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NeoThetis LIQUID BIOPSY

Liquid biopsy for therapy selection

OVERVIEW

WHAT IS NEOTHETIS?

NeoThetis is a non-invasive genetic test that can guide therapy selection for people diagnosed with cancer via a simple blood draw. During cancer development and growth, cancer cells release DNA into the bloodstream known as circulating tumor DNA (ctDNA). ctDNA contains genetic characteristics of the tumor which contribute to cancer development and therapy resistance.

NeoThetis is a novel liquid biopsy test that accurately detects and analyses the ctDNA released from both primary and metastatic tumors of patients diagnosed with cancer. It is specifically designed to maximize the available therapeutic opportunities which are based on precision medicine while guiding therapy selection and treatment re-evaluation tailored to each patient.

THE UNIQUE CHARACTERISTICS OF NEOTHETIS

Performed non-invasively, using a simple blood draw
Guides therapy selection, and treatment re-evaluation for therapy resistance.
Provides therapy solutions approved by professional cancer societies and bodies.
Suggests available ongoing clinical trials.
Identifies potential mutations that might arise in distant non-operable metastatic lesions.
Captures the genetic characteristics of the tumor offering a deep investigation of the genetic alterations and immunotherapy biomarkers.
Offers fast turnaround results, ensuring treatment can begin faster.

WHEN TO PERFORM NEOTHETIS?

NeoThetis can be performed at initial diagnosis and during disease progression:
when tumor is inaccessible
when tissue biopsy is limited or not available
when the patient is unfit for tumor biopsy
if additional tumor biopsy procedures are not clinically recommended
when fast turnaround time is required for therapy selection
when the patient does not respond to current treatment and re-evaluation is needed

OUR TESTS

NeoThetis tests are designed to detect clinically actionable genetic alterations, including Single Nucleotide Variants (SNVs), Insertions and Deletions (INDELs), Copy Number Amplifications (CNAs), and Rearrangements, that drive cancer or are associated with response to treatment.

All NeoThetis tests also assess Microsatellite Instability (MSI) immunotherapy biomarker, with the Pan-Cancer Plus test additionally testing for blood Tumor Mutational Burden (bTMB) immunotherapy biomarker.

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INNOVATIVE TECHNOLOGICAL DESIGN

Targeted technology and novel bioinformatics
Unparalleled workflow which combines our proprietary targeted capture enrichment technology along with novel bioinformatic pipelines, to provide accurate detection of genetic variants even at low allele frequencies. Our high read depth analysis enables for increased sensitivity and specificity providing reliable results.

Genetic alteration detection
NeoThetis screens clinically important coding regions and selected non-coding regions in genes of interest, to identify genetic alterations which:
are included in NCCN, ESMO and ASCO guidelines
are associated with FDA/EMA approved therapies
serve as selection criteria in clinical trials
are associated with therapy resistance

MSI assessment
MSI is an immunotherapy biomarker caused by defects in the mismatch repair mechanism.
MSI testing via Next Generation Sequencing (NGS) detects a higher number of clinically significant loci compared to other MSI testing methods, such as immunohistochemistry, with high accuracy and sensitivity. MSI assessment:
has been emphasized by cancer societies including NCCN, ESMO and ASCO
is associated with FDA/EMA approved immunotherapy drugs

bTMB assessment
bTMB is an emerging immunotherapy which indicates the total number of mutations found in a tumor per megabase and it is obtained from analyzing ctDNA. bTMB is tumor agnostic and can guide healthcare providers to identify patients who might benefit from immunotherapy.

Extended Test
NeoThetis Pan-Cancer Plus
NeoThetis Pan-Cancer
Cancer-Specific Tests
NeoThetis Breast / Gynecological
NeoThetis Colorectal
NeoThetis Gastric
NeoThetis Melanoma
NeoThetis Non-Small Cell Lung Cancer
NeoThetis Pancreatic
NeoThetis Prostate

GENETIC ALTERATIONS AND BIOMARKERS TESTED

RECOMMENDATIONS OF LIQUID BIOPSY BY PROFESSIONAL BODIES AND SOCIETIES

The use of cell-free/circulating tumor DNA testing can be considered when a patient is medically unfit for invasive tissue sampling, or if in the initial diagnostic setting there is insufficient material for molecular analysis following pathologic confirmation.

