Iowa Cancer Mutation Profiling and Interpretation
Label Mnemonic: ECMP
Epic code: LAB8948
Downtime form: A-1a Doctor/Provider Orders - Pathology Molecular
Molecular Pathology
6240 RCP
384-9568
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.
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.
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
CPT Code:
81445