Molecular Profiling Technology

Caris Life Sciences offers unique precision medicine services that are designed to maximize the chances of success for clinical trials and address many patient accrual challenges facing biopharma partners in the world of precision medicine.

DNA Sequencing

Technical Specs

Technical Information Next-Generation Sequencing
Sample Requirements FFPE block or 10 unstained slides with a minimum of 20% malignant origin for DNA. Needle biopsy is also acceptable (4-6 cores).
Tumor 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 tumor samples
Number of Genes ~22,000 genes
Average Depth of Coverage 500x for 700+ clinical and research genes and 200x for all other genes
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 alterations (amplifications ≥ 6 copies)
Negative Percent Agreement (NPA) >99%
Genomic Signatures Microsatellite Instability (MSI), Tumor Mutational Burden (TMB) MI FOLFOXai™ – AI predictor of FOLFOX response in metastatic colorectal adenocarcinoma MI GPS™ Genomic Prevalence Score – CUP, atypical presentation or clinical ambiguity cases

Mutations

Point Mutations and Indels (DNA)

ABI1BRD4CRLF2FOXO4HOXC11KLF4MUC1PAK3RHOHTAL2
ABL1BTG1DDB2FSTL3HOXC13KLK2MUTYHPATZ1RNF213TBL1XR1
ACKR3BTKDDIT3GATA1HOXD11LASP1MYCL (MYCL1)PAX8RPL10TCEA1
AKT1C15orf65DNM2GATA2HOXD13LMO1NBNPDE4DIPSEPT5TCL1A
AMER1 (FAM123B)CBLCDNMT3AGNA11HRASLMO2NDRG1PHF6SEPT6TERT
ARCD79BEIF4A2GPC3IKBKEMAFBNKX2-1PHOX2BSFPQTFE3
ARAFCDH1ELF4HEY1INHBAMAXNONOPIK3CGSLC45A3TFPT
ATP2B3CDK12ELNHIST1H3BIRS2MECOMNOTCH1PLAG1SMARCA4THRAP3
ATRXCDKN2BERCC1HIST1H4IJUNMED12NRASPMS1SOCS1TLX3
BCL11BCDKN2CETV4HLFKAT6A (MYST3)MKL1NUMA1POU5F1SOX2TMPRSS2
BCL2CEBPAFAM46CHMGN2P46KAT6BMLLT11NUTM2BPPP2R1ASPOPUBR5
BCL2L2CHCHD7FANCFHNF1AKCNJ5MN1OLIG2PRF1SRCVHL
BCORCNOT3FEVHOXA11KDM5CMPLOMDPRKDCSSX1WAS
BCORL1COL1A1FOXL2HOXA13KDM6AMSNP2RY8RAD21STAG2ZBTB16
BRD3COX6CFOXO3HOXA9KDSRMTCP1PAFAH1B2RECQL4TAL1ZRSR2

Copy Number Alterations

Point Mutations, Indels and Copy Number Alterations* (DNA)

