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.

Pan-Cancer Solid Tumor Panel includes:

In bold and marked with an asterisk (*) are 84 cancer predisposition genes for which we report incidental pathogenic and likely pathogenic variants detected in the submitted normal comparator (blood or saliva).
ABCB1CCT6BEEF2GAB2IL2RGMIB1PHF6RNF111TAF1
ABL1CD19EGFL7GABRA6IL3MIDEASPHOX2B*RNF139TAL1
ABL2CD22EGFR*GADD45BIL4RMIR142PICALMRNF43TAP1
ABRAXAS1CD274EGLN1GALNT12IL6STMITF*PIGAROBO1TAP2
ACTA2CD276EGR1GATA1IL7RMKI67PIK3C2BROS1TAPBP
ACTBCD27EGR2GATA2*ING1MKNK1PIK3C2GRPA1TBL1XR1
ACVR1BCD28EGR3GATA3INHAMLH1*PIK3C3RPL10TBX3
ACVR1CD33EIF1AXGATA4INHBAMLH3PIK3CARPL22TCF12
ACVR2ACD36EIF3EGATA6INO80MLLT10PIK3CBRPL5TCF3
ADGRA2CD40EIF4A2GEMINPP4AMLLT1PIK3CDRPS15TCF7L2
ADGRB1CD58EIF4EGEN1INPP4BMLLT3PIK3CGRPS20TCL1A
AGO1CD70ELANEGID4INPP5DMPLPIK3R1RPS3ATCL1B
AGO2CD74ELF3GLI1INPPL1MR1PIK3R2RPS6KA3TDG
AJUBACD79AELOCGLI2INSRMRE11PIK3R3RPS6KA4TEK
AKT1CD79BELP2GLIS2IRF1MRTFAPIM1RPS6KB1TENT5C
AKT2CD80EML4GNA11IRF2MRTFBPKN1RPS6KB2TENT5D
AKT3CDC73*EMSYGNA12IRF4MSH2*PLAG1RPTORTERC*
ALBCDH10ENGGNA13IRF6MSH3*PLCB4RRAGCTERF1
ALK*CDH1*EP300GNAI2IRF8MSH6*PLCG1RRAS2TERT*
ALOX12BCDH4EPAS1GNAQIRS1MSI2PLCG2RRASTET1
AMER1CDK12EPC1GNASIRS2MSMBPLK2RSPO2TET2
ANKRD11CDK4*EPCAM*GNB1IRS4MST1PLXNB2RSPO3TET3
ANKRD26CDK6EPHA2GPC3*ITGAMMST1RPMAIP1RTEL1TFE3
APC*CDK8EPHA3GPS2ITKMT1JPPMLRUNX1*TFEB
APH1ACDKN1AEPHA5GREM1*ITPKBMTAPPMS1RUNX1T1TFG
APLNRCDKN1B*EPHA7GRIN2AJAK1MTORPMS2*RXRATGFBR1
APOBCDKN1C*EPHB1GRIN2DJAK2MUC17PNRC1RYBPTGFBR2
ARAFCDKN2A*EPHB4GRM3JAK3MUC6POLD1*S1PR2TGIF1
ARCDKN2BEPORGSK3BJARID2MUSKPOLE*SALL4THADA
ARFRP1CDKN2CERBB2GTF2IJAZF1MUTYH*POLHSAMD9THRAP3
ARHGAP26CEBPA*ERBB3GTSE1JUNMYBPOLQSAMD9LTIPARP
ARHGAP35CENPAERBB4H1-2KANSL1MYBL1POLR2ASAMHD1TLL2
ARHGEF10CFTRERCC1H1-3KAT6AMYCPOLRMTSBDSTLR4
ARHGEF12CHD2ERCC2H1-4KAT6BMYCLPOT1*SCAF4TLR9
ARID1ACHD3ERCC3H19KBTBD4MYCNPOU2F2SCG5TLX3
