NGS data analysis

Convert sequencing data to meaningful insights with confidence and ease.

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Intuitive, integrated NGS data analysis software for complex workflows

Roche’s comprehensive portfolio of sequencing solutions enables you to generate high-quality sequencing data from even the most challenging sample types. Nevertheless, the analysis and interpretation/reporting of complex data sets against a tsunami of evolving research and evidence remains a major obstacle in realizing the promise of NGS in precision medicine. 

For this reason, Roche offers integrated, user-friendly NGS data analysis software for converting raw sequencing data into features such as QC metrics and variant calls (secondary analysis).

  • If you are performing comprehensive genomic profiling (CGP) with an AVENIO Tumor Tissue CGP Kit, push-button secondary analysis is performed with the carefully curated, cloud-based FoundationOne® Analysis Platform1
  • For AVENIO ctDNA Analysis Kits V2 and AVENIO Tumor Tissue Analysis Kits V2, the AVENIO Oncology Analysis Software offers simple, efficient, and accurate sequencing data analysis
  • Seamless, cloud-based secondary analysis and visualization of target enrichment data generated with a KAPA custom or catalog panel is offered through third-party partnerships, such as Roche’s collaboration with DNAnexus®

Once high-confidence variant calls have been generated, we make it easy to extract deep biological meaning, identify significant findings, and present these in a comprehensible way with the navify® Mutation Profiler or a tertiary analysis platform of your choice. 

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AVENIO Oncology Analysis Software enables the end-to-end workflow. the software is for research use only. The AVENIO Oncology Analysis Software allows labs to quickly and easily transform data from enriched DNA and ctDNA processed on an Illumina NextSeq into meaningful insights for profiling mutations and monitoring how they evolve over time.The AVENIO Oncology Analysis Software is run on a server that is connected to on-premise shared network storage. The Oncology Analysis Server is required and available from Roche. After the AVENIO Oncology Analysis Software completes the workflow and report, the shared network storage will contain both the sequencing output files and the analysis output files.
The FoundationOne® Analysis Platform enables the end-to-end workflow from sample extraction to data analysis. The software is for research use only. The FoundationOne® Analysis Platform allows labs to quickly and easily transform data from enriched DNA processed on an Illumina NextSeq into meaningful insights for comprehensive genomic profiling.The FoundationOne® Analysis Platform is a cloud-based software that processes the sequencing data from the NextSeq instruments, and produces files with filtered variant calls and QC metrics which are made available to through AVENIO Connect Software.The AVENIO Connect Software is a cloud solution and the user interface for the FoundationOne® Analysis Platform. The AVENIO Connect Software is used to manage analyses, view sample results, and download results output files. The AVENIO Connect Software is configured to on-premise shared network storage to enable upload of NextSeq BCL files and download results output files.The AVENIO Connect Software and FoundationOne® Analysis Platform are required and available from Roche.The AVENIO Connect Software User Assistance is available to provide guidance on the use of the software. Please consult your local Roche representative.
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Benefits of NGS data analysis solutions from Roche

Convenient

Effortless NGS data analysis with intuitive, integrated software

With our broad portfolio of NGS data analysis software, Roche provides convenient, end-to-end (sample to insight) NGS workflows. 

  • AVENIO Tumor Tissue CGP and oncology kits include access to integrated secondary analysis software1 
  • Cloud-based software with intuitive user interfaces obviates the need for complex hardware integration or bioinformatics expertise1
  • Outputs from secondary analysis software are fully compatible with the navify Mutation Profiler and other tertiary analysis platforms
Comprehensive

Obtain comprehensive genomic insights across applications

Our NGS data analysis software:

  • Identifies all four major types of genetic variants, including single-nucleotide variants (SNVs), indels, copy number alterations, and rearrangements (fusions) for AVENIO Tumor Tissue CGP and oncology assays,1 as well as KAPA HyperCap and KAPA HyperPETE workflows 
  • Calculates complex genomic signatures, such as tumor mutation burden (TMB), microsatellite instability (MSI), genomic loss of heterozygosity (LOH), and homologous recombination deficiency (HRD)1
  • Returns variant calls in all captured regions, not just in pre-defined sets of hotspots1
Reliable

Designed to deliver high-confidence variant calls and meaningful insights

Whether developed in-house (with proprietary algorithms and error-suppression strategies) or in collaboration with external partners (using open-source tools and pipelines), our NGS analysis solutions are tailored to our sample preparation chemistries to ensure reliable and accurate results.

  • Key sequencing QC metrics are considered in the calling and filtering of variants to ensure high-confidence results1
  • The FoundationOne® Analysis Platform and navify Mutation Profiler offer evidence-based secondary and tertiary analysis based on highly curated, continuously evolving databases1,2
  • Five leading oncology databases, a curated loci of interest list, and a customizable annotation database are integrated into the AVENIO Oncology Analysis Software

Brochure: FoundationONE® Analysis Platform + AVENIO Connect Software

Discover how to gain access to clear information and results with our secondary analysis and workflow manager software

Brochure: Target enrichment secondary data analysis with DNAnexus®

Learn about the benefits and find out how to access Roche secondary analysis RUO (Research Use Only) pipelines on DNAnexus for somatic, germline, and longitudinal mutation analysis.

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Do you have questions about our products or services? We’re here to help. Contact a Roche representative in your region.

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KAPA products are for Research Use Only, not for use in diagnostics procedures.

AVENIO products are for Research Use Only. Not for use in diagnostic procedures.

navify® Mutation Profiler is CE-IVD in EU. This product is For Research Use Only, not for use in diagnostic procedures in the US and other countries when used with the AVENIO Tumor Tissue CGP Kits.

Tertiary analysis with navify® Mutation Profiler is not part of the AVENIO Tumor Tissue CGP Automated Kit and may be purchased as an add on.

References

  1. F. Hoffman-La Roche Ltd. AVENIO Tumor Tissue CGP Kit V2 Instructions for Use. (v3.0). 2026.
  2. Yaung SJ et al. Assessment of a Highly Curated Somatic Oncology Database to Aid in the Interpretation of Clinically Important Variants in Next-Generation Sequencing Results. J Mol Diagn. 2020 Nov;22(11):1356-1366.