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Comprehensive Tumour Profiling from Caris Molecular Intelligence®

The Caris Molecular Intelligence® comprehensive tumour profiling approach to assess DNA, RNA and proteins reveals a molecular blueprint to guide more precise and individualised treatment decisions from among 60+ FDA-approved therapies.

Comprehensive tumour profiling

Technical Specifications

Sufficient tumour content (>20% tumour nuclei) must be present to complete all analysis. If you have any questions, please contact our AUS/NZ distributor Precision Oncology on +61 8 6245 2020.

Technical InformationIHCCISHFISH
Sample Requirements

(see requsition for full details)

1 unstained slide at 4μm thickness from FFPE block, with evaluable tumour present, per IHC test1 unstained slide at 4μm thickness from FFPE block, with at least 100 evaluable tumour cells present, per CISH test2 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 InformationNext-Generation Sequencing (DNA)Whole Transcriptome Sequencing (RNA)
Sample RequirementsFFPE block or 10 unstained slides with a minimum of 20% malignant origin for DNA and 10% malignant origin for RNA. Needle biopsy is also acceptable (4-6 cores).
Tumour Enrichment
(when necessary)
Microdissection to isolate and increase the number of cancer cells to improve test performance and increase the chance for successful testing from small tumour samples.
Number of Genes592 genes~22,000 genes
Average Depth of Coverage (DNA) Average Read Count (RNA)> 750X60 million
Positive Percent Agreement (PPA)> 95% for base substitutions at ≥ 5% mutant allele frequency;
> 95% for indels at ≥ 5% mutant allele frequency;
> 90% for copy number variations (amplifications ≥ 6 copies)
> 97%
Negative Percent Agreement (NPA)> 99%> 99%
Genomic SignaturesMicrosatellite Instability (MSI),
Tumour Mutational Burden (TMB)

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. The current and definitive list menu can be found online at www.CarisMolecularIntelligence.com/profiling-menu. Individual assay results are always included with the final report.

BiomarkerTechnologyAgent
ALKIHC, WTS Fusioncrizotinib, ceritinib, alectinib, brigatinib (NSCLC only)
NGS Mutationresistance to crizotinib
ARIHCbicalutamide, leuprolide (salivary gland tumours only)
enzalutamide, bicalutamide (TNBC only)
ATMNGS Mutationcarboplatin, cisplatin, oxaliplatin
olaparib (prostate only)
BRAFNGS Mutationvemurafenib, dabrafenib, cobimetinib, trametinib
vemurafenib +(cetuximab or panitumumab)+irinotecan (CRC only)
encorafenib + binimetinib (melanoma only)
dabrafenib+trametinib (anaplastic thyroid and NSCLC only)
cetuximab, panitumumab with BRAF and or MEK inhibitors (CRC only)
BRCA1/2NGS Mutationcarboplatin, cisplatin, oxaliplatin
olaparib, niraparib (ovarian only), rucaparib (ovarian only), talazoparib (breast only)
resistance to olaparib, niraparib, rucaparib with reversion mutation
EGFRNGS Mutationafatinib (NSCLC only)
afatinib + cetuximab (T790M; NSCLC only)
erlotinib, gefitinib (NSCLC and CUP only)
osimertinib, dacomitinib (NSCLC only)
ERIHCendocrine therapies
everolimus, temsirolimus (breast only)
palbociclib, ribociclib, abemaciclib (breast only)
ERBB2 (HER2)IHC, CISH, NGS CNAtrastuzumab, lapatinib, neratinib (breast only), pertuzumab, T-DM1
NGS MutationT-DM1 (NSCLC only)
ESR1NGS Mutationexemestane + everolimus, fulvestrant, palbociclib combination therapy (breast only)
resistance to aromatase inhibitors (breast only)
FGFR2/3NGS Mutation, WTS Fusionerdafitinib (urothelial bladder only)
IDH1NGS Mutationtemozolomide (high grade glioma only)
KITNGS Mutationimatinib
regorafenib, sunitinib (both GIST only)
KRASNGS Mutationresistance to cetuximab, panitumumab (CRC only)
resistance to erlotinib/gefitinib (NSCLC only)
METWTS Exon Skippingcabozantinib (NSCLC only)
WTS Exon Skipping, CNA, NGS Exon
Skipping
crizotinib (NSCLC only)
MGMTPyrosequencing (Methylation)temozolomide (high grade glioma only)
MMR DeficiencyIHC, NGSpembrolizumab
MSInivolumab, nivolumab+ipilimumab (CRC only)
MMR ProficiencyIHC, NGSpembrolizumab + lenvatinib (endometrial only)
MSS
NRASNGS Mutationresistance to cetuximab, panitumumab (CRC only)
NTRK1/2/3WTS Fusionlarotrectinib
NGS Mutationresistance to larotrectinib
PDGFRANGS Mutationimatinib
PD-L1IHCpembrolizumab (22c3 TPS in NSCLC; 22c3 CPS in cervical, GEJ/gastric, head & neck, urothelial, vulvar)
atezolizumab (NSCLC, non-urothelial bladder, SP142 IC urothelial)
atezolizumab + nab-paclitaxel (SP142 IC in TNBC only)
nivolumab (28-8 in melanoma)
avelumab (non-urothelial bladder and Merkel cell only)
PIK3CANGS Mutationalpelisib + fulvestrant (breast only)
PRIHCendocrine therapies
RETWTS Fusioncabozantinib
NGS Mutation, WTS Fusionvandetanib
ROS1WTS Fusioncrizotinib, ceritinib (NSCLC only)
TOP2ACISHdoxorubicin, liposomal doxorubicin, epirubicin (all breast only)