ABL2BRCA1CREB3L1ETV1GAS7KMT2A (MLL)MYCNPER1RUNX1TFEB
ACSL3BRCA2CREB3L2ETV5GATA3KMT2C (MLL3)MYD88PICALMRUNX1T1TFG
ACSL6BRIP1CREBBPETV6GID4 (C17orf39)KMT2D (MLL2)MYH11PIK3CASBDSTFRC
ADGRA2BUB1BCRKLEWSR1GMPSKNL1MYH9PIK3R1SDC4TGFBR2
AFDNCACNA1DCRTC1EXT1GNA13KRASNACAPIK3R2SDHAF2TLX1
AFF1CALRCRTC3EXT2GNAQKTN1NCKIPSDPIM1SDHBTNFAIP3
AFF3CAMTA1CSF1REZH2GNASLCKNCOA1PMLSDHCTNFRSF14
AFF4CANT1CSF3REZRGOLGA5LCP1NCOA2PMS2SDHDTNFRSF17
AKAP9CARD11CTCFFANCAGOPCLGR5NCOA4POLESEPT9TOP1
AKT2CARSCTLA4FANCCGPHNLHFPL6NF1POT1SETTP53
AKT3CASP8CTNNA1FANCD2GRIN2ALIFRNF2POU2AF1SETBP1TPM3
ALDH2CBFA2T3CTNNB1FANCEGSK3BLPPNFE2L2PPARGSETD2TPM4
ALKCBFBCYLDFANCGH3F3ALRIG3NFIBPRCCSF3B1TPR
APCCBLCYP2D6FANCLH3F3BLRP1BNFKB2PRDM1SH2B3TRAF7
ARFRP1CBLBDAXXFASHERPUD1LYL1NFKBIAPRDM16SH3GL1TRIM26
ARHGAP26CCDC6DDR2FBXO11HGFMAFNINPRKAR1ASLC34A2TRIM27
ARHGEF12CCNB1IP1DDX10FBXW7HIP1MALT1NOTCH2PRRX1SMAD2TRIM33
ARID1ACCND1DDX5FCRL4HMGA1MAML2NPM1PSIP1SMAD4TRIP11
ARID2CCND2DDX6FGF10HMGA2MAP2K1 (MEK1)NR4A3PTCH1SMARCB1TRRAP
ARNTCCND3DEKFGF14HNRNPA2B1MAP2K2 (MEK2)NSD1PTENSMARCE1TSC1
ASPSCR1CCNE1DICER1FGF19HOOK3MAP2K4NSD2PTPN11SMOTSC2
ASXL1CD274 (PDL1)DOT1LFGF23HSP90AA1MAP3K1NSD3PTPRCSNX29TSHR
ATF1CD74EBF1FGF3HSP90AB1MCL1NT5C2RABEP1SOX10TTL
ATICCD79AECT2LFGF4IDH1MDM2NTRK1RAC1SPECC1U2AF1
ATMCDC73EGFRFGF6IDH2MDM4NTRK2RAD50SPENUSP6
ATP1A1CDH11ELK4FGFR1IGF1RMDS2NTRK3RAD51SRGAP3VEGFA
ATRCDK4ELLFGFR1OPIKZF1MEF2BNUP214RAD51BSRSF2VEGFB
AURKACDK6EML4FGFR2IL2MEN1NUP93RAF1SRSF3VTI1A
AURKBCDK8EMSYFGFR3IL21RMETNUP98RALGDSSS18WDCP
AXIN1CDKN1BEP300FGFR4IL6STMITFNUTM1RANBP17SS18L1WIF1
AXLCDKN2AEPHA3FHIL7RMLF1PALB2RAP1GDS1STAT3WISP3
BAP1CDX2EPHA5FHITIRF4MLH1PAX3RARASTAT4WRN
BARD1CHEK1EPHB1FIP1L1ITKMLLT1PAX5RB1STAT5BWT1
BCL10CHEK2EPS15FLCNJAK1MLLT10PAX7RBM15STILWWTR1
BCL11ACHIC2ERBB2 (HER2/NEU)FLI1JAK2MLLT3PBRM1RELSTK11XPA
BCL2L11CHN1ERBB3 (HER3)FLT1JAK3MLLT6PBX1RETSUFUXPC
BCL3CICERBB4 (HER4)FLT3JAZF1MNX1PCM1RICTORSUZ12XPO1
BCL6CIITAERC1FLT4KDM5AMRE11PCSK7RMI2SYKYWHAE
BCL7ACLP1ERCC2FNBP1KDR (VEGFR2)MSH2PDCD1 (PD1)RNF43TAF15ZMYM2
BCL9CLTCERCC3FOXA1KEAP1MSH6PDCD1LG2 (PDL2)ROS1TCF12ZNF217
BCRCLTCL1ERCC4FOXO1KIAA1549MSI2PDGFBRPL22TCF3ZNF331
BIRC3CNBPERCC5FOXP1KIF5BMTORPDGFRARPL5TCF7L2ZNF384
BLMCNTRLERGFUBP1KITMYBPDGFRBRPN1TET1ZNF521
BMPR1ACOPB1ESR1FUSKLHL6MYCPDK1RPTORTET2ZNF703
BRAFCREB1

Microsatellite Instability (MSI)

Caris Molecular Intelligence® tumor profiling includes microsatellite instability (MSI) testing via next-generation sequencing (NGS). MSI is caused by failure of the DNA mismatch repair (MMR) system. High levels of MSI correlate to an increased neoantigen burden, which may make the tumor more sensitive to immunotherapy. MSI status is reported on pages one and two of the MI Profile Report, as well as in the NGS section in the Appendix.

