Oncofocus

WHAT IS THE ONCOFOCUS TEST?

Oncofocus is an NGS-based assay that includes a panel of genes concurred for the clinical use of approved targeted drugs and drugs from prospective clinical trials.

Alterations in these genes lead to tumor development and are used as diagnostic, prognostic, and predictive cancer markers.

"First Genetics Lab" performs testing using the high‑throughput sequencing system named "F‑Genetics" and reagents for high‑throughput next generation sequencing (NGS) of genes associated with human cancer genesis, that are registered as medical devices (Federal Service for Surveillance in Healthcare: РЗН 2020/10521, РЗН 2022/16970)

Oncofocus assay consists of 52 genes

Hotspots (SNV/InDels)
Gene copy number variation (CNV)

Chromosomal aberrations (Gene fusions)

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

Hotspots (SNV/InDels)

35 genes

AKT1

ALK

BRAF

CDK4

CTNNB1

DDR2

EGFR

ERBB2

ERBB3

ERBB4

ESR1

FGFR2

FGFR3

GNA11

GNAQ

HRAS

IDH1

IDH2

JAK1

JAK2

JAK3

KIT

KRAS

MAP2K1

MAP2K2

MET

MTOR

NRAS

PDGFRA

PIK3CA

RAF1

RET

ROS1

SMO

Gene copy number variation (CNV)

19 genes

ALK

BRAF

CCND1

CDK4

CDK6

EGFR

ERBB2

FGFR1

FGFR2

FGFR3

FGFR4

KIT

KRAS

MET

MYC

MYCN

PDGFRA

PIK3CA

Chromosomal aberrations (Gene fusions)

23 genes

ABL1

AKT3

ALK

AXL

BRAF

EGFR

ERBB2

ERG

ETV1

ETV4

ETV5

FGFR1

FGFR2

FGFR3

MET

NTRK1

NTRK2

NTRK3

PDGFRA

PPARG

RAF1

RET

ROS1

Indications for Oncofocus testing

For patients diagnosed with cancer for:

Therapy selection
Therapy monitoring and correction if the cancer recurrence occurs

3 928 338 people

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)
сtumor-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

single nucleotide variants, insertions/deletions (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
Fast turnaround time
Simultaneous detection of all types of mutations, including chromosomal aberrations
Minimum requirements for sample quantity and quality
Shorter testing times