ARID1BCHD4ERCC4H2AC11KDM2BMYD88PPARGSDC4TMEM127*
ARID2CHD7ERCC5H2AC16KDM4CMYH11PPM1DSDHA*TMEM30A
ARID3ACHD8ERCC6H2AC17KDM5AMYH9PPP2R1ASDHAF2*TMPRSS2
ARID4BCHEK1ERFH2AC6KDM5CMYO18APPP2R2ASDHB*TMSB4X
ARID5BCHEK2*ERGH2BC11KDM6AMYOD1PPP4R2SDHC*TMSB4XP8
ASMTLCICERRFI1H2BC12KDM6BNADKPPP6CSDHD*TNFAIP3
ASXL1CIITAESR1H2BC17KDRNBN*PRDM14SERP2TNFRSF11A
ASXL2CILK1ESRRAH2BC4KEAP1NCOA2PRDM1SERPINA1TNFRSF14
ATF7IPCKS1BETNK1H2BC5KELNCOA3PREX2SERPINB3TNFRSF17
ATM*CLIP1ETS1H3-3AKIF1ANCOR1PRF1SERPINB4TNFRSF18
ATP6AP1CMTR2ETV1H3-3BKIF1BNCOR2PRKACASESN2TNFRSF4
ATP6V1B2CNBD1ETV4H3-4KIF5BNCSTNPRKAR1A*SESN3TNFRSF9
ATRCNOT9ETV5H3-5KIR3DL1NECTIN4PRKCASETBP1TOP1
ATRXCOL1A1ETV6H3C10KIT*NEGR1PRKCBSETD1BTOP2A
ATXN3COL5A1EWSR1H3C11KLF2NEIL2PRKCDSETD2TP53BP1
ATXN7COL7A1EXO1H3C12KLF3NF1*PRKCISETDB1TP53*
AURKACOP1EXOSC6H3C13KLF4NF2*PRKD1SETDB2TP63
AURKBCPS1EXT1H3C14KLF5NFATC2PRKDCSF1TPMT
AXIN1CRBNEXT2H3C15KLHL6NFE2PRKNSF3A1TPTE2
AXIN2*CREB3L3EZH1H3C1KLLNNFE2L2PRPF40BSF3B1TRAF2
AXLCREBBPEZH2H3C2KMT2ANFKBIAPRPF8SGK1TRAF3
B2MCRKLEZHIPH3C3KMT2BNFKBIEPRPS1SH2B3TRAF5
BABAM1CRLF1EZRH3C4KMT2CNIPBLPRSS1SH2D1ATRAF7
BAP1*CRLF2FAF1H3C6KMT2DNKX2-1PRSS8SHHTRIP13
BARD1*CRTC1FAM135BH3C7KNSTRNNKX3-1PSIP1SHOC2TRPA1
BBC3CSDE1FANCAH3C8KRASNOD1PSMB5SHQ1TSC1*
BCL10CSF1RFANCBHAVCR2KRT222NOTCH1PTCH1*SIN3ATSC2*
BCL11BCSF3RFANCCHDAC1LAG3NOTCH2PTCH2SIRPATSHR
BCL2CSNK1A1FANCD2HDAC2LATS1NOTCH3PTEN*SLC26A3TSLP
BCL2L11CTC1FANCEHDAC4LATS2NOTCH4PTK2BSLC34A2TUSC3
BCL2L12CTCFFANCFHDAC7LCKNPM1PTK2SLFN11TXNIP
BCL2L1CTDNEP1FANCGHDAC9LDB1NPRL2PTMASLIT2TYK2
BCL2L2CTLA4FANCIHGFLEF1NR4A3PTP4A1SLX4TYRO3
BCL6CTNNA1*FANCLHIF1ALEMD2NRASPTPDC1SMAD2U2AF1
BCL7ACTNNB1FANCMHLA-ALIFRNRG1PTPN11SMAD3U2AF2
BCL9CTNND1FASHLA-BLMO1NSD1PTPN13SMAD4*UBE2T
BCLAF1CTR9FASLGHLA-CLRP1BNSD2PTPN14SMARCA1UBR5
BCORCUL1FAT1HLA-DMALRP5NSD3PTPN1SMARCA2UNCX
BCORL1CUL3FBXO11HLA-DMBLRP6NT5C2PTPN2SMARCA4*USP6
