Test Name

Pan-Cancer Solid Tumor Panel

Test Number

LAB9055

CPT Codes

81455

Test Includes

The Pan-Cancer Solid Tumor Panel is a custom target enrichment and sequencing platform for detection of somatic substitutions, small indels (insertions and deletions <1000 base-pairs in length), tumor mutation burden (TMB) and microsatellite instability (MSI) in tumor samples by next-generation sequencing (NGS) technology. The Pan-Cancer Panel (PCP) involves hybridization capture and deep sequencing of all protein-coding exons of 1080 cancer-associated genes as well as clinically relevant regions near those genes.

Gene list in the panel:
In bold* 82 cancer predisposition genes that we report incidental pathogenic and likely pathogenic variants detected in the submitted normal comparator (blood/saliva).
ABCB1 CCT6B EEF2 GAB2 IL2RG MIB1 PHF6 RNF111 TAF1
ABL1 CD19 EGFL7 GABRA6 IL3 MIDEAS PHOX2B* RNF139 TAL1
ABL2 CD22 EGFR* GADD45B IL4R MIR142 PICALM RNF43 TAP1
ABRAXAS1 CD274 EGLN1 GALNT12 IL6ST MITF* PIGA ROBO1 TAP2
ACTA2 CD276 EGR1 GATA1 IL7R MKI67 PIK3C2B ROS1 TAPBP
ACTB CD27 EGR2 GATA2* ING1 MKNK1 PIK3C2G RPA1 TBL1XR1
ACVR1B CD28 EGR3 GATA3 INHA MLH1* PIK3C3 RPL10 TBX3
ACVR1 CD33 EIF1AX GATA4 INHBA MLH3 PIK3CA RPL22 TCF12
ACVR2A CD36 EIF3E GATA6 INO80 MLLT10 PIK3CB RPL5 TCF3
ADGRA2 CD40 EIF4A2 GEM INPP4A MLLT1 PIK3CD RPS15 TCF7L2
ADGRB1 CD58 EIF4E GEN1 INPP4B MLLT3 PIK3CG RPS20 TCL1A
AGO1 CD70 ELANE GID4 INPP5D MPL PIK3R1 RPS3A TCL1B
AGO2 CD74 ELF3 GLI1 INPPL1 MR1 PIK3R2 RPS6KA3 TDG
AJUBA CD79A ELOC GLI2 INSR MRE11 PIK3R3 RPS6KA4 TEK
AKT1 CD79B ELP2 GLIS2 IRF1 MRTFA PIM1 RPS6KB1 TENT5C
AKT2 CD80 EML4 GNA11 IRF2 MRTFB PKN1 RPS6KB2 TENT5D
AKT3 CDC73* EMSY GNA12 IRF4 MSH2* PLAG1 RPTOR TERC*
ALB CDH10 ENG GNA13 IRF6 MSH3* PLCB4 RRAGC TERF1
ALK* CDH1* EP300 GNAI2 IRF8 MSH6* PLCG1 RRAS2 TERT*
ALOX12B CDH4 EPAS1 GNAQ IRS1 MSI2 PLCG2 RRAS TET1
AMER1 CDK12 EPC1 GNAS IRS2 MSMB PLK2 RSPO2 TET2
ANKRD11 CDK4* EPCAM* GNB1 IRS4 MST1 PLXNB2 RSPO3 TET3
ANKRD26 CDK6 EPHA2 GPC3* ITGAM MST1R PMAIP1 RTEL1 TFE3
APC* CDK8 EPHA3 GPS2 ITK MT1JP PML RUNX1* TFEB
APH1A CDKN1A EPHA5 GREM1* ITPKB MTAP PMS1 RUNX1T1 TFG
APLNR CDKN1B* EPHA7 GRIN2A JAK1 MTOR PMS2* RXRA TGFBR1
APOB CDKN1C* EPHB1 GRIN2D JAK2 MUC17 PNRC1 RYBP TGFBR2
ARAF CDKN2A* EPHB4 GRM3 JAK3 MUC6 POLD1* S1PR2 TGIF1
AR CDKN2B EPOR GSK3B JARID2 MUSK POLE* SALL4 THADA
ARFRP1 CDKN2C ERBB2 GTF2I JAZF1 MUTYH* POLH SAMD9 THRAP3
ARHGAP26 CEBPA* ERBB3 GTSE1 JUN MYB POLQ SAMD9L TIPARP
