VarSome Clinical is a CE IVD-certified and HIPAA-compliant platform allowing fast and accurate variant discovery, annotation, and interpretation of NGS data for whole genomes, exomes, and gene panels. VarSome Clinical helps molecular geneticists and clinicians increase the diagnostic yield and support treatment decisions for genetic conditions.

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End-to-End Bioinformatics Solution for Next-Generation Sequencing

VarSome Clinical is a CE-IVDR medical device online software application that can process the results of Next Generation Sequencing (NGS), generating genetic variation information based on standard guidelines and databases with clinical evidence.

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How does VarSome Clinical work?

1.Upload FASTQ or VCF

VarSome Clinical accepts Illumina as well as MGI FASTQ data and any VCF file. You can upload the data easily and securely through its web interface or you can harness VarSome's powerful API for an automated and secure data transfer. Once the files are uploaded, you can start the analysis!

Annotate VCF

With VarSome Clinical you can upload a VCF file containing single or multiple samples (tracks) for variant annotation and classification. Subsequently, you can apply any number of sophisticated dynamic and/or algorithmic filters to quickly find the causative variants or other variants of interest. Learn more about VarSome's variant filtering options.

Annotate FASTQ

With VarSome Clinical you can upload Illumina and MGI FASTQ files for variant discovery, annotation, and classification. You can perform analysis for multiple samples, such as risk carrier screening for couples, analysis of tumor-normal samples, studies of trios and families or comparative analysis of families of any size or small cohorts. Learn more about VarSome's alignment, joint calling, and variant calling.

Multi-sample Analysis

With VarSome Clinical, you can perform analysis for multiple samples, such as risk carrier screening for couples, analysis of tumor-normal samples, studies of trios and families or comparative analysis of families of any size or small cohorts. Learn more about VarSome's multi-sample analysis.

2.Annotation & Classification

VarSome Clinical's robust pipeline is capable of analyzing gene panels, exomes, and whole genomes for individual samples, trios, families, and cohorts in just minutes. VarSome Clinical leverages the massive cross-referenced knowledge base of the free VarSome.com platform, and also offers access to licensed databases.

Quality Control Reports

VarSome Clinical comes with an extensive Quality Control Report which covers pipeline settings as well as statistics for alignment, variant calling, ACMG and more. Gene Coverage Report and Coding Coverage Report is also available.

Germline and Somatic Variant Classification for SNVs, Indels, and CNVs

VarSome Clinical displays automated variant classification according to the guidelines of the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP). VarSome Clinical has also implemented the ACMG guidelines for CNV interpretation. Each ACMG and AMP rule is explained, along with why it has been triggered, or why not. If you have some additional evidence, you can manually turn on or off other ACMG rules and easily reach the final verdict for your variant. Learn more about VarSome's ACMG, AMP and CNV ACMG variant interpretation guidelines implementation.

140+ Data Resources

VarSome Clinical offers a massive cross-referenced knowledge base consisting of 140+ public genomic databases, representing over 33 billion data points, plus contributions from a 500 000-strong community. But there is more to it: whenever a public database is updated, VarSome processes it and makes it available for annotation and classification! Learn more about databases available in VarSome.

Proprietary Data Resources

With VarSome Clinical you can access proprietary and licensed data sets of 3rd party data providers on a condition you possess a corresponding license. You can also import your own local database with allele frequencies and integrate it privately in VarSome Clinical for annotation and classification of your variants.

3.Intuitive Web Portal

VarSome Clinical's feature-rich and intuitive web interface allows for variant filtering according to pathogenicity, Germline and Somatic classification, allele frequency, gene list or phenotype, and many more. Dynamic and algorithmic filters allow you to perform simple or advanced filtering like segregation analysis, identification of de novo variants or variants in imprinted genes.

Dynamic Filters

Dynamic filters are combinations of conditions to apply to your samples in order to reduce your search space. They are powerful, yet easy to set up, modify and apply in seconds to any of your samples. You can filter variants based on allele frequency, pathogenicity, ACMG, zygosity, function or gene list, to name a few. Learn more about dynamic filters.

Algorithmic Filters

Algorithmic filters are sophisticated filters that can be fully customized according to your workflow and other specific needs. With algorithmic filters, you can perform segregation or gene list-based analysis, find compound heterozygous variants, identify de novo variants or variants in imprinted genes, to name a few. Learn more about algorithmic filters.

Sample Cross-referencing

VarSome Clinical allows you to build your own database of samples and variants. You can comment on variants and set up custom variant classifications to be shared with the members of your team. You may even share data at a single variant level with your partner institutions on the condition that both parties consent in writing. With VarSome Clinical you can also import your own local database with allele frequencies and use it for variant annotation and classification.

Variant Sharing Program

On top of custom variant classifications and comments sharing with the members of your team, you may even share data at a single variant level with your partner institutions on the condition that both parties consent in writing. Learn more about the variant sharing program.

4.Report Generation

Once you have narrowed down the list of variants of interest, you can proceed with report generation, which includes all the details of your variants, including literature references and your custom comments. The layout of the report is fully customizable according to your unique logos and branding policy.

Compliance

VarSome Clinical is certified as an In-vitro Diagnostic (IVD) Medical Device according to the requirements of EC 98/79/EEC. In addition, we are certified as a company with ISO 13485 and ISO 27001 for quality management systems for medical devices and information security management. Learn more in the Compliance Whitepaper.