BCRCUL4AFBXO31HLA-DOALRRK2NT5EPTPN6SMARCAL1USP8
BIRC3CUL4BFBXW7HLA-DOBLTBNTHL1*PTPRCSMARCB1*USP9X
BLM*CUX1FCGR2AHLA-DPA1LTKNTRK1PTPRDSMARCD1VAV1
BMPR1A*CXCR4FCGR3AHLA-DPB1LUC7L2NTRK2PTPROSMARCE1*VEGFA
BRAFCYLDFGF10HLA-DPB2LYNNTRK3PTPRSSMC1AVHL*
BRCA1*CYP17A1FGF12HLA-DQA1LZTR1*NUDT15PTPRTSMC3VTCN1
BRCA2*CYP19A1FGF14HLA-DQA2MACF1NUF2QKISMOWAS
BRCC3CYP2D6FGF19HLA-DQB1MAD2L2NUMBLRAB35SMYD3WDR90
BRD3CYSLTR2FGF1HLA-DQB2MAFBNUP133RABEP1SNCAIPWEE1
BRD4DACH1FGF23HLA-DRAMAFNUP214RAC1SOCS1WIF1
BRD7DAXXFGF2HLA-DRB1MAGED1NUP93RAC2SOCS2WNK2
BRINP3DAZAP1FGF3HLA-DRB5MAGI2NUP98RAD21SOCS3WRN*
BRIP1*DCSTAMPFGF4HLA-DRB6MALT1NUTM1RAD50*SOS1WT1*
BRSK1DCUN1D1FGF5HLA-EMAML2P2RY8RAD51BSOX10WWTR1
BTG1DDB2FGF6HLA-FMAMLD1PABPC1RAD51C*SOX17XBP1
BTG2DDR1FGF7HLA-GMAP2K1PAG1RAD51D*SOX2XIAP
BTKDDR2FGF8HLTFMAP2K2PAK1RAD51SOX9XPA
BTLADDX3XFGF9HMGA2MAP2K4PAK3RAD52SP140XPC
BUB1BDDX41FGFR1HNF1AMAP3K13PAK5RAD54BSPENXPO1
C3orf70DEKFGFR2HNRNPKMAP3K14PALB2*RAD54LSPOPXRCC1
C8orf34DHX9FGFR3HOXA11MAP3K1PARP1RAF1SPRED1XRCC2
CACNA1ADIAPH2FGFR4HOXB13*MAP3K4PARP2RANBP17SPRTNXRCC3
CACNA1DDICER1*FGRHRAS*MAP3K6PARP3RANBP2SPTA1YAP1
CADDIS3FH*HSD3B1MAP3K7PARP4RARASPTAN1YEATS4
CALRDIS3L2*FHITHSP90AA1MAPK1PARPBPRASA1SRCYES1
CAMTA1DKC1FLCN*HSP90AB1MAPK3PASKRASGEF1ASRP72YWHAE
CARD11DKK4FLI1HUWE1MAST1PAX3RB1*SRSF2YY1AP1
CARM1DMDFLNAICOSMAST2PAX5RBM10SS18ZBTB20
CASP8DNAJB1FLT1ICOSLGMAX*PAX7RBM15SSBP2ZBTB2
CBFA2T3DNM2FLT3ID3MBD4*PAX8RBM38STAG1ZBTB7B
CBFBDNMT1FLT4IDH1MC1RPAXIP1RECQL4*STAG2ZC3H12A
CBLBDNMT3AFLYWCH1IDH2MCL1PBRM1RECQLSTAT1ZCCHC12
CBLCDNMT3BFOXA1IDO1MDC1PCBP1RELASTAT2ZFHX3
CBLDOCK8FOXA2IFNAR1MDM2PCRELSTAT3ZFP36L1
CBWD3DOT1LFOXD4L1IFNGR1MDM4PCLORELNSTAT4ZFP36L2
CCDC6DROSHAFOXL2IFNGR2MEAF6PDCD11RESTSTAT5AZMYM2
CCL2DTX1FOXO1IGF1MECOMPDCD1RET*STAT5BZMYM3
CCN6DUSP22FOXO3IGF1RMED12PDCD1LG2RFC1STAT6ZNF133
CCNB3DUSP2FOXP1IGF2MEF2BPDGFBRGPD3STK11*ZNF217
CCND1DUSP4FOXQ1IKBKEMEF2CPDGFRA*RHEBSTK19ZNF24