ARHGAP35 CENPA ERBB4 H1-2 KANSL1 MYBL1 POLR2A SAMHD1 TLL2
ARHGEF10 CFTR ERCC1 H1-3 KAT6A MYC POLRMT SBDS TLR4
ARHGEF12 CHD2 ERCC2 H1-4 KAT6B MYCL POT1* SCAF4 TLR9
ARID1A CHD3 ERCC3 H19 KBTBD4 MYCN POU2F2 SCG5 TLX3
ARID1B CHD4 ERCC4 H2AC11 KDM2B MYD88 PPARG SDC4 TMEM127*
ARID2 CHD7 ERCC5 H2AC16 KDM4C MYH11 PPM1D SDHA* TMEM30A
ARID3A CHD8 ERCC6 H2AC17 KDM5A MYH9 PPP2R1A SDHAF2* TMPRSS2
ARID4B CHEK1 ERF H2AC6 KDM5C MYO18A PPP2R2A SDHB* TMSB4X
ARID5B CHEK2* ERG H2BC11 KDM6A MYOD1 PPP4R2 SDHC* TMSB4XP8
ASMTL CIC ERRFI1 H2BC12 KDM6B NADK PPP6C SDHD* TNFAIP3
ASXL1 CIITA ESR1 H2BC17 KDR NBN* PRDM14 SERP2 TNFRSF11A
ASXL2 CILK1 ESRRA H2BC4 KEAP1 NCOA2 PRDM1 SERPINA1 TNFRSF14
ATF7IP CKS1B ETNK1 H2BC5 KEL NCOA3 PREX2 SERPINB3 TNFRSF17
ATM* CLIP1 ETS1 H3-3A KIF1A NCOR1 PRF1 SERPINB4 TNFRSF18
ATP6AP1 CMTR2 ETV1 H3-3B KIF1B NCOR2 PRKACA SESN2 TNFRSF4
ATP6V1B2 CNBD1 ETV4 H3-4 KIF5B NCSTN PRKAR1A* SESN3 TNFRSF9
ATR CNOT9 ETV5 H3-5 KIR3DL1 NECTIN4 PRKCA SETBP1 TOP1
ATRX COL1A1 ETV6 H3C10 KIT* NEGR1 PRKCB SETD1B TOP2A
ATXN3 COL5A1 EWSR1 H3C11 KLF2 NEIL2 PRKCD SETD2 TP53BP1
ATXN7 COL7A1 EXO1 H3C12 KLF3 NF1* PRKCI SETDB1 TP53*
AURKA COP1 EXOSC6 H3C13 KLF4 NF2* PRKD1 SETDB2 TP63
AURKB CPS1 EXT1 H3C14 KLF5 NFATC2 PRKDC SF1 TPMT
AXIN1 CRBN EXT2 H3C15 KLHL6 NFE2 PRKN SF3A1 TPTE2
AXIN2* CREB3L3 EZH1 H3C1 KLLN NFE2L2 PRPF40B SF3B1 TRAF2
AXL CREBBP EZH2 H3C2 KMT2A NFKBIA PRPF8 SGK1 TRAF3
B2M CRKL EZHIP H3C3 KMT2B NFKBIE PRPS1 SH2B3 TRAF5
BABAM1 CRLF1 EZR H3C4 KMT2C NIPBL PRSS1 SH2D1A TRAF7
BAP1* CRLF2 FAF1 H3C6 KMT2D NKX2-1 PRSS8 SHH TRIP13
BARD1* CRTC1 FAM135B H3C7 KNSTRN NKX3-1 PSIP1 SHOC2 TRPA1
BBC3 CSDE1 FANCA H3C8 KRAS NOD1 PSMB5 SHQ1 TSC1*
BCL10 CSF1R FANCB HAVCR2 KRT222 NOTCH1 PTCH1* SIN3A TSC2*
BCL11B CSF3R FANCC HDAC1 LAG3 NOTCH2 PTCH2 SIRPA TSHR
BCL2 CSNK1A1 FANCD2 HDAC2 LATS1 NOTCH3 PTEN* SLC26A3 TSLP
BCL2L11 CTC1 FANCE HDAC4 LATS2 NOTCH4 PTK2B SLC34A2 TUSC3
BCL2L12 CTCF FANCF HDAC7 LCK NPM1 PTK2 SLFN11 TXNIP
BCL2L1 CTDNEP1 FANCG HDAC9 LDB1 NPRL2 PTMA SLIT2 TYK2
BCL2L2 CTLA4 FANCI HGF LEF1 NR4A3 PTP4A1 SLX4 TYRO3
BCL6 CTNNA1* FANCL HIF1A LEMD2 NRAS PTPDC1 SMAD2 U2AF1
BCL7A CTNNB1 FANCM HLA-A LIFR NRG1 PTPN11 SMAD3 U2AF2
BCL9 CTNND1 FAS HLA-B LMO1 NSD1 PTPN13 SMAD4* UBE2T
BCLAF1 CTR9 FASLG HLA-C LRP1B NSD2 PTPN14 SMARCA1 UBR5
BCOR CUL1 FAT1 HLA-DMA LRP5 NSD3 PTPN1 SMARCA2 UNCX
BCORL1 CUL3 FBXO11 HLA-DMB LRP6 NT5C2 PTPN2 SMARCA4* USP6
BCR CUL4A FBXO31 HLA-DOA LRRK2 NT5E PTPN6 SMARCAL1 USP8
