Oncomine Focus Assay

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ABOUT THE ONCOMINE FOCUS ASSAY

Oncomine Focus Assay is an NGS-based analysis encompassing genes focused on the clinical use of approved targeted drugs and medications from prospective clinical trials.

Сhanges in these genes lead to tumor development and serve as diagnostic, prognostic, and predictive markers of cancer.

Oncomine Focus Assay contains 52 genes

SNV/indels hotspots
copy number variations (CNV)

chromosomal rearrangements (gene fusions)

To interpret the results of the Oncomine Focus Assay and further cancer therapy choosing, a consultation with a clinical geneticist and an oncologist is required.

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

Copy number variations (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 Oncomine Focus Assay

Patients diagnosed with cancer:

Choice of cancer therapy
Monitoring and adjustment of therapy in case of relapse

At the moment, in oncology, great importance is given to timely and accurate cancer diagnostics, as well as the choosing of the «correct» personalized therapy for patients with malignant neoplasms.

NGS concurrently reads

hundreds of millions of short DNA sequences

all types of mutations, including structural rearrangements, that сompares favorably with PCR analysis and Sanger sequencing

NGS Data Handling

allows to find differences in the DNA sequence of the tumor from the reference genomic sequence

The identified differences are called variants of the nucleotide sequence or:

Nucleotide variants

germinal (congenital — pathogenic, or polymorphisms)
somatic mutations typical for the tumor process

Next Generation Sequencing (NGS) method principle

The NGS method allows reading concurrently of hundreds of millions of short DNA sequences and detection of all types of mutations, including

full-coding sequences

hotspots (SNV/indels)

copy number variations (CNV)

chromosomal aberrations (gene fusions)

These «reads» contain a huge volume of genetic information. Subsequent bioinformatic analysis of the NGS data makes it possible to find discrepancies in the tumor DNA sequence from the reference genomic sequence (the «gold standard»). The time-consuming analysis of NGS data requires to use of special software and various bioinformatic algorithms.

The large list of identified variants is then «interpreted» by comparing the results with databases that contain known or newly identified variants associated with various cancers. Interpretation, as well as sequence identification, is a complex and time-consuming step in the study, as it involves the work of many specialists to determine the clinical and therapeutic significance of each discovered variant.

Pros

Superior sensitivity and specificity of the method
Fast turnaround time
Concurrent identification of all types of mutations, including structural rearrangements
Minimum requirements for the quantity and quality of samples
Reducing time of analysis