GatorSeq NGS Panel

Additional Information:

UFHPL Epic order code: LAB5622
The GatorSeq NGS Panel is a hybridization capture-based next-generation targeted sequencing assay for deep sequencing of 718 key cancer genes. Tumor samples are macrodissected to increase tumor cell percentage in the analyzed sample and sequenced on an Illumina NovaSeq 6000 to high-uniform depth (targeting 500X coverage by non-polymerase chain reaction- (PCR) duplicate read pairs, with more than 99 percent of exons at coverage greater than 100X). Sequence data are processed using a customized analysis pipeline that is designed to accurately detect base substitutions and insertions/deletions. Copy number variations are also detectable in a subset of genes. Annotated reports are generated using variant analysis software and databases and each report is reviewed by a qualified pathologist.

The entire coding sequences of the following genes are covered by this assay:

ABCB1 AXL DEK ERBB3 HDAC6 IGF2 MYB NTHL1 RHEB SETBP1 XIAP
ABL1 B2M DICER1 ERBB4 HGF IGF2R MYBL1 NTRK1 RHOA SETD2 XPA
ABL2 BAP1 DIS3 ERCC1 HIF1A IKBKB MYBL1 NTRK2 RICTOR SF1 XPC
ABRAXAS1 BARD1 DKC1 ERCC2 HIST1H1C IKBKE MYC NTRK3 RINT1 SF3A1 XPO1
ACD BBC3 DNAJB1 ERCC3 HIST1H1E IKZF1 MYCL NUP214 RIPK1 SF3B1 XRCC1
ACVR1 BCL10 DNM2 ERCC4 HIST1H2BD IKZF2 MYCN NUP93 RIT1 SGK1 XRCC2
ACVR1B BCL11B DNMT1 ERCC5 HIST1H3A IKZF3 MYD88 NUTM1 RNF43 SH2B3 XRCC3
ADA BCL2 DNMT3A ERCC6 HIST1H3B IL10 MYH11 P2RY8 ROS1 SH2D1A YAP1
AK2 BCL2L1 DNMT3B ERG HIST1H3C IL2RG MYH9 PAK1 RPA1 SHQ1 YES1
AKT1 BCL2L11 DOT1L ERRFI1 HIST1H3D IL7R MYOD1 PAK3 RPN1 SLIT2 YWHAE
AKT2 BCL2L2 E2F3 ESR1 HIST1H3E INHBA NAB2 PAK7 RPS15 SLX4 ZBTB2
AKT3 BCL6 EBF1 ETNK1 HIST1H3G INPP4A NBN PALB2 RPS20 SMAD2 ZFHX3
ALK BCL7A EED ETS1 HIST1H3H INPP4B NCOA2 PARP1 RPS6KA4 SMAD3 ZFHX4
ALOX12B BCOR EFNB2 ETV1 HIST1H3I INSR NCOA3 PAX3 RPS6KB1 SMAD4 ZMYM3
AMER1 BCORL1 EGFL7 ETV4 HIST1H3J IRF2 NCOR1 PAX5 RPS6KB2 SMARCA2 ZNF217
ANKRD26 BCR EGFR ETV5 HLA-A IRF4 NF1 PAX7 RPTOR SMARCA4 ZNF703
APC BIRC2 EGLN1 ETV6 HLA-B IRF8 NF2 PAX8 RRAGC SMARCB1 ZNF750
APOB BIRC3 EGR2 EWSR1 HLA-DRB1 IRS1 NFE2 PBRM1 RSPO2 SMARCD1 ZRSR2
AR BLM EIF1AX EXO1 HMGA2 IRS2 NFE2L2 PDCD1 RSPO3 SMC1A
ARAF BMPR1A EIF4A2 EXT1 HNF1A ITK NFKBIA PDCD1LG2 RTEL1 SMC3
ARFRP1 BRAF EIF4E EXT2 HNRNPK ITPKB NFKBIE PDGFB RUNX1 SMO
ARID1A BRCA1 ELANE EZH2 HOXA11 JAGN1 NHP2 PDGFRA RUNX1T1 SNCAIP
ARID1B BRCA2 ELOC FANCA HOXA9 JAK1 NKX2-1 PDGFRB RYBP SOCS1
ARID2 BRCC3 EML4 FANCB HOXB13 JAK2 NKX3-1 PDK1 S1PR2 SOS1
ARID5B BRD3 EP300 FANCC HRAS JAK3 NOP10 PDPK1 SAMD9 SOX10