BIRC3 CUL4B FBXW7 HLA-DOB LTB NTHL1* PTPRC SMARCB1* USP9X
BLM* CUX1 FCGR2A HLA-DPA1 LTK NTRK1 PTPRD SMARCD1 VAV1
BMPR1A* CXCR4 FCGR3A HLA-DPB1 LUC7L2 NTRK2 PTPRO SMARCE1* VEGFA
BRAF CYLD FGF10 HLA-DPB2 LYN NTRK3 PTPRS SMC1A VHL*
BRCA1* CYP17A1 FGF12 HLA-DQA1 LZTR1 NUDT15 PTPRT SMC3 VTCN1
BRCA2* CYP19A1 FGF14 HLA-DQA2 MACF1 NUF2 QKI SMO WAS
BRCC3 CYP2D6 FGF19 HLA-DQB1 MAD2L2 NUMBL RAB35 SMYD3 WDR90
BRD3 CYSLTR2 FGF1 HLA-DQB2 MAFB NUP133 RABEP1 SNCAIP WEE1
BRD4 DACH1 FGF23 HLA-DRA MAF NUP214 RAC1 SOCS1 WIF1
BRD7 DAXX FGF2 HLA-DRB1 MAGED1 NUP93 RAC2 SOCS2 WNK2
BRINP3 DAZAP1 FGF3 HLA-DRB5 MAGI2 NUP98 RAD21 SOCS3 WRN*
BRIP1* DCSTAMP FGF4 HLA-DRB6 MALT1 NUTM1 RAD50* SOS1 WT1*
BRSK1 DCUN1D1 FGF5 HLA-E MAML2 P2RY8 RAD51B SOX10 WWTR1
BTG1 DDB2 FGF6 HLA-F MAMLD1 PABPC1 RAD51C* SOX17 XBP1
BTG2 DDR1 FGF7 HLA-G MAP2K1 PAG1 RAD51D* SOX2 XIAP
BTK DDR2 FGF8 HLTF MAP2K2 PAK1 RAD51 SOX9 XPA
BTLA DDX3X FGF9 HMGA2 MAP2K4 PAK3 RAD52 SP140 XPC
BUB1B DDX41 FGFR1 HNF1A MAP3K13 PAK5 RAD54B SPEN XPO1
C3orf70 DEK FGFR2 HNRNPK MAP3K14 PALB2* RAD54L SPOP XRCC1
C8orf34 DHX9 FGFR3 HOXA11 MAP3K1 PARP1 RAF1 SPRED1 XRCC2
CACNA1A DIAPH2 FGFR4 HOXB13* MAP3K4 PARP2 RANBP17 SPRTN XRCC3
CACNA1D DICER1* FGR HRAS* MAP3K6 PARP3 RANBP2 SPTA1 YAP1
CAD DIS3 FH* HSD3B1 MAP3K7 PARP4 RARA SPTAN1 YEATS4
CALR DIS3L2* FHIT HSP90AA1 MAPK1 PARPBP RASA1 SRC YES1
CAMTA1 DKC1 FLCN* HSP90AB1 MAPK3 PASK RASGEF1A SRP72 YWHAE
CARD11 DKK4 FLI1 HUWE1 MAST1 PAX3 RB1* SRSF2 YY1AP1
CARM1 DMD FLNA ICOS MAST2 PAX5 RBM10 SS18 ZBTB20
CASP8 DNAJB1 FLT1 ICOSLG MAX* PAX7 RBM15 SSBP2 ZBTB2
CBFA2T3 DNM2 FLT3 ID3 MBD4 PAX8 RBM38 STAG1 ZBTB7B
CBFB DNMT1 FLT4 IDH1 MC1R PAXIP1 RECQL4* STAG2 ZC3H12A
CBLB DNMT3A FLYWCH1 IDH2 MCL1 PBRM1 RECQL STAT1 ZCCHC12
CBLC DNMT3B FOXA1 IDO1 MDC1 PCBP1 RELA STAT2 ZFHX3
CBL DOCK8 FOXA2 IFNAR1 MDM2 PC REL STAT3 ZFP36L1
CBWD3 DOT1L FOXD4L1 IFNGR1 MDM4 PCLO RELN STAT4 ZFP36L2
CCDC6 DROSHA FOXL2 IFNGR2 MEAF6 PDCD11 REST STAT5A ZMYM2
CCL2 DTX1 FOXO1 IGF1 MECOM PDCD1 RET* STAT5B ZMYM3
CCN6 DUSP22 FOXO3 IGF1R MED12 PDCD1LG2 RFC1 STAT6 ZNF133
CCNB3 DUSP2 FOXP1 IGF2 MEF2B PDGFB RGPD3 STK11* ZNF217
CCND1 DUSP4 FOXQ1 IKBKE MEF2C PDGFRA* RHEB STK19 ZNF24
CCND2 DUSP9 FRK IKZF1 MEF2D PDGFRB RHOA STK40 ZNF384
CCND3 E2F3 FRS2 IKZF2 MEN1* PDK1 RHOB SUFU* ZNF703
CCNE1 EBF1 FUBP1 IKZF3 MERTK PDPK1 RHPN2 SUSD2 ZNF750
CCR2 ECT2L FUS IL10 MET* PDS5B RICTOR SUZ12 ZNRF3
CCR4 EED FYN IL2 MGA PGBD5 RINT1 SYK ZRANB3
CCR5 EEF1A1 GAB1 IL2RB MGMT PGR RIT1 TAF15 ZRSR2