Customizable Reports

VarSome Clinical allows you to generate a report containing the variants you choose for each sample. The report includes drug-related information (based on genes), literature references, and your custom comments. The layout of the report can be fully customized according to your unique branding policy.

Audit Trail

VarSome Clinical comes with functionality to track the usage of the platform by users for auditing purposes.

Key Benefits

CE-IVD Mark

VarSome Clinical is an In-vitro Diagnostic Medical Device compliant with the Regulation (EU) 2017/746 (IVDR).

HIPAA Compliant

VarSome Clinical is compliant with HIPAA, ensuring that we have the required safeguards in place to protect electronic Personal Health Information (ePHI).

ISO 13485

As part of the compliance to the IVDR, Saphetor has implemented a Quality Management System for medical device manufacturer that is compliant with ISO 13485:2016/A11:2021.

ISO 27001

Saphetor considers the protection of the data as very important, and has demonstrated it through its compliance to the ISO 27001:2022, which is the latest update of the standard related to the Information Security Management System.

Variant Knowledge Base

Cross-referenced data from 140+ genomic databases plus contributions from a 500 000-strong community.

Programming Interface

VarSome Clinical comes with powerful API for automated data transfer in both directions.

Did you know?

Variant Discovery

VarSome Clinical's variant discovery pipelines have been designed to achieve high quality standards, such as reproducibility, sensitivity and precision:

Sensitivity: 99.8% for SNVs and 99.5% for indels
Precision: 99.8% for SNVs and indels

Precision Contests

VarSome Clinical's variant discovery rocks! It received top marks in the recent contest organized by the Food and Drug Administration, and it was steadily in the top ranks in all metrics, as in previous precision FDA contests. These results are a testament to the VarSome team's total commitment to excellence. Check out our blog for more details.

Experts in Big Data

To date, VarSome has aggregated and cross-referenced 140+ leading databases and other data resources, representing over 33 billion data points, and new ones are added constantly over time. But there is more to it - whenever a data resource is updated, VarSome quickly makes it available for annotation and classification of your variants!

Network of Geneticists

As VarSome Clinical has been deployed by dozens of institutional customers across many countries, you can benefit from VarSome's extensive network of molecular geneticists and health care professionals who contribute to the identification of likely causal variants, along with a summary of available therapeutic options.

VarSome Clinical is a Class C per Rule 3 of Annex VIII of the Regulation (EU) 2017/746 on in vitro diagnostic Medical Devices (IVDR).

VarSome Clinical is an in vitro diagnostic medical device software intended to qualitatively process high-throughput human DNA sequencing data to identify genetic variants, annotate them with relevant information from widely recognized databases and report their classification verdict according to broadly recognized professional guidelines. VarSome Clinical is intended to be used by healthcare professionals to obtain information on the genomic status of the adult and pediatric population undergoing next generation sequencing (NGS). The information obtained with VarSome Clinical may be to support patient management decisions. VarSome Clinical does not provide any recommendations or conclusions related to diagnosis, prognosis or treatment. The software is composed of two modules with distinct functions:

· VarSome Clinical - (Module 1) Variant Calling is intended for the qualitative analysis of high throughput human DNA sequencing data, to identify discrepancies (variants) between DNA sequencing reads and the reference human genome. These discrepancies may represent genomic variants caused by single nucleotide mutations, indels and copy number variations. Inputs to Module 1 are next generation FASTQ sequences that meet VarSome Clinical's quality requirements as depicted in the User Manual. The output of the Variant Calling module is a VCF text file format, which is the required input for VarSome Clinical Module 2.

· VarSome Clinical - (Module 2.1) Annotation is intended for automated annotation of genomic variants using relevant information from respected scientific sources. It assigns to the variants state-of-the-art functional information available from widely recognized databases cited within the User Manual. The level of annotated information is representative of the current understanding of the variant characterization, allowing for adequate application of variant classification rules (Module 2.2).

· VarSome Clinical - (Module 2.2) Variant Classification is intended for the classification of the annotated variants, based on semi-automated application of variant classification rules derived from broadly recognized professional guidelines, namely the guidelines published by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP): o For germline variants, classification rules of the ACMG guidelines are followed, providing variants with one of the ACMG pathogenicity verdicts: "Benign", "Likely Benign", "Likely Pathogenic", "Pathogenic" or "VUS" (Variant of Unknown Significance). o For somatic variants, the classification rules of the AMP guidelines are followed, providing variants with one of the AMP pathogenicity verdicts: "Tier 1", "Tier 2", "Tier 3" or "Tier 4".

These verdicts are only reflective of the pathogenicity level as per state-of-the-art ACMG and AMP guidelines and do not directly provide information on the patient's clinical status. The semi-automated application of variant classification rules is intended as a standardized method for reaching an ACMG or AMP verdict, as per the ACMG and AMP guidelines cited in the User Manual, that reflects the current expert consensus at the time of the analysis. VarSome Clinical is indicated to qualitatively process high-throughput human DNA sequencing data to obtain information on the genomic status of the adult and pediatric population undergoing next generation sequencing (NGS).

Read the User Manual before use.

Notified Body: TÜV SÜD Product Service GmbH

Manufacturer: Saphetor EPFL Innovation Park -C, CH-1015 Lausanne Switzerland

EC REP: Saphetor Greek Branch Leocharous 3, 10560 Athens Greece