ASXL1 BRD4 EPAS1 FANCD2 HSD3B1 JAZF1 NOTCH1 PGR SAMD9L SOX17
ASXL2 BRINP3 EPCAM FANCE HSP90AA1 JUN NOTCH2 PHF6 SAMHD1 SOX2
ATM BRIP1 EPHA3 FANCF HSP90AB1 KAT6A NOTCH3 PHOX2B SBDS SOX9
ATR BTG1 EPHA5 FANCG ICOSLG KDM5A NOTCH4 PIGA SBF2 SPEN
ATRX BTG2 EPHA7 FANCI ID3 KDM5C NPM1 PIK3C2B SDHA SPOP
AURKA BTK EPHB1 FANCL IDH1 KDM6A NR0B1 PIK3C2G SDHAF2 SPTA1
AURKB BUB1B EPHB4 FANCM IDH2 KDR NRAS PIK3C3 SDHB SRC
AURKC C11ORF30 EPHB4 FAS IFNGR1 KEAP1 NRG1 PIK3CA SDHC SRSF2
AXIN1 C11ORF95 EPOR FAT1 IGF1 KEL NSD1 PIK3CB SDHD SS18
AXIN2 CALR ERBB2 FAT3 IGF1R KIF1B NT5C2 PIK3CD SEC23B STAG1
CARD11 CDKN2C FBXO11 G6PC3 KIF23 MAP3K14 PIK3CG PTCH1 STAG2 TLR2
CASP8 CEBPA FBXW2 GABRA6 KIF5B MAP3K3 PIK3R1 PTEN STAT3 TLR4
CBFB CHD2 FBXW7 GALNT12 KIT MAP3K7 PIK3R2 PTK2 STAT4 TMEM127
CBL CHD4 FGF1 GATA1 KLF1 MAPK1 PIK3R3 PTPN11 STAT5A TMPRSS2
CBLB CHEK1 FGF10 GATA2 KLF2 MAPK3 PIM1 PTPRD STAT5B TNFAIP3
CBLC CHEK2 FGF14 GATA3 KLF4 MAX PLAG1 PTPRO STAT6 TNFRSF14
CCN6 CIC FGF19 GATA4 KLHL6 MCL1 PLCG1 PTPRS STK11 TNFRSF1A
CCND1 CIITA FGF2 GATA6 KLLN MDC1 PLCG2 PTPRT STK40 TOP1
CCND2 COL1A1 FGF23 GEN1 KMT2A MDM2 PLK2 QKI SUFU TOP2A
CCND3 COP1 FGF3 GFI1 KMT2B MDM4 PMAIP1 RAB35 SUZ12 TP53
CCNE1 CREBBP FGF4 GID4 KMT2C MECOM PML RAC1 SYK TP53BP1
CD19 CRKL FGF5 GLI1 KMT2D MED12 PMS1 RAD21 TAF1 TP63
CD22 CRLF2 FGF6 GLI2 KRAS MEF2B PMS2 RAD50 TAL1 TPMT
CD274 CSF1 FGF7 GNA11 LAMP1 MEN1 PNRC1 RAD51 TBL1XR1 TRAF2
CD276 CSF1R FGF8 GNA13 LATS1 MERTK POLD1 RAD51B TBP TRAF3
CD28 CSF3 FGF9 GNAI2 LATS2 MET POLE RAD51C TBX3 TRAF7
CD40 CSF3R FGFR1 GNAQ LDLR MGA POLH RAD51D TBXT TRIM27
CD58 CSNK1A1 FGFR2 GNAS LIFR MITF POLR2A RAD52 TCF12 TSC1
CD70 CTC1 FGFR3 GNB1 LIG4 MLH1 POT1 RAD54B TCF3 TSC2
CD74 CTCF FGFR4 GPC3 LMO1 MLH3 PPARG RAD54L TCF7L2 TSHR
CD79A CTLA4 FH GPR124 LRP1B MLLT10 PPM1D RAF1 TCIRG1 TYK2
CD79B CTNNA1 FLCN GPS2 LTK MLLT3 PPP2R1A RANBP2 TEK U2AF1
CDAN1 CTNNB1 FLI1 GREM1 LYN MN1 PPP2R2A RARA TEK U2AF2
CDC73 CUL3 FLT1 GRIN2A LYST MN1 PPP6C RASA1 TENT5C UBR5
CDH1 CUX1 FLT3 GRM3 LZTR1 MPL PRDM1 RASA1 TERC USP6
CDIN1 CXCR4 FLT4 GSK3B MAF MRE11 PREX2 RB1 TERF1 VAV1
CDK12 CYLD FOXA1 GUSB MAGI2 MRTFA PRKAR1A RBBP6 TERF2 VEGFA
CDK4 DAXX FOXL2 H2AX MALT1 MSH2 PRKCI RBM10 TERT VHL
CDK6 DCUN1D1 FOXO1 H3-3A MAML1 MSH3 PRKDC RBM15 TET1 VTCN1
CDK8 DDB2 FOXP1 H3-3B MAML2 MSH6 PRKN RBM8A TET2 WAS
CDKN1A DDR1 FOXR2 H3-3C MAP2K1 MST1 PRPF40B RECQL TFE3 WEE1
CDKN1B DDR2 FRS2 HAX1 MAP2K2 MST1R PRPF8 RECQL4 TFEB WHSC1
CDKN1C DDX11 FUBP1 HDAC1 MAP2K4 MTAP PRPS1 REL TFRC WHSC1L1
CDKN2A DDX3X FUS HDAC2 MAP3K1 MTOR PRSS1 RELA TGFBR1 WRN
CDKN2B DDX41 FYN HDAC4 MAP3K13 MUTYH PRSS8 RET TGFBR2 WT1

