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Tumour Profiling Services from Caris Molecular Intelligence®

Multi-platform, solid tumour biomarker analysis for therapeutic decision support.

  • Chemotherapy
  • Immunotherapy
  • Targeted Therapy
  • Protein Expression via IHC
  • DNA Analysis via Pyro Sequencing
  • DNA/RNA Analysis via Fragment Analysis
  • Molecular Analysis via Next-Generation Sequencing: 592 Genes
  • Clinical Trial Opportunities

Technical Specifications

Sufficient tumour must be present to complete all analysis.

Technical Information IHC CISH FISH
Sample Requirements

(see requsition for full details)

1 unstained slide at 4μm thickness from FFPE block, with evaluable tumour present, per IHC test 1 unstained slide at 4μm thickness from FFPE block, with at least 20-100 evaluable tumour cells present, per CISH test 2 unstained slides at 4μm thickness from FFPE block, with at least 100 evaluable cells present and 10% tumour, per FISH test
Sensitivity/Specificity >95% >95% >95%
Technical Information Next-Generation Sequencing
Mutations and Copy Number Variations (DNA) Fusions (RNA)
Sample Requirements FFPE block or 15 unstained slides with a minimum of 20% malignant origin. Needle biopsy is also acceptable (4-6 cores). FFPE block or 2-5 unstained slides with a minimum of 20% malignant origin. Needle biopsy is also acceptable (4-6 cores).
Tumour Enrichment Microdissection performed on all cases resulting in ~25% increase in tumour nuclei and enhances detection of minor clonal variants
Amount of DNA Required 200ng input (50ng)
PPV > 99% > 98%
Sensitivity > 99% for base substitutions at ≥ 5% mutant allele frequency;
> 99% for indels at ≥ 5% mutant allele frequency;
> 95% for copy number variations (amplifications ≥ 8 copies)
> 91%
Average Depth of Coverage (DNA) Average Depth/Count (RNA) > 750X > 30,000 Unique RNA Fragments
Number of Genes 592 genes 10 genes

 

Caris Molecular Intelligence® Associations List

The list below details the biomarkers assessed, technology platforms utilised and associated therapies or clinical trials. Biomarkers and therapy associations may vary by the tumour type submitted.

Individual assay results are always included with the final report.

Agent Biomarker Platform
afatinib
(assoc. in NSCLC only)
EGFR NGS Mutation
ERBB2 (Her2) NGS Mutation
afatinib + cetuximab
(combination assoc. in NSCLC only)
EGFR T790M NGS Mutation
alectinib, ceritinib ALK IHC; NGS Fusion Analysis (RNA)
aspirin
(assoc. in CRC only)
PIK3CA NGS Mutation
atezolizumab
(assoc. in NSCLC only)
PD-L1 IHC
cabozantinib RET NGS Fusion Analysis (RNA)
capecitabine, fluorouracil, pemetrexed TS IHC
carboplatin, cisplatin, oxaliplatin ATM NGS Mutation
BRCA11 NGS Mutation
BRCA21 NGS Mutation
ERCC1 IHC
cetuximab, panitumumab2
(assoc. in CRC only)
BRAF NGS Mutation
KRAS NGS Mutation
NRAS NGS Mutation
PIK3CA NGS Mutation
PTEN IHC
cetuximab EGFR NGS CNV
crizotinib ALK IHC; NGS Mutation (DNA) & Fusion Analysis (RNA)
cMET NGS Mutation, CNV (DNA)
ROS1 NGS Fusion Analysis (RNA)
dabrafenib, vemurafenib2 BRAF NGS Mutation
dacarbazine, temozolomide MGMT IHC
MGMT-Methylation Pyrosequencing
IDH1 (assoc. in High Grade Glioma only) NGS
docetaxel, paclitaxel, nab-paclitaxel TUBB3 IHC
doxorubicin,liposomal-doxorubicin, epirubicin TOP2A IHC
CISH
enzalutamide, bicalutamide AR
(assoc. in TNBC only)
IHC
erlotinib, gefitinib
(assoc. in NSCLC only)
EGFR NGS Mutation
KRAS NGS Mutation
PIK3CA NGS Mutation
cMET NGS CNV (DNA)
PTEN IHC
everolimus, temsirolimus ER
(assoc. in Breast only)
IHC
PIK3CA
(excluding CRC)
NGS Mutation
exemestane + everolimus, fulvestrant, pabociclib combination therapy ER IHC
ESR1 NGS Mutation
gemcitabine RRM1 IHC
hormone therapies3 AR IHC
ER IHC
PR IHC
imatinib cKIT NGS Mutation
PDGFRA NGS Mutation
irinotecan TOPO1 IHC
topotecan
(excluding Breast, CRC, NSCLC)
lapatinib, pertuzumab, T-DM1 Her2/Neu NGS CNV (DNA)
mitomycin-c BRCA11 NGS Mutation
BRCA21
nivolumab, pembrolizumab
(assoc. in Bladder, Kidney, Melanoma, NSCLC only)
PD-L1 IHC
MSI
(pembrolizumab only)
FA
olaparib ATM
(assoc. in Prostate only)
NGS Mutation
BRCA11
BRCA21
osimertinib
(assoc. in NSCLC only)
EGFR T790M NGS Mutation
palbociclib
(assoc. in Breast only)
ER IHC
Her2/Neu IHC
sunitinib
(assoc. in GIST only)
cKIT NGS
trametinib2
(assoc. in Melanoma only)
BRAF NGS
trastuzumab ERBB2 (Her2)
(assoc. in NSCLC only)
NGS
Her2/Neu IHC; NGS CNV (DNA)
PTEN
(assoc. in Breast only)
IHC
PIK3CA
(assoc. in Breast only)
NGS Mutation
vandetanib RET NGS Mutation (DNA) & Fusion Analysis (RNA)