IHC: Immunohistochemistry     CISH: Chromogenic in situ Hybridization     NGS: Next-Generation Sequencing (DNA)     CNA: Copy Number Alteration (DNA)
WTS: Whole Transcriptome Sequencing (RNA)

Note: in certain instances, some biomarkers included in MI Profile or genes ordered individually will not associate with commercially available cancer therapies or clinical trials.

Biomarker Analysis by Tumour Type

The information below details the biomarkers analysed by technology for the tumour type submitted. Before ordering testing services, please refer to the profile menu online (www.CarisMolecularIntelligence.com/profiling-menu) to view the most up-to-date listing of biomarkers that will be performed. Tests may vary if insufficient tumour samples are submitted.

MI Profile™
Tumour TypeImmunohistochemistry (IHC)Next-Generation Sequencing (NGS)
(see below for gene list)
Whole Transcriptome Sequencing (WTS)
Other
DNAGenomic Signatures
RNA
BladderMMR, PD-L1 (SP142 and 22c3)Mutation, CNA AnalysisMSI, TMBFusion Analysis
BreastAR, ER, Her2/Neu, MMR,
PD-L1 (SP142), PR, PTEN
Mutation, CNA AnalysisMSI, TMBFusion AnalysisTOP2A (Chromogenic in situ Hybridization)
Cancer of Unknown Primary – FemaleAR, ER, Her2/Neu, MMR,
PD-L1 (SP142)
Mutation, CNA AnalysisMSI, TMBFusion Analysis
Cancer of Unknown Primary – MaleAR, Her2/Neu, MMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
CervicalER, MMR, PD-L1 (22c3), PRMutation, CNA AnalysisMSI, TMBFusion Analysis
Cholangiocarcinoma/ HepatobiliaryHer2/Neu, MMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion AnalysisHer2 (Chromogenic in situ Hybridization)
Colorectal and Small IntestinalHer2/Neu, MMR, PD-L1 (SP142),
PTEN
Mutation, CNA AnalysisMSI, TMBFusion Analysis
EndometrialER, MMR, PD-L1 (SP142), PR, PTENMutation, CNA AnalysisMSI, TMBFusion Analysis
Esophageal CancerHer2/Neu, MMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Gastric/GEJHer2/Neu, MMR, PD-L1 (22c3)Mutation, CNA AnalysisMSI, TMBFusion AnalysisHer2 (Chromogenic in situ Hybridization)
GISTMMR, PD-L1 (SP142), PTENMutation, CNA AnalysisMSI, TMBFusion Analysis
GliomaMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion AnalysisMGMT Methylation
(Pyrosequencing)
Head & NeckMMR, p16, PD-L1 (22c3)Mutation, CNA AnalysisMSI, TMBFusion AnalysisHPV (Chromogenic in situ
Hybridization), reflex to
confirm p16 result
KidneyMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
MelanomaMMR, PD-L1 (28-8)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Merkel CellMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Neuroendocrine/Small Cell LungMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Non-Small Cell LungALK, MMR, PD-L1 (22c3), PTENMutation, CNA AnalysisMSI, TMBFusion Analysis
OvarianER, MMR, PD-L1 (SP142), PRMutation, CNA AnalysisMSI, TMBFusion Analysis
PancreaticMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
ProstateAR, MMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Salivary GlandAR, Her2/Neu, MMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
SarcomaMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
ThyroidMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis
Uterine SerousER, Her2/Neu, MMR, PD-L1 (SP142),
PR, PTEN
Mutation, CNA AnalysisMSI, TMBFusion AnalysisHer2 (Chromogenic in situ Hybridization)
Vulvar Cancer (SCC)ER, MMR, PD-L1 (22c3), PRMutation, CNA AnalysisMSI, TMBFusion Analysis
Other TumoursMMR, PD-L1 (SP142)Mutation, CNA AnalysisMSI, TMBFusion Analysis