Performing Laboratory / Facility

UCLA Molecular Diagnostics Laboratories (MDL)

Performing Section

Molecular Pathology

Availability

Monday through Friday, 0700-1700

Turnaround Time

14 days from receipt of required FFPE specimen AND matched normal specimen in performing lab

Methodology

Genomic DNA is extracted from FFPE tumor tissue and patient-matched blood/saliva specimen as a normal comparator. Using kits from Twist Bioscience, the DNA undergoes enzymatic fragmentation, library preparation, and target enrichment. The resulting libraries are pooled and sequenced to high uniform depth (600x for tumors, 200x for normals) using the Illumina NovaSeq 6000 sequencer. The sequencing data is processed by the UCLA Molecular Diagnostic Labs’ Analysis Pipeline which uses Illumina Dragen 4.0.3 for primary and secondary analyses against reference genome GRCh38 (hg38), and GoldenHelix VarSeq 2.3.0 for tertiary analyses. Manual assessment of technical accuracy and reportability of each variant is performed in VarSeq’s VSClinical interface in accordance with ACMG and AMP guidelines and following a procedure that emphasizes reproducibility across cases and between performing individuals.

Use

The test is for use by qualified health care providers in accordance with professional guidelines for use of somatic variants as therapeutic, prognostic, and/or diagnostic biomarkers.

Limitations

This assay may not detect certain large structural variants, such as inversions and insertion of retrotransposons, if the breakpoints are not located in the targeted regions. Variants further than 8bp into introns are not analyzed. Variants in certain regions may not be detected due to the presence of pseudogenes, sequence context, and allelic bias. Copy number variants (CNVs) are not reported. The performance of this test might also be limited by factors such as nature of the sample, tumor purity, among other reasons.

Specimen Type

10 unstained formalin-fixed paraffin-embedded (FFPE) slides and a matched normal specimen (blood (preferred) or saliva). FFPE slides must contain ≥20% of neoplastic cells on the entire slide or in the circular tumor area. An H&E from the same tumor block is required.

Matched normal specimen (blood or saliva) is required currently for this test.

Shipping and Handling Instructions

Transport specimen at room temperature.