IHC: Immunohistochemistry CISH: Chromogenic in situ Hybridization FA: Fragment Analysis
NGS: Next-Generation Sequencing CNV: Copy Number Variation by NGS FUS: Fusion Analysis by NGS

Note: Biomarkers listed above may also be assessed for clinical trial opportunities and may include clinical trials associations.

1 May not be available for Medicare patients. Medicare reimburses BRCA1-2 for breast and ovarian cases only.
2 In CRC, cetuximab/panitumumab, vemurafenib/dabrafenib, and trametinib may be reported in combination.
3 Hormone therapies may include: tamoxifen, toremifene, fulvestrant, letrozole, anastrozole, exemestane, megestrol acetate, leuprolide, goserelin, bicalutamide, flutamide, abiraterone, enzalutamide, triptorelin, abarelix, degarelix.

Biomarker Analysis by Tumour Type

The information below details the biomarkers analyzed by technology for the tumour type submitted. Tests may vary if insufficient tumour samples are submitted.

MI Profile™
Tumour Type Immunohistochemistry (IHC) Next-Generation Sequencing (NGS)

(see below for gene list)

Other
Bladder ERCC1, PD-L1, RRM1, TOP2A, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Breast AR, ER, ERCC1, Her2/Neu, PD-L1, PR, PTEN, TOPO1, TRKA/B/C (NTRK), TS Mutation, CNV Analysis (DNA) TOP2A (Chromogenic in situ Hybridization)
Cancer of Unknown Primary ERCC1, PD-L1, RRM1, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Cervix ER, ERCC1, PD-L1, PR, RRM1, TOP2A, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Cholangiocarcinoma/ Hepatobiliary ERCC1, Her2/Neu, PD-L1, RRM1, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Colorectal ERCC1, MLH1, MSH2, MSH6, PD-L1, PMS2, PTEN, TOPO1, TRKA/B/C (NTRK), TS Mutation, CNV Analysis (DNA) MSI1 (Fragment Analysis)
Endometrial ER, ERCC1, MLH1, MSH2, MSH6, PMS2, PR, PD-L1, PTEN, RRM1, TOP2A, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA) MSI1 (Fragment Analysis)
Gastric ERCC1, Her2/Neu, PD-L1, TOP2A, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
GIST PD-L1, PTEN, TRKA/B/C (NTRK) Mutation, CNV Analysis (DNA)
Glioma ERCC1, PD-L1, TOPO1 Mutation, CNV (DNA); Fusion Analysis (RNA) MGMT Methylation

(Pyrosequencing)

Head & Neck ERCC1, PD-L1, RRM1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Kidney ERCC1, PD-L1, RRM1, TOP2A, TRKA/B/C (NTRK), TUBB3 Mutation, CNV Analysis (DNA)
Melanoma ERCC1, MGMT, PD-L1, TRKA/B/C (NTRK), TUBB3 Mutation, CNV Analysis (DNA)
Neuroendocrine/ Small Cell Lung ERCC1, PD-L1, MGMT, TOP2A, TS Mutation, CNV Analysis (DNA)
Non-Small Cell Lung ALK, ERCC1, PD-L1, PTEN, RRM1, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV (DNA); Fusion Analysis (RNA)
Ovarian ER, ERCC1, PD-L1, PR, RRM1, TOP2A, TOPO1, TRKA/B/C (NTRK), TUBB3 Mutation, CNV Analysis (DNA)
Pancreatic ERCC1, MLH1, MSH2, MSH6, PD-L1, PMS2, RRM1, TOPO1, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)
Prostate AR, ERCC1, PD-L1, TRKA/B/C (NTRK), TUBB3 Mutation, CNV Analysis (DNA)
Sarcoma ERCC1, MGMT, PD-L1, RRM1, TOP2A, TOPO1, TRKA/B/C (NTRK), TUBB3 Mutation, CNV Analysis (DNA)
Thyroid ERCC1, PD-L1, TOP2A, TRKA/B/C (NTRK) Mutation, CNV Analysis (DNA)
Other Tumours ERCC1, PD-L1, RRM1, TOP2A, TRKA/B/C (NTRK), TS, TUBB3 Mutation, CNV Analysis (DNA)

