT2, SLX4, SMARCA4, SMARCB1, SMC1A, SMC3, SOX2, STK11, SUFU, TP53, TRAF7, TSC1, TSC2, ZBTB7A
Genes with hotspot coverage* included in the Iowa Cancer Mutation Profile for the detection of substitutions and small indels in specific regions of listed genes: ABL1, ACVR1, AKT1, AKT2, AKT3, ALK, ANKRD26, AR, ARAF, AXL, BIRC3, BLM, BRAF, BTK, CBL, CCND1, CD28, CDK4, CDK6, CHEK2, CSF1R, CSF3R, CTNNB1, DDR2, DHX15, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ESR1, ETV6, ETNK1, EZH2, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FOXL2, GATA1, GATA2, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HIST1H3C, HNF1A, HRAS, IDH1, IDH2, JAK1, JAK2, JAK3, KDR, KLF4, KIT, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAX, MDM4, MED12, MET, MPL, MTOR, MYC, MYCN, MYD88, NFE2L2, NRAS, NTRK1, NTRK2, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PLCG2, PPARG, PPP2R1A, PTPN11, RAC1, RAF1, RET, RHEB, RHOA, ROS1, SETBP1, SF3B1, SMAD4, SMO, SPOP, SRC, SRSF2, STAT3, STAT5B, TERT, TET2, TOP1, TYK2, U2AF1, U2AF2, WT1, XPO1.
*For additional information on gene region coverage, please contact the lab.
Copy Number Variations (CNVs)^ reported for following genes: AAKT1, AKT2, AKT3, ALK, AR, AXL, BRAF, CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN2A, CDKN2B, EGFR, ERBB2, ESR1, FGF19, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, IGF1R, KIT, KRAS, MDM2, MDM4, MET, MYC, MYCL, MYCN, NTRK1, NTRK2, NTRK3, PDGFRA, PDGFRB, PPARG, PIK3CA, PIK3CB, PTEN, RICTOR, SOX2, TERT, TSC1, TSC2.
^Only whole gene copy number changes are tested.
Additional analyses are performed for detection of Microsatellite Instability Status.
Read more....
Genes with full exonic coverage included in the Iowa Cancer Mutation Profile for the detection of substitutions, small insertions and deletions (indels): APC, ARID1A, ATM, ATR, ATRX, AURKA, BAP1, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CHEK1, CIC, CREBBP, CRKL, DAXX, DDX3X, DICER, DNMT3A, DOT1L, EED, EPHA3, ERRFI1, FAM175A, FANCA, FANCC, FANCD2, FANCI, FANCL, FBXW7, FLT1, FUBP1, GATA3, IGF2, KMT2D, MAPK3, MCL1, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, NF2, NFKBIA, NOTCH1, NOTCH2, NOTCH3, PALB2, PARP1, PHF6, PIK3R1, PIK3R2, PMS2, POLD1, POLE, PTCH1, PTEN, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RB1, RNF43, SDHA, SDHB, SDHC, SDHD, SETD2, SIRT2, SLIT2, SLX4, SMARCA4, SMARCB1, SMC1A, SMC3, SOX2, STK11, SUFU, TP53, TRAF7, TSC1, TSC2, ZBTB7A
Genes with hotspot coverage* included in the Iowa Cancer Mutation Profile for the detection of substitutions and small indels in specific regions of listed genes: ABL1, ACVR1, AKT1, AKT2, AKT3, ALK, ANKRD26, AR, ARAF, AXL, BIRC3, BLM, BRAF, BTK, CBL, CCND1, CD28, CDK4, CDK6, CHEK2, CSF1R, CSF3R, CTNNB1, DDR2, DHX15, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ESR1, ETV6, ETNK1, EZH2, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FOXL2, GATA1, GATA2, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HIST1H3C, HNF1A, HRAS, IDH1, IDH2, JAK1, JAK2, JAK3, KDR, KLF4, KIT, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAX, MDM4, MED12, MET, MPL, MTOR, MYC, MYCN, MYD88, NFE2L2, NRAS, NTRK1, NTRK2, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PLCG2, PPARG, PPP2R1A, PTPN11, RAC1, RAF1, RET, RHEB, RHOA, ROS1, SETBP1, SF3B1, SMAD4, SMO, SPOP, SRC, SRSF2, STAT3, STAT5B, TERT, TET2, TOP1, TYK2, U2AF1, U2AF2, WT1, XPO1.
*For additional information on gene region coverage, please contact the lab.
Copy Number Variations (CNVs)^ reported for following genes: AAKT1, AKT2, AKT3, ALK, AR, AXL, BRAF, CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN2A, CDKN2B, EGFR, ERBB2, ESR1, FGF19, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, IGF1R, KIT, KRAS, MDM2, MDM4, MET, MYC, MYCL, MYCN, NTRK1, NTRK2, NTRK3, PDGFRA, PDGFRB, PPARG, PIK3CA, PIK3CB, PTEN, RICTOR, SOX2, TERT, TSC1, TSC2.
^Only whole gene copy number changes are tested.
Additional analyses are performed for detection of Microsatellite Instability Status.
Read more....
Test Limitations:
Testing is not currently validated for mutation load analysis. Large
genomic rearrangements (LRG) such as inversions,
deletions/duplications spanning several exons, and gene fusions are
not detected by this panel. Please contact the laboratory director
for questions. Testing is not validated for use on plasma for
cell-free tumor DNA mutation testing.
Methodology:
Massively parallel Next Generation DNA sequencing by synthesis,
Illumina technology
Instructions:
Specimen requires 20% or greater tumor cell content. Submit formalin
fixed paraffin embedded tissue and ten unstained 4 micron-thick
sections on non-plus slides.
Testing requires dedicated collection tube.
Testing requires dedicated collection tube.
Sample Storage:
Refrigerate.
Transport Instructions:
Place specimen into zip-lock type bag, seal bag.
Recommend early AM overnight shipping or equivalent if not on courier service.
Ship refrigerated.
Place requisition into outside pocket of bag.
Protect phlebotomy tube from excessive heat and ship in cooled container during summer months.
Recommend early AM overnight shipping or equivalent if not on courier service.
Ship refrigerated.
Place requisition into outside pocket of bag.
Protect phlebotomy tube from excessive heat and ship in cooled container during summer months.