Causes for Rejection

Incorrect tissue type, damaged slides, tissue quantity not sufficient
Test Information

Test Name

Pan-Cancer Solid Tumor Panel

Test Number

LAB9055

CPT Codes

81455

Test Includes

The Pan-Cancer Solid Tumor Panel is a custom target enrichment and sequencing platform for detection of somatic substitutions, small indels (insertions and deletions <1000 base-pairs in length), tumor mutation burden (TMB) and microsatellite instability (MSI) in tumor samples by next-generation sequencing (NGS) technology. The Pan-Cancer Panel (PCP) involves hybridization capture and deep sequencing of all protein-coding exons of 1080 cancer-associated genes as well as clinically relevant regions near those genes.

Gene list in the panel:
In bold* 82 cancer predisposition genes that we report incidental pathogenic and likely pathogenic variants detected in the submitted normal comparator (blood/saliva).
ABCB1 CCT6B EEF2 GAB2 IL2RG MIB1 PHF6 RNF111 TAF1
ABL1 CD19 EGFL7 GABRA6 IL3 MIDEAS PHOX2B* RNF139 TAL1
ABL2 CD22 EGFR* GADD45B IL4R MIR142 PICALM RNF43 TAP1
ABRAXAS1 CD274 EGLN1 GALNT12 IL6ST MITF* PIGA ROBO1 TAP2
ACTA2 CD276 EGR1 GATA1 IL7R MKI67 PIK3C2B ROS1 TAPBP
ACTB CD27 EGR2 GATA2* ING1 MKNK1 PIK3C2G RPA1 TBL1XR1
ACVR1B CD28 EGR3 GATA3 INHA MLH1* PIK3C3 RPL10 TBX3
ACVR1 CD33 EIF1AX GATA4 INHBA MLH3 PIK3CA RPL22 TCF12
ACVR2A CD36 EIF3E GATA6 INO80 MLLT10 PIK3CB RPL5 TCF3
ADGRA2 CD40 EIF4A2 GEM INPP4A MLLT1 PIK3CD RPS15 TCF7L2
ADGRB1 CD58 EIF4E GEN1 INPP4B MLLT3 PIK3CG RPS20 TCL1A
AGO1 CD70 ELANE GID4 INPP5D MPL PIK3R1 RPS3A TCL1B
AGO2 CD74 ELF3 GLI1 INPPL1 MR1 PIK3R2 RPS6KA3 TDG
AJUBA CD79A ELOC GLI2 INSR MRE11 PIK3R3 RPS6KA4 TEK
AKT1 CD79B ELP2 GLIS2 IRF1 MRTFA PIM1 RPS6KB1 TENT5C
AKT2 CD80 EML4 GNA11 IRF2 MRTFB PKN1 RPS6KB2 TENT5D
AKT3 CDC73* EMSY GNA12 IRF4 MSH2* PLAG1 RPTOR TERC*
ALB CDH10 ENG GNA13 IRF6 MSH3* PLCB4 RRAGC TERF1
ALK* CDH1* EP300 GNAI2 IRF8 MSH6* PLCG1 RRAS2 TERT*
ALOX12B CDH4 EPAS1 GNAQ IRS1 MSI2 PLCG2 RRAS TET1
AMER1 CDK12 EPC1 GNAS IRS2 MSMB PLK2 RSPO2 TET2
ANKRD11 CDK4* EPCAM* GNB1 IRS4 MST1 PLXNB2 RSPO3 TET3
ANKRD26 CDK6 EPHA2 GPC3* ITGAM MST1R PMAIP1 RTEL1 TFE3
APC* CDK8 EPHA3 GPS2 ITK MT1JP PML RUNX1* TFEB
APH1A CDKN1A EPHA5 GREM1* ITPKB MTAP PMS1 RUNX1T1 TFG
APLNR CDKN1B* EPHA7 GRIN2A JAK1 MTOR PMS2* RXRA TGFBR1
APOB CDKN1C* EPHB1 GRIN2D JAK2 MUC17 PNRC1 RYBP TGFBR2
ARAF CDKN2A* EPHB4 GRM3 JAK3 MUC6 POLD1* S1PR2 TGIF1
AR CDKN2B EPOR GSK3B JARID2 MUSK POLE* SALL4 THADA
