Specimen Collection Manual and Test Catalog

PREFERRED:
FFPE tissue:  Six (6) unstained slides (USS), 10 µm thickness each, in slide folder (protected from light)
Bone marrow: 3 mL lavender-top K2 EDTA tube (part of Bone Marrow Panel Collection – Bone Marrow Aspirate – Two [2] K2 EDTA Tube[s])
Fresh tissue:  Place in liquid medium (e.g., RPMI)
Whole blood:  Two (2) - 6 mL pink-top K2 EDTA tube (minimum of 4 mL in each tube)

ALTERNATE:
Whole blood: Four (4) - 3 mL lavender-top K2 EDTA tubes

FFPE tissue: For non-Geisinger sites, send six (6) USS/10 µm thickness, H&E slide, source of specimen and tumor assessment.  Alternatively, send the FFPE block and additional information. 
Bone marrow: For non-Geisinger sites, collection tube is included in the bone marrow (BM) collection kit.
Whole blood:  Testing is ordered using test Blood Nucleic Acid Extraction, BLDNAE, Lab3520, Test 790019014.

NOTE: Isolated/extracted nucleic acids are acceptable only from CLIA-certified laboratories or a laboratory meeting equivalent requirements as determined by CAP and/or CMS.

Mix well immediately. Do not centrifuge or separate plasma from cells.

FFPE tissue:  Room temperature (18-25°C)
Bone marrow/fresh tissue/whole blood: Refrigerated (2-8°C) 

FFPE Tissue: Room temperature (18-25°C), indefinitely
Bone marrow/fresh tissue/whole blood: Refrigerated (2-8°C), 3 days.  Specimen must be extracted within 3 days.

FFPE blocks containing no tumor (evaluated by pathologist). FFPE tissues that have been decalcified. Insufficient DNA and/or RNA. Wrong collection tube. Improper storage or transport temperature. Stability limits exceeded. Shared or comingled specimens.

Negative (no mutations detected).

For molecular testing, original tube is required.

This custom testing gene panel uses targeted next-generation sequencing (NGS) to detect genomic alterations including: tumor mutation burden (TMB), microsatellite instability (MSI), single base-pair mutations and small insertions/deletions in the coding regions or adjacent intron/exon boundaries, copy number variants (CNV), gene rearrangements (RNA fusion) and exon skipping.            
The following mutations will be reported on the comprehensive solid tumor neoplasm gene panel:

DNA based mutation analysis includes the following genes: ABL1, ABL2, ABRAXAS1, ACVR1, ACVR1B, ACVR2A, ADAMTS12, ADAMTS2 ,AKT1 ,AKT2 ,AKT3, ALK ,AMER1, APC, AR, ARAF, ARHGAP35, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ASXL2, ATM, ATP1A1, ATR, ATRX, AURKA, AURKC, AXIN1, AXIN2, AXL, B2M, BAP1, BARD1, BCL2, BCL2L12, BCL6, BCOR, BCR, BLM, BMP5, BMPR2, BRAF, BRCA1, BRCA2, BRIP1, BTK, CACNA1D, CALR, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274 (PD-L1), CD276, CD79B, CDC73, CDH1, CDH10, CDK12, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CHD4, CHEK1, CHEK2, CIC, CIITA, CREBBP, CSF1R, CSMD3, CTCF, CTLA4, CTNNB1, CUL1, CUL3, CUL4A, CUL4B, CYLD, CYP2C9, CYP2D6, CYSLTR2, DAXX, DDR2, DDX3X, DGCR8, DICER1, DNMT3A, DOCK3, DPYD, DROSHA, DSC1, DSC3, E2F1, EGFR, EIF1AX, ELF3, ENO1, EP300, EPAS1, EPCAM, EPHA2, ERAP1, ERAP2, ERBB2, ERBB3, ERBB4, ERCC2, ERCC4, ERCC5, ERRFI1, ESR1, ETV6, EZH2, FAM135B, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAS, FAT1, FBXW7, FGF7, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FLT4, FOXA1, FOXL2, FOXO1, FUBP1, GATA2, GATA3, GLI1, GNA11, GNA13, GNAQ, GNAS, GPS2, H3F3A, H3F3B, HDAC2, HDAC9, HIF1A, HIST1H2BD, HIST1H3B, HLA-A, HLA-B, HNF1A, HRAS, ID3, IDH1, IDH2, IKBKB, IL6ST, IL7R, INPP4B, IRF4, IRS4, JAK1, JAK2, JAK3, KDM5C, KDM6A, KDR, KEAP1, KIT, KLF4, KLF5, KLHL13, KMT2A, KMT2B, KMT2C, KMT2D, KNSTRN, KRAS, LARP4B, LATS1, LATS2, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAP2K7, MAP3K1, MAP3K4, MAPK1, MAPK8, MAX, MDM4, MECOM, MED12, MEF2B, MEN1, MET, MGA, MITF, MLH1, MLH3, MPL, MRE11, MSH2, MSH3, MSH6, MTAP, MTOR, MTUS2, MUTYH, MYC, MYCN, MYD88, MYOD1, NBN, NCOR1, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NRAS, NSD2, NT5C2, NTRK1, NTRK2, NTRK3, NUP93, PALB2, PARP1, PARP2, PARP3, PARP4, PAX5, PBRM1, PCBP1, PDCD1, PDCD1LG2, PDGFRA, PDGFRB, PDIA3, PGD, PHF6, PIK3C2B, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIM1, PLCG1, PMS1, PMS2, POLD1, POLE, POT1, PPM1D, PPP2R1A, PPP2R2A, PPP6C, PRDM1, PRDM9, PRKACA, PRKAR1A, PSMB10, PSMB8, PSMB9, PTCH1, PTEN, PTPN11, PTPRD, PTPRT, PXDNL, RAC1, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RAF1, RARA, RASA1, RASA2, RB1, RBM10, RECQL4, RET, RGS7, RHEB, RHOA, RICTOR, RIT1, RNASEH2A, RNASEH2B, RNASEH2C, RNF43, ROS1, RPA1, RPL10, RPL22, RPL5, RUNX1, RUNX1T1, SDHA, SDHB, SDHC, SDHD, SETBP1, SETD2, SF3B1, SIX1, SIX2, SLCO1B3, SLX4, SMAD2, SMAD4, SMARCA4, SMARCB1, SMC1A, SMO, SNCAIP, SOCS1, SOS1, SOX2, SOX9, SPEN, SPOP, SRC, SRSF2, STAG2, STAT1, STAT3, STAT5B, STAT6, STK11, SUFU, TAF1, TAP1, TAP2, TBX3, TCF7L2, TERT (promoter and coding sequence), TET2, TGFBR1, TGFBR2, TMEM132D, TNFAIP3, TNFRSF14, TOP1, TP53, TP63, TPMT, TPP2, TRRAP, TSC1, TSC2, TSHR, U2AF1, UGT1A1, USP8, USP9X, VHL, WAS, WT1, XPO1, XRCC2, XRCC3, ZBTB20, ZFHX3, ZMYM3, ZNF217, ZNF429, ZRSR2.                 