MMR = Mismatch Repair proteins: MLH1, MSH2, MSH6, PMS2

For PD-L1 IHC testing, the antibody tested is listed above. For non-urothelial bladder cancers, PD-L1 clones SP142 and 22c3 are performed.

Next-Generation Sequencing Gene List

Next-Generation Sequencing

Genomic Stability Testing (DNA)
Microsatellite Instability (MSI)Tumour Mutational Burden (TMB)
Point Mutations and Indels (DNA)
ABI1CEBPAGPC3KLF4NUTM2BSFPQ
ABL1CHCHD7HEY1KLK2OLIG2SLC45A3
ACKR3CNOT3HIST1H3BLASP1OMDSMARCA4
AKT1COL1A1HIST1H4ILMO1P2RY8SOCS1
AMER1 (FAM123B)COX6CHLFLMO2PAFAH1B2SOX2
ARCRLF2HMGN2P46MAFBPAK3SPOP
ARAFDDB2HNF1AMAXPATZ1SRC
ATP2B3DDIT3HOXA11MECOMPAX8SSX1
ATRXDNM2HOXA13MED12PDE4DIPSTAG2
BCL11BDNMT3AHOXA9MKL1PHF6TAL1
BCL2EIF4A2HOXC11MLLT11PHOX2BTAL2
BCL2L2ELF4HOXC13MN1PIK3CGTBL1XR1
BCORELNHOXD11MPLPLAG1TCEA1
BCORL1ERCC1HOXD13MSNPMS1TCL1A
BRD3ETV4HRASMTCP1POU5F1TERT
BRD4FAM46CIKBKEMUC1PPP2R1ATFE3
BTG1FANCFINHBAMUTYHPRF1TFPT
BTKFEVIRS2MYCL (MYCL1)PRKDCTHRAP3
C15orf65FOXL2JUNNBNRAD21TLX3
CBLCFOXO3KAT6A (MYST3)NDRG1RECQL4TMPRSS2
CD79BFOXO4KAT6BNKX2-1RHOHUBR5
CDH1FSTL3KCNJ5NONORNF213VHL
CDK12GATA1KDM5CNOTCH1RPL10WAS
CDKN2BGATA2KDM6ANRASSEPT5ZBTB16
CDKN2CGNA11KDSRNUMA1SEPT6ZRSR2
Point Mutations, Indels and Copy Number Alterations (DNA)
ABL2CDKN1BFASKMT2A (MLL)PALB2SLC34A2
ACSL3CDKN2AFBXO11KMT2C (MLL3)PAX3SMAD2
ACSL6CDX2FBXW7KMT2D (MLL2)PAX5SMAD4
ADGRA2CHEK1FCRL4KNL1PAX7SMARCB1
AFDNCHEK2FGF10KRASPBRM1SMARCE1
AFF1CHIC2FGF14KTN1PBX1SMO
AFF3CHN1FGF19LCKPCM1SNX29
AFF4CICFGF23LCP1PCSK7SOX10
AKAP9CIITAFGF3LGR5PDCD1 (PD1)SPECC1
AKT2CLP1FGF4LHFPL6PDCD1LG2 (PDL2)SPEN
AKT3CLTCFGF6LIFRPDGFBSRGAP3
ALDH2CLTCL1FGFR1LPPPDGFRASRSF2
ALKCNBPFGFR1OPLRIG3PDGFRBSRSF3
APCCNTRLFGFR2LRP1BPDK1SS18
ARFRP1COPB1FGFR3LYL1PER1SS18L1
ARHGAP26CREB1FGFR4MAFPICALMSTAT3
ARHGEF12CREB3L1FHMALT1PIK3CASTAT4
ARID1ACREB3L2FHITMAML2PIK3R1STAT5B
ARID2CREBBPFIP1L1MAP2K1 (MEK1)PIK3R2STIL
ARNTCRKLFLCNMAP2K2 (MEK2)PIM1STK11
ASPSCR1CRTC1FLI1MAP2K4PMLSUFU
ASXL1CRTC3FLT1MAP3K1PMS2SUZ12
ATF1CSF1RFLT3MCL1POLESYK
ATICCSF3RFLT4MDM2POT1TAF15
