Oncoprofile

What is the oncoprofile test?

Oncoprofile is an NGS-based assay that includes a panel of genes frequently involved in carcinogenesis.

Unlike Oncofocus, Oncoprofile includes an expanded spectrum of genes whose abnormalities are responsible for both «adult» and juvenile forms of cancer, as well as identifying genetic variants associated with hereditary cancer syndromes such as:

Hereditary breast and ovarian cancer syndrome
Li-Fraumeni syndrome
Ataxia telangiectasia (Louis-Bar syndrome)
Fanconi anemia
Lynch syndrome
Peutz-Jeghers syndrome
PTEN-associated hamartoma tumor syndrome (Cowden syndrome)
Neurofibromatosis types I and II
Familial atypical nevi and melanoma syndrome/Dysplastic nevus syndrome/Melanoma-astrocytoma syndrome
Hereditary retinoblastoma
Tuberous sclerosis (Burneville’s disease)

Oncoprofile assay contains 161 genes

Hotspots (SNV/InDels)
Full coding sequence of genes

copy number variations (CNV)
inter and intra chromosomal rearrangements (chimeric gene variants)

Consulting with a clinical geneticist and an oncologist to interpret Oncoprofile test results and select cancer therapy is required.

Hotspots (SNV/InDels)

87 genes

AKT1

AKT2

AKT3

ALK

ARAF

AXL

BRAF

BTK

CBL

CCND1

CDK4

CDK6

CHEK2

CSF1R

CTNNB1

DDR2

EGFR

ERBB2

ERBB3

ERBB4

ERCC2

ESR1

EZH2

FGFR1

FGFR2

FGFR3

FGFR4

FLT3

FOXL2

GATA2

GNA11

GNAQ

GNAS

H3F3A

HIST1H3B

HNF1A

HRAS

IDH1

IDH2

JAK1

JAK2

JAK3

KDR

KIT

KNSTRN

KRAS

MAGOH

MAP2K1

MAP2K2

MAP2K4

MAPK1

MAX

MDM4

MED12

MET

MTOR

MYC

MYCN

MYD88

FE2L2

NRAS

NTRK1

NTRK2

NTRK3

PDGFRA

PDGFRB

PIK3CB

PIK3CA

PPP2R1A

PTPN11

RAC1

RAF1

RET

RHEB

RHOA

ROS1

SF3B1

SMAD4

SMO

SPOP

SRC

STAT3

TERT

TOP1

U2AF1

XPO1

Full coding sequence of genes

48 genes

ARID1A

ATM

ATR

ATRX

BAP1

BRCA1

BRCA2

CDK12

CDKN1B

CDKN2A

CDKN2B

CHEK1

CREBBP

FANCA

FANCD2

FANCI

FBXW7

MLH1

MRE11

MSH6

MSH2

NBN

NF1

NF2

NOTCH1

NOTCH2

NOTCH3

PALB2

PIK3R1

PMS2

POLE

PTCH1

PTEN

RAD50

RAD51

RAD51B

RAD51C

RAD51D

RNF43

RB1

SETD2

SLX4

SMARCA4

SMARCB1

STK11

TP53

TSC1

TSC2

Copy number variations (CNV)

43 genes

AKT1

AKT2

AKT3

ALK

AXL

BRAF

CCND1

CCND2

CCND3

CCNE1

CDK2

CDK4

CDK6

EGFR

ERBB2

ESR1

FGF19

FGF3

FGFR1

FGFR2

FGFR3

FGFR4

FLT3

IGF1R

KIT

KRAS

MDM2

MDM4

MET

MYC

MYCL

MYCN

NTRK1

NTRK2

NTRK3

PDGFRA

PDGFRB

PIK3CB

PIK3CA

PPARG

RICTOR

TERT

Inter and intrachromosomal rearrangements (Gene fusions)

51 genes

AKT2

ALK

AXL

BRCA1

BRCA2

BRAF

CDKN2A

EGFR

ERBB2

ERBB4

ERG

ESR1

ETV1

ETV4

ETV5

FGFR1

FGFR2

FGFR3

FGR

FLT3

JAK2

KRAS

MDM4

MET

MYB

MYBL1

NF1

NOTCH1

NOTCH4

NRG1

NTRK1

NTRK2

NTRK3

NUTM1

PDGFRA

PDGFRB

PIK3CA

PRKACA

PRKACB

PTEN

PPARG

RAD51B

RAF1

RB1

RELA

RET

ROS1

RSPO2

RSPO3

TERT

Indications for the Oncoprofile

The Oncoprofile test is indicated in patients with a confirmed diagnosis of cancer and when one of the above syndromes is suspected for:

Tumor molecular profiling
Therapy selection
Evaluation of unfavorable prognosis
Therapy monitoring and correction if the cancer recurrence occurs
Detection of several hereditary cancer syndromes (*The confirmation test in the patient’s blood sample is required if a pathogenic genetic variant is found in the tumor)

3 928 338people

with a cancer diagnosis are registered in Russia in 2019

640 391 cases

when cancer was first detected

21.7%

of patients with malignant tumors died within the first year after diagnosis in 2019

Accurate and on-time cancer diagnostics and the «right» personalized therapy selection are crucial for cancer patients and are a primary direction for national oncology.

NGS can simultaneously read

hundreds of millions of short DNA sequences

all types of mutations, including structural rearrangements, which distinguishes it favorably from PCR analysis and sequencing by Sanger

NGS Data Processing

makes it possible to find differences in the tumor DNA sequence from the reference genomic sequence

The revealed differences are called nucleotide sequence variants or:

Nucleotide variants

germinal (congenital — pathogenic, or polymorphisms)
tumor-specific somatic mutations

How exactly does Next Generation Sequencing (NGS) work?

NGS can simultaneously read hundreds of millions of short sequences of DNA and detect all types of mutations, including

Full-length genes

Hotspots (SNV/InDels)

Copy number variations (CNV)

Chromosomal aberrations (gene fusions)

«These „„reads““ contain a large amount of information about the genetic sequence. The following bioinformatic data analysis finds differences between the tumor DNA sequence and the reference genomic („„golden standard““). NGS data analysis is time-consuming and requires specific software and various bioinformatics algorithms.»

The massive list of detected variants is then «interpreted» by comparing the results with databases that list known or newly seen variants associated with various cancers. Interpretation and sequencing are complex and time-consuming because it involves the work of many specialists to determine the clinical and therapeutic significance of each detected variant.

Advantages

High sensitivity and specificity of the method
Fast turnaround time of the test
Simultaneous detection of all types of mutations, including structural rearrangements
Minimum requirements for sample quantity and quality
Shorter testing times