oncominefocus

A solid tumor next-generation sequencing assay for biomarker analysis

The Oncomine Focus Assay is a targeted, multi-biomarker assay that enables detection of hotspots, SNVs, indels, CNVs, and gene fusions from DNA and RNA in a single workflow. This comprehensive assay design is further enhanced with workflow automation, delivering insights quickly and helping accelerate your research towards that next companion diagnostic or therapy in the future.

Designed for clinical and translational cancer research, the Oncomine Focus Assay leverages proprietary Ion AmpliSeq technology to enable robust results, low input amounts, and analysis of low quality samples, and is compatible with FFPE fine needle aspirates and core needle biopsies.

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Content

Simultaneous detection of hundreds of variants across 52 genes relevant to solid tumors.

  • Targets relevant hotspots, SNVs, indels, CNVs, and gene fusions from DNA or RNA in a single workflow
  • Enables detection of NTRK1, NTRK2, and NTRK3 gene fusions
  • Includes solid tumor genes targeted by on-market oncology drugs and published evidence
  • Content driven by the Oncomine Knowledgebase, which includes content aligned to approved therapies and indications

NTRK

NTRK fusion detection

Oncomine Focus Assay gene list

Hotspot genes
(35 genes)

AKT1
ALK
AR
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 genes
(19 genes)

AKT1
ALK
AR
BRAF
CCND1
CDK4
CDK6
EGFR
ERBB2
FGFR1
FGFR2
FGFR3
FGFR4
KIT
KRAS
MET
MYC
MYCN
PDGFRA

 

PIK3CA
 

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

 


A 3-day NGS workflow from tissue sample to report

oncomine-cell-free-dna-assays-liquid-biopsy-clinical-research-banner

Prep

From FFPE samples including fine needle aspirates and needle biopsies, DNA and RNA is extracted, amplified, and templated into amplicon-based libraries ready to be sequenced.

Sequence

Ion GeneStudio S5 Series enables high-throughput sequencing of 2M to 130M reads per run.

Analyze

Seamless integration of our informatics solutions with our sequencing platforms enable quick and intuitive analysis and reporting.

Sample extraction

From FFPE samples including fine needle aspirates and needle biopsies, DNA and RNA is extracted, amplified, and templated into amplicon-based libraries ready to be sequenced.

Library preparation

Oncomine Focus Assay is a targeted, multi-biomarker NGS assay that enables analysis on all classes of variants from DNA and RNA across 52 unique genes in a single workflow.

Library templating

The Ion Chef System enables hands-free library templating of the Oncomine libraries into the Ion Chip for downstream sequencing.

Step4

The Ion GeneStudio S5 Series enable throughput capacity from 2 million to 130 million reads per run.  Simply select the Ion Chip that provides the throughput and coverage needed for your application.

Torrent Suite

Plan, monitor, and track your runs all within a web interface while reviewing the quality and accuracy of your sequencing run, in addition to variant calling, detecting SNPs and indels.

Ion Reporter

Call and annotate SNPs/InDels, CNVs, and fusions. Interpret your DNA and RNA variants faster and more easily from semiconductor sequencing data using a web-enabled solution.

Oncomine Reporter

Find the relevant cancer drivers in a report that enables contextual investigation of sample-specific variants to understand their use with respect to labels, guidelines, and current global clinical trials.

oncomine-cell-free-dna-assays-liquid-biopsy-clinical-research-banner

Prep

From FFPE samples including fine needle aspirates and needle biopsies, DNA and RNA is extracted, amplified, and templated into amplicon-based libraries ready to be sequenced.

Sequence

Ion GeneStudio S5 Series enables high-throughput sequencing of 2M to 130M reads per run.

Analyze

Seamless integration of our informatics solutions with our sequencing platforms enable quick and intuitive analysis and reporting.

Sample extraction

From FFPE samples including fine needle aspirates and needle biopsies, DNA and RNA is extracted, amplified, and templated into amplicon-based libraries ready to be sequenced.

Library preparation

Oncomine Focus Assay is a targeted, multi-biomarker NGS assay that enables analysis on all classes of variants from DNA and RNA across 52 unique genes in a single workflow.

Library templating

The Ion Chef System enables hands-free library templating of the Oncomine libraries into the Ion Chip for downstream sequencing.

Step4

The Ion GeneStudio S5 Series enable throughput capacity from 2 million to 130 million reads per run.  Simply select the Ion Chip that provides the throughput and coverage needed for your application.

Torrent Suite

Plan, monitor, and track your runs all within a web interface while reviewing the quality and accuracy of your sequencing run, in addition to variant calling, detecting SNPs and indels.

Ion Reporter

Call and annotate SNPs/InDels, CNVs, and fusions. Interpret your DNA and RNA variants faster and more easily from semiconductor sequencing data using a web-enabled solution.

Oncomine Reporter

Find the relevant cancer drivers in a report that enables contextual investigation of sample-specific variants to understand their use with respect to labels, guidelines, and current global clinical trials.


Comparison of Oncomine assay and Ion AmpliSeq panel content

Targeted next-generation sequencing (NGS) is empowering laboratories of all sizes to confidently pioneer breakthroughs in cancer research. At the core of these breakthroughs are assays and panels designed to achieve highly sensitive results from minimal sample input—to help deliver information that may lead to the next companion diagnostic test or therapy in the future.

Clinical cancer research requires countless decisions. Of critical importance are the decisions you make about assay content. The Oncomine Focus Assay provides a robust assay where all genes provide actionable insights across a range of different cancer types.

Examples-oncomine-assays

 Click to enlarge

Examples of Oncomine assays and Ion AmpliSeq panels and a subset of their associated genes and tumor types for research use. The Oncomine Knowledgebase shows that the specific gene had a variant detected in specific tumor type at a minimum of a 1% frequency. Additional genes are available on these and other Oncomine assays and Ion AmpliSeq panels.


Performance

  • Reproducible and sensitive detection of variants across multiple cancer types
  • Compatible with as little as 10 ng sample, including FFPE fine needle biopsies and core needle aspirates
  • Enables results from up to six samples and two controls per run for DNA and RNA in a single workflow
  • NGS results in days rather than weeks, leveraging Ion Torrent sequencing technology, optional Ion Chef library preparation, and the Ion GeneStudio S5 Systems

 

Analytical performance summary

Across variant types, the Oncomine Focus Assay achieves high sensitivity, specificity, and reproducibility using clinical research samples sequenced on the Ion GeneStudio S5 System.

  Sensitivity PPV (Specificity) Reproducibility
SNVs 98.77% 99.63% 99.6%
Indels 100% 100% 100%
CNVs 96.42% 100% 96.42%
Gene fusion 100% 100% 100%
Overall 98.70% 99.67% 99.01%
Table 1. Sensitivity, specificity, and reproducibility across variant types using the Oncomine Focus Assay on the Ion GeneStudio S5 System.


Reporting

Features enabled with Oncomine informatics:

  • Prioritize variants, find the relevant few
  • Call variants, identify and annotate cancer drivers
  • Quickly create custom, lab-generated reports
  • Customizable report templates available in 11 languages