MSI-High Status Across Caris Molecular Intelligence Cases

Earlier studies have associated MSI-High status with benefit to immunotherapy in metastatic colorectal cancer. Recent data, however, show that MSI is a useful indicator for predicting response to pembrolizumab in any solid tumor type.1

Traditionally, MSI is detected through polymerase chain reaction (PCR) by fragment analysis (FA) of five conserved satellite regions and comparing cancer tissue to normal tissue to identify differences in tandem repeats. To validate MSI testing via NGS, Caris evaluated more than 7,000 target microsatellite loci and compared the results from PCR for 2,189 cases across 26 different tumor types. This data was published in Cancer Medicine and demonstrated that MSI testing with Caris’ NGS platform is highly concordant with the traditional standard method of PCR-FA and is a more efficient and cost-effective approach to identifying patient candidates for immunotherapy.2

Traditional Approach: normal and cancer tissue required

Caris Approach: no normal tissue required; saving resources, costs and time

Attributions:

  1. D. T. Le, et al. Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science. Published Online 8 June 2017. DOI: 10.1126/science.aan6733.
  2. Vanderwalde, A., Spetzler, D., Xiao, N., Gatalica, Z. and Marshall, J. (2018), Microsatellite instability status determined by next-generation sequencing and compared with PD-L1 and tumor mutational burden in 11,348 patients. Cancer Med. doi:10.1002/cam4.1372

Tumor Mutational Burden (TMB)

Tumor Mutational Burden (TMB) is an emerging, quantitative indicator for predicting response to novel immune checkpoint inhibitors across a wide spectrum of tumor types.1-6 TMB measures the total number of non-synonymous, somatic mutations identified per megabase of the genome coding area (a megabase is 1,000,000 DNA basepairs).

Tumors with high TMB likely harbor neoantigens and may respond more favorably to immune checkpoint inhibitors. 1-2 Caris Molecular Intelligence defines TMB as 17 or more mutations per megabase. TMB is included for all MI Profile orders, at no additional cost, added tissue or delay in turnaround time.

How Tumor Mutational Burden Works:

  • Non-synonymous mutations are changes in DNA that result in amino acid changes in the protein.2,6
  • The new protein changes result in new shapes (neo-antigens) that are considered to be foreign to the immune system.2,4
  • Immune checkpoint inhibitors are able to stimulate and allow the immune system to detect these neoantigens and destroy the tumor.2
  • Germline (inherited) mutations are not included in TMB because the immune system has a higher likelihood of recognizing these alterations as normal.7

Attributions:

  1. Rizvi NA. Science. 2015; 384(6230):124-128.doi:10.1126/science.aaa1348.
  2. Snyder A. N Engl J Med. 2014; 371:2189-2199. doi:10.1056/NEJMoa1406498.
  3. Campesato LF. Oncotarget. 2015; 6(33):34221-34227. doi:10.18632/oncotarget.5950.
  4. Rosenberg JE. The Lancet. 2016; 387(10031):1909-1920. doi:10.1016/S0140-6736(16)00561-4.
  5. Strickland KC. Oncotarget. 2016; 7(12):13587-13598. doi:10.18632/oncotarget.7277.
  6. Le DT. N Engl J Med. 2015;372:2509-2520. doi:10.1056/NEJMoa1500596.
  7. Stewart TJ. Oncogene. 2008;27:5894-5903. doi:10.1038/onc.2008.268.

Loss of Heterozygosity (LOH)

Caris Life Sciences® utilizes MI Exome™ (Whole Exome Sequencing) to analyze 250,000 evenly-spaced single nucleotide polymorphisms (SNP) to measure genomic instability in the tumor. Genomic Loss of Heterozygosity (LOH) or genomic instability is often related to defective homologous recombination repair mechanisms and may be indicative of PARP-inhibitor and platinum therapy response.

Genomic LOH testing is provided at no additional cost and no increase in specimen requirements or turnaround time when MI Profile™ or MI Tumor Seek™ are ordered. The results can be found in the Genomic Signatures section of the Caris Molecular Intelligence® report, alongside Microsatellite Instability (MSI) and Tumor Mutational Burden (TMB) results. 

RNA Sequencing

Technical Specs

Technical Information Whole Transcriptome Sequencing
Sample Requirements FFPE block or 2-5 unstained slides with a minimum of 20% malignant origin. Needle biopsy is also acceptable (4-6 cores).
Tumor 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 tumor samples
Number of Genes ~22,000 genes
Average Read Count 60 million
Positive Percent Agreement (PPA) >97%
Negative Percent Agreement (NPA) >99%
Genomic Signatures MI GPS™ Genomic Prevalence Score – CUP, atypical presentation or clinical ambiguity cases

Fusions

ABL BRD3 FGFR3 INSR MYB NUMBL PRKCA RSPO3
AKT3 BRD4 ERG MAML2 NOTCH1 NUTM1 PRKCB TERT
ALK EGFR ESR1 MAST1 NOTCH2 PDGFRA RAF1 TFE3
ARHGAP26 EWSR1 ETV1 MAST2 NRG1 PDGFRB RELA TFEB
AXL FGR ETV4 MET NTRK1 PIK3CA RET THADA
BCR FGFR1 ETV5 MSMB NTRK2 PKN1 ROS1 TMPRSS2
BRAF FGFR2 ETV6 MUSK NTRK3 PPARG RSPO2

Variant Transcripts

AR-V7
EGFR vIII
MET Exon 14 Skipping

Artificial Intelligence

MI FOLFOXai™

MI FOLFOXai™, from Caris Life Sciences®, is an Artificial Intelligence-powered predictor of FOLFOX response that utilizes Caris Molecular Intelligence® tumor profiling results. It is intended to be used as an aid in gauging a patient’s likelihood to benefit from FOLFOX chemotherapy (in combination with bevacizumab) as the first-line chemotherapy regimen in metastatic colorectal adenocarcinoma.