ARFRP1 CDKN2C ERBB2 GTF2I JAZF1 MUTYH* POLH SAMD9 THRAP3
ARHGAP26 CEBPA* ERBB3 GTSE1 JUN MYB POLQ SAMD9L TIPARP
ARHGAP35 CENPA ERBB4 H1-2 KANSL1 MYBL1 POLR2A SAMHD1 TLL2
ARHGEF10 CFTR ERCC1 H1-3 KAT6A MYC POLRMT SBDS TLR4
ARHGEF12 CHD2 ERCC2 H1-4 KAT6B MYCL POT1* SCAF4 TLR9
ARID1A CHD3 ERCC3 H19 KBTBD4 MYCN POU2F2 SCG5 TLX3
ARID1B CHD4 ERCC4 H2AC11 KDM2B MYD88 PPARG SDC4 TMEM127*
ARID2 CHD7 ERCC5 H2AC16 KDM4C MYH11 PPM1D SDHA* TMEM30A
ARID3A CHD8 ERCC6 H2AC17 KDM5A MYH9 PPP2R1A SDHAF2* TMPRSS2
ARID4B CHEK1 ERF H2AC6 KDM5C MYO18A PPP2R2A SDHB* TMSB4X
ARID5B CHEK2* ERG H2BC11 KDM6A MYOD1 PPP4R2 SDHC* TMSB4XP8
ASMTL CIC ERRFI1 H2BC12 KDM6B NADK PPP6C SDHD* TNFAIP3
ASXL1 CIITA ESR1 H2BC17 KDR NBN* PRDM14 SERP2 TNFRSF11A
ASXL2 CILK1 ESRRA H2BC4 KEAP1 NCOA2 PRDM1 SERPINA1 TNFRSF14
ATF7IP CKS1B ETNK1 H2BC5 KEL NCOA3 PREX2 SERPINB3 TNFRSF17
ATM* CLIP1 ETS1 H3-3A KIF1A NCOR1 PRF1 SERPINB4 TNFRSF18
ATP6AP1 CMTR2 ETV1 H3-3B KIF1B NCOR2 PRKACA SESN2 TNFRSF4
ATP6V1B2 CNBD1 ETV4 H3-4 KIF5B NCSTN PRKAR1A* SESN3 TNFRSF9
ATR CNOT9 ETV5 H3-5 KIR3DL1 NECTIN4 PRKCA SETBP1 TOP1
ATRX COL1A1 ETV6 H3C10 KIT* NEGR1 PRKCB SETD1B TOP2A
ATXN3 COL5A1 EWSR1 H3C11 KLF2 NEIL2 PRKCD SETD2 TP53BP1
ATXN7 COL7A1 EXO1 H3C12 KLF3 NF1* PRKCI SETDB1 TP53*
AURKA COP1 EXOSC6 H3C13 KLF4 NF2* PRKD1 SETDB2 TP63
AURKB CPS1 EXT1 H3C14 KLF5 NFATC2 PRKDC SF1 TPMT
AXIN1 CRBN EXT2 H3C15 KLHL6 NFE2 PRKN SF3A1 TPTE2
AXIN2* CREB3L3 EZH1 H3C1 KLLN NFE2L2 PRPF40B SF3B1 TRAF2
AXL CREBBP EZH2 H3C2 KMT2A NFKBIA PRPF8 SGK1 TRAF3
B2M CRKL EZHIP H3C3 KMT2B NFKBIE PRPS1 SH2B3 TRAF5
BABAM1 CRLF1 EZR H3C4 KMT2C NIPBL PRSS1 SH2D1A TRAF7
BAP1* CRLF2 FAF1 H3C6 KMT2D NKX2-1 PRSS8 SHH TRIP13
BARD1* CRTC1 FAM135B H3C7 KNSTRN NKX3-1 PSIP1 SHOC2 TRPA1
BBC3 CSDE1 FANCA H3C8 KRAS NOD1 PSMB5 SHQ1 TSC1*
BCL10 CSF1R FANCB HAVCR2 KRT222 NOTCH1 PTCH1* SIN3A TSC2*
BCL11B CSF3R FANCC HDAC1 LAG3 NOTCH2 PTCH2 SIRPA TSHR
BCL2 CSNK1A1 FANCD2 HDAC2 LATS1 NOTCH3 PTEN* SLC26A3 TSLP
BCL2L11 CTC1 FANCE HDAC4 LATS2 NOTCH4 PTK2B SLC34A2 TUSC3
BCL2L12 CTCF FANCF HDAC7 LCK NPM1 PTK2 SLFN11 TXNIP
BCL2L1 CTDNEP1 FANCG HDAC9 LDB1 NPRL2 PTMA SLIT2 TYK2
BCL2L2 CTLA4 FANCI HGF LEF1 NR4A3 PTP4A1 SLX4 TYRO3
BCL6 CTNNA1* FANCL HIF1A LEMD2 NRAS PTPDC1 SMAD2 U2AF1
BCL7A CTNNB1 FANCM HLA-A LIFR NRG1 PTPN11 SMAD3 U2AF2
BCL9 CTNND1 FAS HLA-B LMO1 NSD1 PTPN13 SMAD4* UBE2T
BCLAF1 CTR9 FASLG HLA-C LRP1B NSD2 PTPN14 SMARCA1 UBR5
BCOR CUL1 FAT1 HLA-DMA LRP5 NSD3 PTPN1 SMARCA2 UNCX
BCORL1 CUL3 FBXO11 HLA-DMB LRP6 NT5C2 PTPN2 SMARCA4* USP6