“Validated and sensitive ctDNA assays can be used to genotype advanced cancers and select patients for targeted therapies”

POSSIBLE OUTCOMES OF THE TEST

A detailed report outlining the results of the genetic test is provided:

IMMUNOTHERAPY BIOMARKERS
MSI status and bTMB score is reported, accompanied with available FDA/EMA approved drugs which are eligible for the variants detected.

GENOMIC FINDINGS
All the genetic variants identified are reported. The results will also indicate which approved FDA/EMA targeted therapies are suitable as treatment options. Depending on the results identified, the report will also provide information on the drugs the patient will not benefit from.
Variants of strong and of potential clinical significance as well as variants of uncertain significance (VUS) are also reported.

CLINICAL TRIALS
Provides information on clinical trials which are relevant to the genetic variants identified.

INTERPRETATION
The biological and therapeutical classification of results are reported in detail according to NCCN guidelines

WHAT CAN I DO AFTER NEOTHETIS LIQUID BIOPSY?

NeoThetis liquid biopsy can enable the healthcare provider to take the most informed and accurate decisions on the best clinical management for cancer treatment

Personalised targeted therapy and immunotherapy options which provide novel therapeutic avenues, can enhance clinical care and treatment, improving quality of life

Identification and enrolment of patients in applicable ongoing clinical trials

Expert medical genetic counselling and support is provided to help patients through their journey for cancer treatment

HOW CAN I TAKE THE NEOTHETIS LIQUID BIOPSY TEST?
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Ask your healthcare provider about NeoThetis

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Your healthcare provider will collect a blood sample from you

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The sample will be sent to our laboratory

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The sample will be analyzed in our laboratory

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Results will be available within 6-9 days and a detailed report will be sent to your healthcare provider

ACCEPTED MATERIAL

Two (2) sterile Streck Cell-Free DNA BCT blood collection tubes provided in the NeoThetis kit.

TURNAROUND TIME

6-9 working days

TECHNOLOGY

Circulating cell-free DNA (cf-DNA) is extracted from blood samples using a standardized methodology, followed by DNA library preparation. DNA enrichment for the genomic regions of interest is carried out using a solution-based hybridization method followed by next generation sequencing (NGS). Sequence data is aligned to a reference genome and variants are identified using proprietary bioinformatics pipelines. NeoThetis can be used for the identification of selected single nucleotide variants (SNVs), small insertions and deletions (Indels, ≤50bp), rearrangements, copy number amplifications (CNAs) and microsatellite instability (MSI). Tumor-related actionable and clinically relevant alterations are classified and reported according to recommendations set by the Association for Molecular Pathology (AMP) (Li MM et al. J Mol Diagn. 2017 Jan; 19(1): 4–23) and is according to published knowledge at the time of reporting.

Test Methodology
SEQUENCING

Next generation sequencing (Illumina)

ENRICHMENT

Proprietary Target Capture Enrichment Technology (Click here to see our Publications)

SNV AND CNV DATA ANALYSIS

Vardict variant caller, targeted CNV calling using a proprietary bioinformatics pipeline utilizing a circular binary segmentation algorithm, Rearrangement calling utilizing discordant pair and split-read alignments following local assembly, realignment, and a filtering pipeline to refine the set of candidate events

DATA EVALUATION

Varsome Clinical by Saphetor

REFERENCE GENOME

hg19, NCBI GRCh37

QUALITY CRITERIA

≥Q30, 99.9% base call accuracy in >80% of the bases

CLASSIFICATION OF VARIANTS

MM Li et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.J Mol Diagn. 2017 Jan;19(1):4-23.