CCND2DUSP9FRKIKZF1MEF2DPDGFRBRHOASTK40ZNF384
CCND3E2F3FRS2IKZF2MEN1*PDK1RHOBSUFU*ZNF703
CCNE1EBF1FUBP1IKZF3MERTKPDPK1RHPN2SUSD2ZNF750
CCR2ECT2LFUSIL10MET*PDS5BRICTORSUZ12ZNRF3
CCR4EEDFYNIL2MGAPGBD5RINT1SYKZRANB3
CCR5EEF1A1GAB1IL2RBMGMTPGRRIT1TAF15ZRSR2

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

Patient-matched blood/saliva specimen is required as a normal comparator. Genomic DNA is extracted from FFPE tumor tissue and normal comparator sample. DNA undergoes enzymatic fragmentation, library preparation, and target enrichment. The resulting sample libraries are sequenced by the Illumina NovaSeq 6000 sequencer. The sequencing data is processed by the UCLA Molecular Diagnostic Labs’ Analysis Pipeline (PCPDx v2.0.0) for primary and secondary analyses against reference genome GRCh38 (hg38). Manual assessment of technical accuracy and reportability of each variant is performed 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.

Pan-Cancer Solid Tumor Panel includes:

In bold and marked with an asterisk (*) are 84 cancer predisposition genes for which we report incidental pathogenic and likely pathogenic variants detected in the submitted normal comparator (blood or saliva).
ABCB1CCT6BEEF2GAB2IL2RGMIB1PHF6RNF111TAF1
ABL1CD19EGFL7GABRA6IL3MIDEASPHOX2B*RNF139TAL1
ABL2CD22EGFR*GADD45BIL4RMIR142PICALMRNF43TAP1
ABRAXAS1CD274EGLN1GALNT12IL6STMITF*PIGAROBO1TAP2
ACTA2CD276EGR1GATA1IL7RMKI67PIK3C2BROS1TAPBP
ACTBCD27EGR2GATA2*ING1MKNK1PIK3C2GRPA1TBL1XR1
ACVR1BCD28EGR3GATA3INHAMLH1*PIK3C3RPL10TBX3
ACVR1CD33EIF1AXGATA4INHBAMLH3PIK3CARPL22TCF12
ACVR2ACD36EIF3EGATA6INO80MLLT10PIK3CBRPL5TCF3
ADGRA2CD40EIF4A2GEMINPP4AMLLT1PIK3CDRPS15TCF7L2
ADGRB1CD58EIF4EGEN1INPP4BMLLT3PIK3CGRPS20TCL1A
AGO1CD70ELANEGID4INPP5DMPLPIK3R1RPS3ATCL1B
AGO2CD74ELF3GLI1INPPL1MR1PIK3R2RPS6KA3TDG
AJUBACD79AELOCGLI2INSRMRE11PIK3R3RPS6KA4TEK
AKT1CD79BELP2GLIS2IRF1MRTFAPIM1RPS6KB1TENT5C