Copy number variant analysis includes the following genes: ABCB1, ABL1, ABL2, ABRAXAS1, ACVR1B, ACVR2A, ADAMTS12, ADAMTS2, AKT1, AKT2, AKT3, ALK, AMER1, APC, AR, ARAF, ARHGAP35, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ASXL2, ATM, ATR, ATRX, AURKA, AURKC, AXIN1, AXIN2, AXL, B2M, BAP1, BARD1, BCL2, BCL2L12, BCL6, BCOR, BLM, BMPR2, BRAF, BRCA1, BRCA2, BRIP1, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274, CD276, CDC73, CDH1, CDH10 ,CDK12, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CHD4, CHEK1, CHEK2, CIC, CREBBP, CSMD3, CTCF, CTLA4, CTNND2, CUL3, CUL4A, CUL4B, CYLD, CYP2C9, DAXX, DDR1, DDR2, DDX3X, DICER1, DNMT3A, DOCK3, DPYD, DSC1, DSC3, EGFR, EIF1AX, ELF3, EMSY, ENO1, EP300, EPCAM, EPHA2, ERAP1, ERAP2, ERBB2, ERBB3, ERBB4, ERCC2, ERCC4, ERRFI1, ESR1, ETV6, EZH2, FAM135B, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAT1, FBXW7, FGF19, FGF23, FGF3, FGF4, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FLT4, FOXA1, FUBP1, FYN, GATA2, GATA3, GLI3, GNA13, GNAS, GPS2, H3F3A,, H3F3B, HDAC2, HDAC9, HLA-A, HLA-B, HNF1A, IDH2, IGF1R, IKBKB, IL7R, INPP4B, JAK1, JAK2, JAK3, KDM5C, KDM6A, KDR, KEAP1, KIT, KLF5, KMT2A, KMT2B, KMT2C, KMT2D, KRAS, LARP4B, LATS1, LATS2, MAGOH, MAP2K1, MAP2K4, MAP2K7, MAP3K1, MAP3K4, MAPK1, MAPK8, MAX, MCL1, MDM2, MDM4, MECOM, MEF2B, MEN1, MET, MGA, MITF, MLH1, MLH3, MPL, MRE11, MSH2, MSH3, MSH6, MTAP, MTOR, MUTYH, MYC, MYCL, MYCN, MYD88, NBN, NCOR1, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NRAS, NTRK1, NTRK3, PALB2, PARP1, PARP2, PARP3, PARP4, PBRM1, PCBP1, PDCD1, PDCD1LG2, PDGFRA, PDGFRB, PDIA3, PGD, PHF6, PIK3C2B, PIK3CA, PIK3CB, PIK3R1, PIK3R2, PIM1, PLCG1, PMS1, PMS2, POLD1, POLE, POT1, PPM1D, PPP2R1A, PPP2R2A, PPP6C, PRDM1, PRDM9, PRKACA, PRKAR1A, PTCH1, PTEN, PTPN11, PTPRT, PXDNL, RAC1, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RAF1, RARA, RASA1, RASA2, RB1, RBM10, RECQL4, RET, RHEB, RICTOR, RIT1, RNASEH2A, RNASEH2B, RNF43, ROS1, RPA1, RPS6KB1, RPTOR, RUNX1, SDHA, SDHB, SDHD, SETBP1, SETD2, SF3B1, SLCO1B3, SLX4, SMAD2, SMAD4, SMARCA4, SMARCB1, SMC1A, SMO, SOX9, SPEN, SPOP, SRC, STAG2, STAT3, STAT6, STK11, SUFU, TAP1, TAP2, TBX3, TCF7L2, TERT, TET2, TGFBR2, TNFAIP3, TNFRSF14, TOP1, TP53, TP63, TPMT, TPP2, TSC1, TSC2, U2AF1, USP8, USP9X, VHL, WT1, XPO1, XRCC2, XRCC3, YAP1, YES1, ZFHX3, ZMYM3, ZNF217, ZNF429, ZRSR2.

RNA based fusion analysis includes the following driver genes: AKT1, AKT2, AKT3, ALK, AR, BRAF, BRCA1, CDKN2A, ERBB2, ERBB4, EGFR, ERG, ESR1, ETV1, ETV4, ETV5, FGFR1, FGFR2, FGFR3, MAP3K8, MET, MYB, MTAP, MYBL1, NOTCH1, NOTCH2, NOTCH3, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PIK3CA, PIK3CB, PPARG, PRKACA, PRKACB, RAF1, RARA, RELA, RET, ROS1, RSPO2, RSPO3, STAT6, TERT, TFE3, TFEB, YAP1.

RNA based exon analysis includes the following genes: AR, BRAF, BRCA1, EGFR, MET, NTRK1, RELA.

DNA/RNA Extraction
Next Generation Sequencing

Oncomine Comprehensive Assay Plus, Solid Tumor Gene Panel, Solid Tumor DNA/RNA Gene Panel, NGS, Next-Generation Sequencing

The MyGenVar Comprehensive Solid Tumor Gene Panel targets DNA and RNA variants by high-throughput sequencing. It helps determine diagnostic classification and provide prognostic or therapeutic information for clinical management.

Yi Ding MD, PhD