IN SILICO ALGORITHMS

ALoFT, BayesDel, DEOGEN2, Eigen, Eigen-PC, FATHMM, FATHMM-XF, FATHMM-MKL, fitCons, LIST-S2, LRT, M-CAP, MetaLR, MetaRNN, MetaSVM, MPC, MutationAssessor, MutationTaster, MutPred, MVP, Polyphen-2, PrimateAI, PROVEAN, REVEL, SIFT, SIFT4G, dbscSNV

DATABASES

Over 100 databases; Cancer somatic databases: COSMIC, ICGC, cbio portal, IARC TP53 somatic, Cancer hotspots, GDC, Fusion GDB. Somatic variant interpr. databases: JAX CKB, PMKB, CIViC, OncoKB, DoCM. Drug-gene interaction databases: PharmGKB, FDA, DGI. Clinical trials databases: AACT Clinical trials

PAN-CANCER PLUS SENSITIVITY AND SPECIFICITY OF TESTED VARIANTS

SNVs and INDELs(VAF>0.25%-0.5%)

Sensitivity: 91% (95%CI: 86-94%)
Specificity: 99.998% (95%CI: 99.9969-99.9989%)

SNVs and INDELs(VAF>0.5%)

Sensitivity: 99% (95%CI: 95-99.8%)
Specificity: 99.998% (95%CI: 99.9969-99.9989%)

CNAs(>2.8 copies)

Sensitivity: 100% (95%CI: 74-100%)
Specificity: 100% (95%CI:92-100%)

Rearrangements(VAF≥0.5%)

Sensitivity: 100% (95%CI:69-100%)
Specificity: 100% (95%CI:92-100%)

MSI(VAF>0.25%)

Sensitivity: 100% (95%CI: 79-100%)
Specificity: 100% (95%CI: 93-100%

bTMB

Concordance correlation coefficient: 0.979 (95%CI: 0.966-0.987)

PAN-CANCER AND CANCER-SPECIFIC SENSITIVITY AND SPECIFICITY OF TESTED VARIANTS

SNVs and INDELs (VAF=0.1-0.5%)

Sensitivity: 92% (95%CI:81-97%)
Specificity: >99.99%

SNVs and INDELs(VAF≥ 0.5%)

Sensitivity: 100% (95%CI:92-100%)
Specificity: >99.99%

CNAs (>2.8 copies)

Sensitivity:100% (95%CI:77-100%)
Specificity: 100% (95%CI:93-100%)

Rearrangements (VAF≥0.5%)

Sensitivity:100% (95%CI:66-100%)
Specificity:100% (95%CI:93-100%)

MSI (VAF≥0.25%)

Sensitivity:100% (95%CI:98.8-100%)
Specificity:100% (95%CI:92.9-100%)

OUR TESTS

Genes: AKT1, ATM, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CHEK2, CTNNB1, DICER1, EGFR, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FOXA1, FOXL2, GATA3, KIT, KRAS, MAP3K1, MET, MLH1, MRE11A, MSH2, MSH6, MTOR, NBN, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PIK3CA, PIK3CB, PMS2, POLE, PTEN, RAD51C, RAD51D, RAF1, RET, RUNX1, SMAD4, TP53

Genes: AKT1, APC, ATM, BRAF, BRCA1, BRCA2, CTNNB1, EGFR, ERBB2, FBXW7, FGFR1, FGFR2, FGFR3, GNAS, KRAS, MET, MLH1, MSH2, MSH6, MTOR, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PIK3CA, PIK3CB, PMS2, POLE, PTEN, RAF1, SMAD4, TP53

Genes: APC, CDH1, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, KIT, KRAS, MET, MLH1, MSH2, MSH6, NF1, NTRK1, NTRK2, NTRK3, PDGFRA, PIK3CA, PMS2, SMAD4, STK11, TP53

Genes: AKT1, ALK, BRAF, CTNNB1, ERBB2, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, KIT, KRAS, MAP2K1, MET, MYC, NF1, NRAS, NTRK1, NTRK2, NTRK3, PDGFRA, PIK3CA, POLE, PTEN, RET, ROS1, STK11, TP53

Genes: AKT1, ALK, APC, ARAF, ATM, BRAF, BRCA2, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, JAK2, KEAP1, KRAS, MAP2K1, MET, NRAS, NTRK1, NTRK2, NTRK3, PDGFRA, PIK3CA, POLE, PTEN, RAF1, RET, ROS1, SMAD4, STK11, TP53