AKT2CD80EML4GNA11IRF2MRTFBPKN1RPS6KB2TENT5D
AKT3CDC73*EMSYGNA12IRF4MSH2*PLAG1RPTORTERC*
ALBCDH10ENGGNA13IRF6MSH3*PLCB4RRAGCTERF1
ALK*CDH1*EP300GNAI2IRF8MSH6*PLCG1RRAS2TERT*
ALOX12BCDH4EPAS1GNAQIRS1MSI2PLCG2RRASTET1
AMER1CDK12EPC1GNASIRS2MSMBPLK2RSPO2TET2
ANKRD11CDK4*EPCAM*GNB1IRS4MST1PLXNB2RSPO3TET3
ANKRD26CDK6EPHA2GPC3*ITGAMMST1RPMAIP1RTEL1TFE3
APC*CDK8EPHA3GPS2ITKMT1JPPMLRUNX1*TFEB
APH1ACDKN1AEPHA5GREM1*ITPKBMTAPPMS1RUNX1T1TFG
APLNRCDKN1B*EPHA7GRIN2AJAK1MTORPMS2*RXRATGFBR1
APOBCDKN1C*EPHB1GRIN2DJAK2MUC17PNRC1RYBPTGFBR2
ARAFCDKN2A*EPHB4GRM3JAK3MUC6POLD1*S1PR2TGIF1
ARCDKN2BEPORGSK3BJARID2MUSKPOLE*SALL4THADA
ARFRP1CDKN2CERBB2GTF2IJAZF1MUTYH*POLHSAMD9THRAP3
ARHGAP26CEBPA*ERBB3GTSE1JUNMYBPOLQSAMD9LTIPARP
ARHGAP35CENPAERBB4H1-2KANSL1MYBL1POLR2ASAMHD1TLL2
ARHGEF10CFTRERCC1H1-3KAT6AMYCPOLRMTSBDSTLR4
ARHGEF12CHD2ERCC2H1-4KAT6BMYCLPOT1*SCAF4TLR9
ARID1ACHD3ERCC3H19KBTBD4MYCNPOU2F2SCG5TLX3
ARID1BCHD4ERCC4H2AC11KDM2BMYD88PPARGSDC4TMEM127*
ARID2CHD7ERCC5H2AC16KDM4CMYH11PPM1DSDHA*TMEM30A
ARID3ACHD8ERCC6H2AC17KDM5AMYH9PPP2R1ASDHAF2*TMPRSS2
ARID4BCHEK1ERFH2AC6KDM5CMYO18APPP2R2ASDHB*TMSB4X
ARID5BCHEK2*ERGH2BC11KDM6AMYOD1PPP4R2SDHC*TMSB4XP8
ASMTLCICERRFI1H2BC12KDM6BNADKPPP6CSDHD*TNFAIP3
ASXL1CIITAESR1H2BC17KDRNBN*PRDM14SERP2TNFRSF11A
ASXL2CILK1ESRRAH2BC4KEAP1NCOA2PRDM1SERPINA1TNFRSF14
ATF7IPCKS1BETNK1H2BC5KELNCOA3PREX2SERPINB3TNFRSF17
ATM*CLIP1ETS1H3-3AKIF1ANCOR1PRF1SERPINB4TNFRSF18
ATP6AP1CMTR2ETV1H3-3BKIF1BNCOR2PRKACASESN2TNFRSF4
ATP6V1B2CNBD1ETV4H3-4KIF5BNCSTNPRKAR1A*SESN3TNFRSF9
ATRCNOT9ETV5H3-5KIR3DL1NECTIN4PRKCASETBP1TOP1
ATRXCOL1A1ETV6H3C10KIT*NEGR1PRKCBSETD1BTOP2A
ATXN3COL5A1EWSR1H3C11KLF2NEIL2PRKCDSETD2TP53BP1
ATXN7COL7A1EXO1H3C12KLF3NF1*PRKCISETDB1TP53*
AURKACOP1EXOSC6H3C13KLF4NF2*PRKD1SETDB2TP63
AURKBCPS1EXT1H3C14KLF5NFATC2PRKDCSF1TPMT
AXIN1CRBNEXT2H3C15KLHL6NFE2PRKNSF3A1TPTE2
AXIN2*CREB3L3EZH1H3C1KLLNNFE2L2PRPF40BSF3B1TRAF2