In certain instances, some biomarkers included in MI Profile or genes ordered individually will not associate with commercially available cancer therapies or clinical trials. For PD-L1 IHC testing, Dako antibody 22c3 is available upon request.

1 If MSI is ordered and the tumour percentage is 20-49% or MSI testing is not possible, MMR IHCs (MLH1, MSH2, MSH6, PMS2) will be performed.

Next-Generation Sequencing Expanded NGS Gene List

Mutations (DNA)
ABI1 CEBPA GPC3 KLF4 NUTM2B SFPQ
ABL1 CHCHD7 HEY1 KLK2 OLIG2 SLC45A3
ACKR3 CNOT3 HIST1H3B LASP1 OMD SMARCA4
AKT1 COL1A1 HIST1H4I LMO1 P2RY8 SOCS1
AMER1 (FAM123B) COX6C HLF LMO2 PAFAH1B2 SOX2
AR CRLF2 HMGN2P46 MAFB PAK3 SPOP
ARAF DDB2 HNF1A MAX PATZ1 SRC
ATP2B3 DDIT3 HOXA11 MECOM PAX8 SSX1
ATRX DNM2 HOXA13 MED12 PDE4DIP STAG2
BCL11B DNMT3A HOXA9 MKL1 PHF6 TAL1
BCL2 EIF4A2 HOXC11 MLLT11 PHOX2B TAL2
BCL2L2 ELF4 HOXC13 MN1 PIK3CG TBL1XR1
BCOR ELN HOXD11 MPL PLAG1 TCEA1
BCORL1 ERCC1 HOXD13 MSN PMS1 TCL1A
BRD3 ETV4 HRAS MTCP1 POU5F1 TERT
BRD4 FAM46C IKBKE MUC1 PPP2R1A TFE3
BTG1 FANCF INHBA MUTYH PRF1 TFPT
BTK FEV IRS2 MYCL (MYCL1) PRKDC THRAP3
C15orf65 FOXL2 JUN NBN RAD21 TLX3
CBLC FOXO3 KAT6A (MYST3) NDRG1 RECQL4 TMPRSS2
CD79B FOXO4 KAT6B NKX2-1 RHOH UBR5
CDH1 FSTL3 KCNJ5 NONO RNF213 VHL
CDK12 GATA1 KDM5C NOTCH1 RPL10 WAS
CDKN2B GATA2 KDM6A NRAS SEPT5 ZBTB16
CDKN2C GNA11 KDSR NUMA1 SEPT6 ZRSR2
Mutations and Copy Number Variations (DNA)
ABL2 CDK8 FAS KLHL6 PAX3 SMAD2
ACSL3 CDKN1B FBXO11 KMT2A (MLL) PAX5 SMAD4
ACSL6 CDKN2A FBXW7 KMT2C (MLL3) PAX7 SMARCB1
AFF1 CDX2 FCRL4 KMT2D (MLL2) PBRM1 SMARCE1
AFF3 CHEK1 FGF10 KRAS PBX1 SMO
AFF4 CHEK2 FGF14 KTN1 PCM1 SNX29
AKAP9 CHIC2 FGF19 LCK PCSK7 SOX10
AKT2 CHN1 FGF23 LCP1 PDCD1 (PD1) SPECC1
AKT3 CIC FGF3 LGR5 PDCD1LG2 (PDL2) SPEN
ALDH2 CIITA FGF4 LHFP PDGFB SRGAP3
ALK CLP1 FGF6 LIFR PDGFRA SRSF2
APC CLTC FGFR1 LPP PDGFRB SRSF3
ARFRP1 CLTCL1 FGFR1OP LRIG3 PDK1 SS18
ARHGAP26 CNBP FGFR2 LRP1B PER1 SS18L1
ARHGEF12 CNTRL FGFR3 LYL1 PICALM STAT3
ARID1A COPB1 FGFR4 MAF PIK3CA STAT4
ARID2 CREB1 FH MALT1 PIK3R1 STAT5B
ARNT CREB3L1 FHIT MAML2 PIK3R2 STIL
ASPSCR1 CREB3L2 FIP1L1 MAP2K1 PIM1 STK11
ASXL1 CREBBP FLCN MAP2K2 PML SUFU
ATF1 CRKL FLI1 MAP2K4 PMS2 SUZ12