Genes tested for copy number alterations: ALK, ATM, ATRX, BAP1, BRAF, BRCA1, BRCA2, CCND1, CCND3, CCNE1, CDK4, CDK6, CDKN2A, CDKN2B, CHEK1, CIC, CTNNB1, EGFR, ERBB2, ERBB3, ESR1, FGF10, FGF14, FGF19, FGF23, FGF3, FGF4, FGF6, FGFR1, FGFR2, FGFR3, FGFR4, FUBP1, HRAS, IDH2, JAK2, KIT, KRAS, MDM2, MDM4, MET, MTAP, MYC, MYCN, NF1, NF2, NRAS, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PTCH1, PTEN, RAF1, RB1, RET, RICTOR, SETD2, SMO, TERT, TFEB, TP53

Specimen Requirements:

Acceptable sample type: The samples should be specifically chosen by a pathologist to include at least 5 % tumor cells without significant necrosis or inflammation. The following types of samples are accepted:

a. FFPE (formalin fixed, paraffin embedded) block
b. Unstained slides (USS) from FFPE
c. Bone marrow aspirate
d. Peripheral blood
Formalin Fixed Parafin Embedded (FFPE) specimens
Must be accompanied by 1 corresponding H&E from the same block with the tumor circled by a qualified pathologist AND the estimated percentage of tumor cells present in the circled area(s).
1. Circle the area(s) on the H&E slide where tumor cells are present with a marking pen.
2. Write the percent tumor on the H&E slide with a marking pen.

Unstained Slides (USS) prepared from FFPE specimens
For 10mmx10mm sized tissue or larger, send 10 USS. For smaller tissues, send 20 USS
Must be accompanied by 1 corresponding H&E from the same block with the tumor circled by a qualified pathologist AND the estimated percentage of tumor cells present in the circled area(s).
1. Circle the area(s) on the H&E slide where tumor cells are present with a marking pen.
2. Write the percent tumor on the H&E slide with a marking pen.

Bone marrow aspirate or Peripheral blood
Container/Tube: Lavender top (EDTA)
Specimen Volume: 3mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot. Do not freeze or centrifuge.
Specimen Stability Information: Ambient 24 Hours/ Refrigerated 1 Week/ Frozen Unacceptable
Transport to the laboratory as soon as possible for testing.

Unacceptable conditions:
Tissues that are not fixed in 10% formalin, or has been fixed for longer than 3 days in 10% formalin.
Clotted or frozen blood.
Specimens received beyond recommended stability.
Less than the minimum volume requirements for blood collection.
Failure to indicate tumor and/or percent tumor will result in delayed specimen processing or specimen rejection.
Tumor percent cannot be zero (0) or unknown.
A percent tumor of less than 5 will be reviewed on a case by case basis by the director of molecular pathology.”

Use:

This test is used to determine a prognosis and/or treatment options for individuals with cancer at initial diagnosis or with refractory disease. This assay is intended to detect somatic alterations present in tumor cells and should not be used to determine the presence or absence of germline alterations.

Reported:

10 – 14 days

Reference Range:

No variants detected.