AXLCREBBPEZH2H3C2KMT2ANFKBIAPRPF8SGK1TRAF3
B2MCRKLEZHIPH3C3KMT2BNFKBIEPRPS1SH2B3TRAF5
BABAM1CRLF1EZRH3C4KMT2CNIPBLPRSS1SH2D1ATRAF7
BAP1*CRLF2FAF1H3C6KMT2DNKX2-1PRSS8SHHTRIP13
BARD1*CRTC1FAM135BH3C7KNSTRNNKX3-1PSIP1SHOC2TRPA1
BBC3CSDE1FANCAH3C8KRASNOD1PSMB5SHQ1TSC1*
BCL10CSF1RFANCBHAVCR2KRT222NOTCH1PTCH1*SIN3ATSC2*
BCL11BCSF3RFANCCHDAC1LAG3NOTCH2PTCH2SIRPATSHR
BCL2CSNK1A1FANCD2HDAC2LATS1NOTCH3PTEN*SLC26A3TSLP
BCL2L11CTC1FANCEHDAC4LATS2NOTCH4PTK2BSLC34A2TUSC3
BCL2L12CTCFFANCFHDAC7LCKNPM1PTK2SLFN11TXNIP
BCL2L1CTDNEP1FANCGHDAC9LDB1NPRL2PTMASLIT2TYK2
BCL2L2CTLA4FANCIHGFLEF1NR4A3PTP4A1SLX4TYRO3
BCL6CTNNA1*FANCLHIF1ALEMD2NRASPTPDC1SMAD2U2AF1
BCL7ACTNNB1FANCMHLA-ALIFRNRG1PTPN11SMAD3U2AF2
BCL9CTNND1FASHLA-BLMO1NSD1PTPN13SMAD4*UBE2T
BCLAF1CTR9FASLGHLA-CLRP1BNSD2PTPN14SMARCA1UBR5
BCORCUL1FAT1HLA-DMALRP5NSD3PTPN1SMARCA2UNCX
BCORL1CUL3FBXO11HLA-DMBLRP6NT5C2PTPN2SMARCA4*USP6
BCRCUL4AFBXO31HLA-DOALRRK2NT5EPTPN6SMARCAL1USP8
BIRC3CUL4BFBXW7HLA-DOBLTBNTHL1*PTPRCSMARCB1*USP9X
BLM*CUX1FCGR2AHLA-DPA1LTKNTRK1PTPRDSMARCD1VAV1
BMPR1A*CXCR4FCGR3AHLA-DPB1LUC7L2NTRK2PTPROSMARCE1*VEGFA
BRAFCYLDFGF10HLA-DPB2LYNNTRK3PTPRSSMC1AVHL*
BRCA1*CYP17A1FGF12HLA-DQA1LZTR1*NUDT15PTPRTSMC3VTCN1
BRCA2*CYP19A1FGF14HLA-DQA2MACF1NUF2QKISMOWAS
BRCC3CYP2D6FGF19HLA-DQB1MAD2L2NUMBLRAB35SMYD3WDR90
BRD3CYSLTR2FGF1HLA-DQB2MAFBNUP133RABEP1SNCAIPWEE1
BRD4DACH1FGF23HLA-DRAMAFNUP214RAC1SOCS1WIF1
BRD7DAXXFGF2HLA-DRB1MAGED1NUP93RAC2SOCS2WNK2
BRINP3DAZAP1FGF3HLA-DRB5MAGI2NUP98RAD21SOCS3WRN*
BRIP1*DCSTAMPFGF4HLA-DRB6MALT1NUTM1RAD50*SOS1WT1*
BRSK1DCUN1D1FGF5HLA-EMAML2P2RY8RAD51BSOX10WWTR1
BTG1DDB2FGF6HLA-FMAMLD1PABPC1RAD51C*SOX17XBP1
BTG2DDR1FGF7HLA-GMAP2K1PAG1RAD51D*SOX2XIAP
BTKDDR2FGF8HLTFMAP2K2PAK1RAD51SOX9XPA
BTLADDX3XFGF9HMGA2MAP2K4PAK3RAD52SP140XPC
BUB1BDDX41FGFR1HNF1AMAP3K13PAK5RAD54BSPENXPO1
C3orf70DEKFGFR2HNRNPKMAP3K14PALB2*RAD54LSPOPXRCC1
C8orf34DHX9FGFR3HOXA11MAP3K1PARP1RAF1SPRED1XRCC2