MI FOLFOXai™ is included for all metastatic colorectal adenocarcinoma cases. The MI FOLFOXai™ results appear on the front page of the Caris report as INCREASED BENEFIT or DECREASED BENEFIT – with additional detail provided about the results on page two of the report. This information provides additional insight for patient response to FOLFOX as a first-line therapeutic option.

MI FOLFOXai™ was validated using two independent data sets:

  • 296 manually curated cases with real-world evidence (data acquired from insurance claims records, electronic medical records and death registries)
    • Median Overall Survival difference between the increased benefit arm and the decreased benefit arm: 11.2 months
  • 149 cases analyzed retrospectively from the randomized, prospective Phase III TRIBE2 study
    • Median Overall Survival difference between the increased benefit arm and the decreased benefit arm: 6.0 months

Patients predicted to have increased benefit to FOLFOX may achieve optimal results by receiving a FOLFOX regimen first
in their chemotherapy sequencing plan. Patients predicted to have decreased benefit to FOLFOX may achieve results by
receiving an alternate regimen, such as FOLFOXIRI or FOLFIRI, prior to the administration of a FOLFOX regimen.

Decisions on patient care and treatment must be based on the independent medical judgment of the treating physician, taking into consideration all available information concerning the patient’s condition.

MI GPSai™

Caris has one of the largest and most comprehensive databases of combined molecular and clinical outcomes data in the world, and we are actively employing advanced machine learning capabilities with the database to identify unique molecular signatures. These molecular signatures can be used to better identify cancer subtypes and predict patient response to certain therapies. We are pleased to introduce a tool to help manage cancer of unknown primary (CUP) or cases identified by the ordering physician with atypical clinical presentation or clinical ambiguity.

MI GPSai™ provides a cancer type similarity assessment that compares the genomic (DNA) and transcriptomic (RNA) characteristics of the patient’s tumor against other tumors in the Caris database (e.g. lung cancer tumor submitted for testing has a similar molecular signature as the lung cancers found in the Caris Database, or conversely the molecular signature is not similar to lung cancer, but similar to another tumor type’s molecular signature).

MI GPS ai™ can be added to any solid tumor order by selecting the appropriate box on the tumor profiling requisition. The result is presented as a prevalence score in a convenient tabular format and is populated onto the final Caris report. These results will provide additional insight by assessing how closely tumors match the genomic and transcriptomic signatures of tissue types to help you make more informed treatment decisions.

Caris Molecular Artificial Intelligence (MAI™) uses the power of DEAN (Deliberation Analytics) and machine learning technology to provide oncologists with the most thorough genomic and transcriptomic classifications to inform decision making. Caris MAI™ analyzes historical clinical and outcome data and learns from the past to provide for a better future via molecular subtyping.

Other

IHC

Immunohistochemistry (IHC) determines the level of protein expression in a tumor, which can be used in conjunction with CISH or FISH to validate date or provide complementary information that provides greater insights into various cancer types.

CISH

Chromogenic in situ hybridization (CISH) is an assay that uses chromogenic probes to visualize specific regions of DNA in a tissue specimen using a bright-field microscope, similar to standard immunohistochemistry. CISH allows for the enumeration of a variety of chromosomal abnormalities including gene amplifications, deletions, and translocations. This assay is often utilized at Caris Life Sciences in the reflex setting; for instance, when further clarity is needed to substantiate a result or when tissue is limited. CISH can be performed as a tissue-sparing alternative to analyze a specific gene of interest.

FISH

Fluorescence in situ hybridization (FISH) is an assay that uses fluorescent probes to visualize specific nucleic acid regions (DNA or RNA) in a tissue specimen using a fluorescent microscope. FISH allows for the enumeration of a variety of chromosomal abnormalities including gene amplifications, deletions, and translocations. This assay is often employed at Caris Life Sciences in the reflex setting; for instance, when further clarity is needed to substantiate a result or when tissue is limited. FISH can be performed as a tissue-sparing alternative to analyze a specific gene of interest.
Need Support?
Contact Us
or call 1.888.979.8669 (international: +41 21 533 53 00)