BCR CUL4A FBXO31 HLA-DOA LRRK2 NT5E PTPN6 SMARCAL1 USP8
BIRC3 CUL4B FBXW7 HLA-DOB LTB NTHL1* PTPRC SMARCB1* USP9X
BLM* CUX1 FCGR2A HLA-DPA1 LTK NTRK1 PTPRD SMARCD1 VAV1
BMPR1A* CXCR4 FCGR3A HLA-DPB1 LUC7L2 NTRK2 PTPRO SMARCE1* VEGFA
BRAF CYLD FGF10 HLA-DPB2 LYN NTRK3 PTPRS SMC1A VHL*
BRCA1* CYP17A1 FGF12 HLA-DQA1 LZTR1 NUDT15 PTPRT SMC3 VTCN1
BRCA2* CYP19A1 FGF14 HLA-DQA2 MACF1 NUF2 QKI SMO WAS
BRCC3 CYP2D6 FGF19 HLA-DQB1 MAD2L2 NUMBL RAB35 SMYD3 WDR90
BRD3 CYSLTR2 FGF1 HLA-DQB2 MAFB NUP133 RABEP1 SNCAIP WEE1
BRD4 DACH1 FGF23 HLA-DRA MAF NUP214 RAC1 SOCS1 WIF1
BRD7 DAXX FGF2 HLA-DRB1 MAGED1 NUP93 RAC2 SOCS2 WNK2
BRINP3 DAZAP1 FGF3 HLA-DRB5 MAGI2 NUP98 RAD21 SOCS3 WRN*
BRIP1* DCSTAMP FGF4 HLA-DRB6 MALT1 NUTM1 RAD50* SOS1 WT1*
BRSK1 DCUN1D1 FGF5 HLA-E MAML2 P2RY8 RAD51B SOX10 WWTR1
BTG1 DDB2 FGF6 HLA-F MAMLD1 PABPC1 RAD51C* SOX17 XBP1
BTG2 DDR1 FGF7 HLA-G MAP2K1 PAG1 RAD51D* SOX2 XIAP
BTK DDR2 FGF8 HLTF MAP2K2 PAK1 RAD51 SOX9 XPA
BTLA DDX3X FGF9 HMGA2 MAP2K4 PAK3 RAD52 SP140 XPC
BUB1B DDX41 FGFR1 HNF1A MAP3K13 PAK5 RAD54B SPEN XPO1
C3orf70 DEK FGFR2 HNRNPK MAP3K14 PALB2* RAD54L SPOP XRCC1
C8orf34 DHX9 FGFR3 HOXA11 MAP3K1 PARP1 RAF1 SPRED1 XRCC2
CACNA1A DIAPH2 FGFR4 HOXB13* MAP3K4 PARP2 RANBP17 SPRTN XRCC3
CACNA1D DICER1* FGR HRAS* MAP3K6 PARP3 RANBP2 SPTA1 YAP1
CAD DIS3 FH* HSD3B1 MAP3K7 PARP4 RARA SPTAN1 YEATS4
CALR DIS3L2* FHIT HSP90AA1 MAPK1 PARPBP RASA1 SRC YES1
CAMTA1 DKC1 FLCN* HSP90AB1 MAPK3 PASK RASGEF1A SRP72 YWHAE
CARD11 DKK4 FLI1 HUWE1 MAST1 PAX3 RB1* SRSF2 YY1AP1
CARM1 DMD FLNA ICOS MAST2 PAX5 RBM10 SS18 ZBTB20
CASP8 DNAJB1 FLT1 ICOSLG MAX* PAX7 RBM15 SSBP2 ZBTB2
CBFA2T3 DNM2 FLT3 ID3 MBD4 PAX8 RBM38 STAG1 ZBTB7B
CBFB DNMT1 FLT4 IDH1 MC1R PAXIP1 RECQL4* STAG2 ZC3H12A
CBLB DNMT3A FLYWCH1 IDH2 MCL1 PBRM1 RECQL STAT1 ZCCHC12
CBLC DNMT3B FOXA1 IDO1 MDC1 PCBP1 RELA STAT2 ZFHX3
CBL DOCK8 FOXA2 IFNAR1 MDM2 PC REL STAT3 ZFP36L1
CBWD3 DOT1L FOXD4L1 IFNGR1 MDM4 PCLO RELN STAT4 ZFP36L2
CCDC6 DROSHA FOXL2 IFNGR2 MEAF6 PDCD11 REST STAT5A ZMYM2
CCL2 DTX1 FOXO1 IGF1 MECOM PDCD1 RET* STAT5B ZMYM3
CCN6 DUSP22 FOXO3 IGF1R MED12 PDCD1LG2 RFC1 STAT6 ZNF133
CCNB3 DUSP2 FOXP1 IGF2 MEF2B PDGFB RGPD3 STK11* ZNF217
CCND1 DUSP4 FOXQ1 IKBKE MEF2C PDGFRA* RHEB STK19 ZNF24
CCND2 DUSP9 FRK IKZF1 MEF2D PDGFRB RHOA STK40 ZNF384
CCND3 E2F3 FRS2 IKZF2 MEN1* PDK1 RHOB SUFU* ZNF703
CCNE1 EBF1 FUBP1 IKZF3 MERTK PDPK1 RHPN2 SUSD2 ZNF750
CCR2 ECT2L FUS IL10 MET* PDS5B RICTOR SUZ12 ZNRF3
CCR4 EED FYN IL2 MGA PGBD5 RINT1 SYK ZRANB3
CCR5 EEF1A1 GAB1 IL2RB MGMT PGR RIT1 TAF15 ZRSR2