CACNA1ADIAPH2FGFR4HOXB13*MAP3K4PARP2RANBP17SPRTNXRCC3
CACNA1DDICER1*FGRHRAS*MAP3K6PARP3RANBP2SPTA1YAP1
CADDIS3FH*HSD3B1MAP3K7PARP4RARASPTAN1YEATS4
CALRDIS3L2*FHITHSP90AA1MAPK1PARPBPRASA1SRCYES1
CAMTA1DKC1FLCN*HSP90AB1MAPK3PASKRASGEF1ASRP72YWHAE
CARD11DKK4FLI1HUWE1MAST1PAX3RB1*SRSF2YY1AP1
CARM1DMDFLNAICOSMAST2PAX5RBM10SS18ZBTB20
CASP8DNAJB1FLT1ICOSLGMAX*PAX7RBM15SSBP2ZBTB2
CBFA2T3DNM2FLT3ID3MBD4*PAX8RBM38STAG1ZBTB7B
CBFBDNMT1FLT4IDH1MC1RPAXIP1RECQL4*STAG2ZC3H12A
CBLBDNMT3AFLYWCH1IDH2MCL1PBRM1RECQLSTAT1ZCCHC12
CBLCDNMT3BFOXA1IDO1MDC1PCBP1RELASTAT2ZFHX3
CBLDOCK8FOXA2IFNAR1MDM2PCRELSTAT3ZFP36L1
CBWD3DOT1LFOXD4L1IFNGR1MDM4PCLORELNSTAT4ZFP36L2
CCDC6DROSHAFOXL2IFNGR2MEAF6PDCD11RESTSTAT5AZMYM2
CCL2DTX1FOXO1IGF1MECOMPDCD1RET*STAT5BZMYM3
CCN6DUSP22FOXO3IGF1RMED12PDCD1LG2RFC1STAT6ZNF133
CCNB3DUSP2FOXP1IGF2MEF2BPDGFBRGPD3STK11*ZNF217
CCND1DUSP4FOXQ1IKBKEMEF2CPDGFRA*RHEBSTK19ZNF24
CCND2DUSP9FRKIKZF1MEF2DPDGFRBRHOASTK40ZNF384
CCND3E2F3FRS2IKZF2MEN1*PDK1RHOBSUFU*ZNF703
CCNE1EBF1FUBP1IKZF3MERTKPDPK1RHPN2SUSD2ZNF750
CCR2ECT2LFUSIL10MET*PDS5BRICTORSUZ12ZNRF3
CCR4EEDFYNIL2MGAPGBD5RINT1SYKZRANB3
CCR5EEF1A1GAB1IL2RBMGMTPGRRIT1TAF15ZRSR2

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

Patient-matched blood/saliva specimen is required as a normal comparator. Genomic DNA is extracted from FFPE tumor tissue and normal comparator sample. DNA undergoes enzymatic fragmentation, library preparation, and target enrichment. The resulting sample libraries are sequenced by the Illumina NovaSeq 6000 sequencer. The sequencing data is processed by the UCLA Molecular Diagnostic Labs’ Analysis Pipeline (PCPDx v2.0.0) for primary and secondary analyses against reference genome GRCh38 (hg38). Manual assessment of technical accuracy and reportability of each variant is performed 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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