Genes: AKT1, ALK, APC, AR, ARAF, ATM, ATRX, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHEK2, CIC, CTNNB1, DDR2, DICER1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, FOXA1, FOXL2, FUBP1, GATA3, GNA11, GNAQ, GNAS, H3F3A, IDH1, IDH2, JAK2, KEAP1, KIT, KRAS, MAP2K1, MAP3K1, MET, MLH1, MRE11A, MSH2, MSH6, MTOR, MYC, MYCN, NBN, NF1, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PIK3CA, PIK3CB, PMS2, POLE, PTEN, RAD51C, RAD51D, RAF1, RB1, RET, ROS1, RUNX1, SMAD4, SPOP, STK11, TERT, TMPRSS2, TP53

Genes: ABL1, ABL2, AKT1, AKT2, ALK, ANKRD26, APC, AR, ARAF, ASXL1, ATM, ATRX, B2M, BAP1, BARD1, BCL2, BCL6, BCOR, BCORL1, BCR, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, CALR, CBFB, CBL, CBLB, CBLC, CCND1, CCND2, CCND3, CCNE1, CD274, CD74, CDC25C, CDH1, CDK12, CDK4, CDK6, CDKN2A, CEBPA, CHEK2, CIC, CSF1R, CSF3R, CTLA4, CTNNB1, CUX1, CXCR4, DCK, DDR2, DDX41, DEK, DHX15, DICER1, DNMT3A, DUSP22, EGFR, EIF1AX, EPCAM, ERBB2, ERBB3, ERBB4, ERCC4, ERG, ESR1, ETNK1, ETV1, ETV4, ETV6, EWSR1, EZH2, FANCA, FBXW7, FGF13, FGF19, FGF2, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FLT4, FOXA1, FOXL2, FOXO1, FRS2, FUBP1, GATA1, GATA2, GATA3, GNA11, GNAQ, GNAS, H3F3A, HDAC2, HOXB13, HRAS, IDH1, IDH2, IKZF1, IL3, INHA, INSRR, IRF4, JAK1, JAK2, JAK3, KDM6A, KDR, KEAP1, KIT, KMT2A, KMT2C, KMT2D, KRAS, LUC7L2, MALT1, MAP2K1, MAP2K2, MAP3K1, MDM2, MECOM, MET, MITF, MLH1, MLLT3, MPL, MRE11, MSH2, MSH6, MTOR, MUTYH, MYC, MYCN, MYD88, MYH11, MYOD1, NBN, NCOA3, NF1, NF2, NFE2L2, NOTCH1, NPM1, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUP214, NUTM1, PALB2, PARP1, PBX1, PDCD1, PDCD1LG2, PDGFRA, PDGFRB, PGR, PHF6, PIK3CA, PIK3CB, PIK3R1, PML, PMS2, POLD1, POLE, PPM1D, PPP2R1A, PTCH1, PTEN, PTPN11, RAD21, RAD51C, RAD51D, RAF1, RARA, RB1, RBBP6, RET, RNF43, ROS1, RPS14, RUNX1, RUNX1T1, SETBP1, SF3B1, SH2B3, SLC29A1, SMAD4, SMARCA4, SMARCB1, SMC1A, SMC3, SMO, SOX10, SPOP, SRSF2, STAG2, STAT3, STAT5B, STK11, SUZ12, TCF3, TCL1A, TERT, TET2, TMPRSS2, TP53, TSC1, TSC2, U2AF1, VEGFA, VHL, WT1, XPO1, ZRSR2

Genes: ALK, ATM, BRAF, BRCA1, BRCA2, CDKN2A, CHEK2, ERBB2, FBXW7, FGFR1, FGFR2, FGFR3, KRAS, MLH1, MSH2, MSH6, MYC, NTRK1, NTRK2, NTRK3, PALB2, PMS2, ROS1, SMAD4, STK11, TP53

Genes: AKT1, APC, AR, ATM, BARD1, BRAF, BRCA1, BRCA2, CHEK2, CTNNB1, ERBB2, FGFR1, FGFR2, FGFR3, FOXA1, MLH1, MSH2, MSH6, MYC, MYCN, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PIK3CA, PIK3CB, PMS2, POLE, PTEN, RAD51C, RAD51D, SPOP, TMPRSS2, TP53

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