Performing Laboratory / Facility

UCLA Molecular Diagnostics Laboratories (MDL)

Performing Section

Molecular Pathology

Availability

Monday through Friday, 0700-1700

Turnaround Time

14 days from receipt of required FFPE specimen AND matched normal specimen in performing lab

Methodology

Genomic DNA is extracted from FFPE tumor tissue and patient-matched blood/saliva specimen as a normal comparator. Using kits from Twist Bioscience, the DNA undergoes enzymatic fragmentation, library preparation, and target enrichment. The resulting libraries are pooled and sequenced to high uniform depth (600x for tumors, 200x for normals) using the Illumina NovaSeq 6000 sequencer. The sequencing data is processed by the UCLA Molecular Diagnostic Labs’ Analysis Pipeline which uses Illumina Dragen 4.0.3 for primary and secondary analyses against reference genome GRCh38 (hg38), and GoldenHelix VarSeq 2.3.0 for tertiary analyses. Manual assessment of technical accuracy and reportability of each variant is performed in VarSeq’s VSClinical interface in accordance with ACMG and AMP guidelines and following a procedure that emphasizes reproducibility across cases and between performing individuals.

Use

The test is for use by qualified health care providers in accordance with professional guidelines for use of somatic variants as therapeutic, prognostic, and/or diagnostic biomarkers.

Limitations

This assay may not detect certain large structural variants, such as inversions and insertion of retrotransposons, if the breakpoints are not located in the targeted regions. Variants further than 8bp into introns are not analyzed. Variants in certain regions may not be detected due to the presence of pseudogenes, sequence context, and allelic bias. Copy number variants (CNVs) are not reported. The performance of this test might also be limited by factors such as nature of the sample, tumor purity, among other reasons.
Specimen Collection and Handling

Specimen Type

10 unstained formalin-fixed paraffin-embedded (FFPE) slides and a matched normal specimen (blood (preferred) or saliva). FFPE slides must contain ≥20% of neoplastic cells on the entire slide or in the circular tumor area. An H&E from the same tumor block is required.

Matched normal specimen (blood or saliva) is required currently for this test.

Shipping and Handling Instructions

Transport specimen at room temperature.

Causes for Rejection

Incorrect tissue type, damaged slides, tissue quantity not sufficient
Result Interpretation

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