Beginning Tuesday, June 23, 2020.
Expanded cancer molecular biomarker testing will be available from the Molecular Pathology Laboratory for identification of DNA variations in up to 214 genes and include evaluation for copy number alterations in a subset of those genes. The EPIC order for the DNA analysis is the Iowa Cancer Mutation Profile with interpretation (LAB8948). This change will impact testing by expanding the gene list included in the orders for both the Iowa Cancer Mutation and RNA Fusion Profile (LAB8955) and the Comprehensive Lung Panel (LAB8580). These comprehensive panels should be used for detecting mutations in cancer to help in determining therapy options and combine the expanded panel of DNA variations with RNA fusion detection using next generation sequencing.

Key features:

• Substitutions and small insertion/deletions are detected in these genes: ABL1, ACVR1, AKT1, AKT2, AKT3, ALK, ANKRD26, APC, AR, ARAF, ARID1A, ATM, ATR, ATRX, AURKA, AXL, BAP1, BARD1, BIRC3, BLM, BRAF, BRCA1, BRCA2, BRIP1, BTK, CBL, CCND1, CCND2, CCND3, CCNE1, CD28, CDH1, CDK12, CDK2, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CHEK1, CHEK2, CIC, CREBBP, CRKL, CSF1R, CSF3R, CTNNB1, DAXX, DDR2, DDX3X, DHX15, DICER, DNMT3A, DOT1L, EED, EGFR, EPHA3, ERBB2, ERBB3, ERBB4, ERCC2, ERRFI1, ESR1, ETNK1, ETV6, EZH2, FAM175A, FANCA, FANCC, FANCD2, FANCI, FANCL, FBXW7, FGF19, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FOXL2, FUBP1, GATA1, GATA2, GATA3, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HIST1H3C, HNF1A, HRAS, IDH1, IDH2, IGF1R, IGF2, JAK1, JAK2, JAK3, KDR, KIT, KLR4, KMT2D, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAPK3, MAX, MCL1, MDM2, MDM4, MED12, MET, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MYC, MYCL, MYCN, MYD88, NBN, NF1, NF2, NFE2L2, NFKBIA, NOTCH1, NOTCH2, NOTCH3, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PARP1, PDGFRA, PDGFRB, PHF6, PIK3CA, PIK3CB, PIK3R1, PIK3R2, PLCG2, PMS2, POLD1, POLE, PPARG, PPP2R1A, PTCH1, PTEN, PTPN11, RAC1, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAF1, RB1, RET, RHEB, RHOA, RICTOR, RNF43, ROS1, SDHA, SDHB, SDHC, SDHD, SETBP1, SETD2, SF3B1, SF3B1, SIRT2, SLIT2, SLX4, SMAD4, SMARCA4, SMARCB1, SMC1A, SMC3, SMO, SOX2, SPOP, SRC, SRSF2, STAT3, STAT5B, STK11, SUFU, TERT, TET2, TOP1, TP53, TRAF7, TSC1, TSC2, TYK2, U2AF1, U2AF2, WT1, XPO1, and ZBTB7A.


• Copy number alterations (gains or losses) are detected in these genes: AKT1, 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, PIK3CA, PIK3CB, PPARG, PTEN, RICTOR, SOX2, TERT, TSC1, and TSC2.


• Fusion transcripts are detected and reported involving rearrangements of these genes: AKT1, ALK, AXL, CCND1, EGFR, FGFR1, FGFR2, FGFR3, MET, NRG1, NTRK1, NTRK2, NTRK3, PPARG, RAF1, RET, and ROS1.


• FDA approved drugs may be available in association with particular mutation profiles for many of the gene targets included in this testing, dependent on tumor type and treatment strategy.

EPIC Test Name and Order Code:
LAB8948 – IOWA CANCER MUTATION PROFILE WITH INTERPRETATION
LAB8955 – IOWA CANCER MUTATION AND RNA FUSION PROFILE WITH INTERPRETATION
LAB8580 – COMPREHENSIVE LUNG PANEL ORDER

Specimen types: Formalin-fixed, paraffin-embedded tissue or cytology fine needle aspirate smears stained or unstained; 5000 tumor cells minimum requirement, or ≥20% tumor cells from tissue sections, bone marrow aspirates collected in EDTA, minimum 3 mL, blood collected in EDTA, minimum 3 mL.

Method: DNA and RNA based next-generation sequencing. Testing is batched. Turnaround time is 10-14 days.

Results Reported: RNA Fusion or DNA variants detected.

Limitations: Testing is not currently validated for microsatellite instability (MSI) or mutation load analyses. Please contact the laboratory director for questions. Testing is not validated for use on plasma for cell-free tumor DNA mutation testing.

Questions concerning testing can be directed to Deqin Ma, MD, PhD (384-5700), Anthony Snow, MD (353-8986), Sharath Bhagavathi MD, (678-8197) or Aaron Bossler, MD, PhD, director (384-9566).