ATIC CRTC1 FLT1 MAP3K1 POLE SYK
ATM CRTC3 FLT3 MCL1 POT1 TAF15
ATP1A1 CSF1R FLT4 MDM2 POU2AF1 TCF12
ATR CSF3R FNBP1 MDM4 PPARG TCF3
AURKA CTCF FOXA1 MDS2 PRCC TCF7L2
AURKB CTLA4 FOXO1 MEF2B PRDM1 TET1
AXIN1 CTNNA1 FOXP1 MEN1 PRDM16 TET2
AXL CTNNB1 FUBP1 MET (cMET) PRKAR1A TFEB
BAP1 CYLD FUS MITF PRRX1 TFG
BARD1 CYP2D6 GAS7 MLF1 PSIP1 TFRC
BCL10 DAXX GATA3 MLH1 PTCH1 TGFBR2
BCL11A DDR2 GID4 (C17orf39) MLLT1 PTEN TLX1
BCL2L11 DDX10 GMPS MLLT10 PTPN11 TNFAIP3
BCL3 DDX5 GNA13 MLLT3 PTPRC TNFRSF14
BCL6 DDX6 GNAQ MLLT4 RABEP1 TNFRSF17
BCL7A DEK GNAS MLLT6 RAC1 TOP1
BCL9 DICER1 GOLGA5 MNX1 RAD50 TP53
BCR DOT1L GOPC MRE11A RAD51 TPM3
BIRC3 EBF1 GPHN MSH2 RAD51B TPM4
BLM ECT2L GPR124 MSH6 RAF1 TPR
BMPR1A EGFR GRIN2A MSI2 RALGDS TRAF7
BRAF ELK4 GSK3B MTOR RANBP17 TRIM26
BRCA11 ELL H3F3A MYB RAP1GDS1 TRIM27
BRCA21 EML4 H3F3B MYC RARA TRIM33
BRIP1 EP300 HERPUD1 MYCN RB1 TRIP11
BUB1B EPHA3 HGF MYD88 RBM15 TRRAP
C11orf30 (EMSY) EPHA5 HIP1 MYH11 REL TSC1
C2orf44 EPHB1 HMGA1 MYH9 RET TSC2
CACNA1D EPS15 HMGA2 NACA RICTOR TSHR
CALR ERBB2 (HER2) HNRNPA2B1 NCKIPSD RMI2 TTL
CAMTA1 ERBB3 (HER3) HOOK3 NCOA1 RNF43 U2AF1
CANT1 ERBB4 (HER4) HSP90AA1 NCOA2 ROS1 USP6
CARD11 ERC1 HSP90AB1 NCOA4 RPL22 VEGFA
CARS ERCC2 IDH1 NF1 RPL5 VEGFB
CASC5 ERCC3 IDH2 NF2 RPN1 VTI1A
CASP8 ERCC4 IGF1R NFE2L2 RPTOR WHSC1
CBFA2T3 ERCC5 IKZF1 NFIB RUNX1 WHSC1L1
CBFB ERG IL2 NFKB2 RUNX1T1 WIF1
CBL ESR1 IL21R NFKBIA SBDS WISP3
CBLB ETV1 IL6ST NIN SDC4 WRN
CCDC6 ETV5 IL7R NOTCH2 SDHAF2 WT1
CCNB1IP1 ETV6 IRF4 NPM1 SDHB WWTR1
CCND1 EWSR1 ITK NR4A3 SDHC XPA
CCND2 EXT1 JAK1 NSD1 SDHD XPC
CCND3 EXT2 JAK2 NT5C2 SEPT9 XPO1
CCNE1 EZH2 JAK3 NTRK1 SET YWHAE
CD274 (PDL1) EZR JAZF1 NTRK2 SETBP1 ZMYM2
CD74 FANCA KDM5A NTRK3 SETD2 ZNF217
CD79A FANCC KDR (VEGFR2) NUP214 SF3B1 ZNF331
CDC73 FANCD2 KEAP1 NUP93 SH2B3 ZNF384
CDH11 FANCE KIAA1549 NUP98 SH3GL1 ZNF521
CDK4 FANCG KIF5B NUTM1 SLC34A2 ZNF703
CDK6 FANCL KIT PALB2

1 May not be available for Medicare patients. Medicare reimburses BRCA1-2 for breast and ovarian cases only.

Gene Fusions (RNA)
ALK NTRK1 NTRK3 RET ROS1 RSPO3
BRAF NTRK2

 

Variant Transcripts (RNA)
EGFR vIII MET Exon 14 Skipping

 

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