ATMCTCFFNBP1MDM4POU2AF1TCF12
ATP1A1CTLA4FOXA1MDS2PPARGTCF3
ATRCTNNA1FOXO1MEF2BPRCCTCF7L2
AURKACTNNB1FOXP1MEN1PRDM1TET1
AURKBCYLDFUBP1METPRDM16TET2
AXIN1CYP2D6FUSMITFPRKAR1ATFEB
AXLDAXXGAS7MLF1PRRX1TFG
BAP1DDR2GATA3MLH1PSIP1TFRC
BARD1DDX10GID4 (C17orf39)MLLT1PTCH1TGFBR2
BCL10DDX5GMPSMLLT10PTENTLX1
BCL11ADDX6GNA13MLLT3PTPN11TNFAIP3
BCL2L11DEKGNAQMLLT6PTPRCTNFRSF14
BCL3DICER1GNASMNX1RABEP1TNFRSF17
BCL6DOT1LGOLGA5MRE11RAC1TOP1
BCL7AEBF1GOPCMSH2RAD50TP53
BCL9ECT2LGPHNMSH6RAD51TPM3
BCREGFRGRIN2AMSI2RAD51BTPM4
BIRC3ELK4GSK3BMTORRAF1TPR
BLMELLH3F3AMYBRALGDSTRAF7
BMPR1AEML4H3F3BMYCRANBP17TRIM26
BRAFEMSYHERPUD1MYCNRAP1GDS1TRIM27
BRCA1EP300HGFMYD88RARATRIM33
BRCA2EPHA3HIP1MYH11RB1TRIP11
BRIP1EPHA5HMGA1MYH9RBM15TRRAP
BUB1BEPHB1HMGA2NACARELTSC1
CACNA1DEPS15HNRNPA2B1NCKIPSDRETTSC2
CALRERBB2 (HER2/NEU)HOOK3NCOA1RICTORTSHR
CAMTA1ERBB3 (HER3)HSP90AA1NCOA2RMI2TTL
CANT1ERBB4 (HER4)HSP90AB1NCOA4RNF43U2AF1
CARD11ERC1IDH1NF1ROS1USP6
CARSERCC2IDH2NF2RPL22VEGFA
CASP8ERCC3IGF1RNFE2L2RPL5VEGFB
CBFA2T3ERCC4IKZF1NFIBRPN1VTI1A
CBFBERCC5IL2NFKB2RPTORWDCP
CBLERGIL21RNFKBIARUNX1WIF1
CBLBESR1IL6STNINRUNX1T1WISP3
CCDC6ETV1IL7RNOTCH2SBDSWRN
CCNB1IP1ETV5IRF4NPM1SDC4WT1
CCND1ETV6ITKNR4A3SDHAF2WWTR1
CCND2EWSR1JAK1NSD1SDHBXPA
CCND3EXT1JAK2NSD2SDHCXPC
CCNE1EXT2JAK3NSD3SDHDXPO1
CD274 (PDL1)EZH2JAZF1NT5C2SEPT9YWHAE
CD74EZRKDM5ANTRK1SETZMYM2
CD79AFANCAKDR (VEGFR2)NTRK2SETBP1ZNF217
CDC73FANCCKEAP1NTRK3SETD2ZNF331
CDH11FANCD2KIAA1549NUP214SF3B1ZNF384
CDK4FANCEKIF5BNUP93SH2B3ZNF521
CDK6FANCGKITNUP98SH3GL1ZNF703
CDK8FANCLKLHL6NUTM1

 

Whole Transcriptome Sequencing – Genes most commonly associated with cancer listed below.

Fusions (RNA)
ABLEWSR1ETV6NOTCH2PKN1TERT
AKT3FGRINSRNRG1PPARGTFE3
ALKFGFR1MAML2NTRK1PRKCATFEB
ARHGAP26FGFR2MAST1NTRK2PRKCBTHADA
AXLFGFR3MAST2NTRK3RAF1TMPRSS2
BCRERGMETNUMBLRELA
BRAFESR1MSMBNUTM1RET
BRD3ETV1MUSKPDGFRAROS1
BRD4ETV4MYBPDGFRBRSPO2
EGFRETV5NOTCH1PIK3CARSPO3
Variant Transcripts (RNA)
AR-V7EGFR vIIIMET Exon 14 Skipping
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