Sample Preparation

Sequencing

Read alignment

Variant calling

VCF

Variant interpretation

Reporting

Clinical report

omnomicsNGS workbench

How it works

Explanation level:

Import or upload VCF file to omnomicsNGS

Import or upload VCF file to omnomicsNGS

Import a VCF in format 4.1 or higher which can include SNPs, InDels, CNVs and gene fusions. Each patient can have multiple samples, and VCF files can be uploaded manually or automatically through integration with other parts of your pipeline, including LIMS for example.

Open sample to see sample information and a summary of the variants present.

Open sample to see sample information and a summary of the variants present.

Open a sample to see sample information and a summary of the variants present. The sample synopsis page allows adding tags and more detailed information about the sample context. Other files such as image data can be attached to the sample. How these functions are used is up to the user. If the user has defined biomarker panels (gene hot-spots, pharmacogenomics signatures, etc.), the summary results are shown. They can be applied for example to get an express view of the sample.

Use the Workbench to analyse data with virtual gene panels and phenotypes

Use the Workbench to analyse data with virtual gene panels and phenotypes

Display all variants in the sample on the Workbench and define user-specific lay-outs for different clinical domains of interest. Filter variants using HPO terms and virtual gene panels to quickly reduce the number of variants in a sample to those which are actionable. The operations on the Workbench are tracked and settings can be locked by an administrator to allow safe regular usage.

Further filter triage using organisation-wide or personal filtering strategies to narrow down to relevant variants in the sample

Further filter triage using organisation-wide or personal filtering strategies to narrow down to relevant variants in the sample

Build filtering strategies using over 150 filterable data columns, including integrated data, population frequencies, predictors, variant classification criteria, and organisation-specific data on local expertise as well as observed and reported variants. Save the strategies for quick automated enaction in routine work.

Automatically classify individual variants through integration of the best public databases and application of ACMG classification criteria for germline samples and AMP/ASCO criteria for somatic samples

Automatically classify individual variants through integration of the best public databases and application of ACMG classification criteria for germline samples and AMP/ASCO criteria for somatic samples

Automatically classify variants using ACMG classification criteria, which can be manually adjusted based on your knowledge. Annotations from databases such as ClinVar, CIViC, Ensembl, RefSeq, OMIM, OrphaNet and more. Apply approved ontologies for diseases, phenotypes and variant consequences. Obtain guidance from effect predictors and around 40 populations, including carrier, allele, and homozygote frequencies. Use manual or automated batch import and annotation curation mechanisms to complement the pool of information with specific expertise.

Report selected primary observations, secondary observations, carrier status and risk factors.

Report selected primary observations, secondary observations, carrier status and risk factors.

Generate clinical reports for selected variants in PDF format, or XML for further treatment in other software such as laboratory information systems. Reports are based on user-defined templates and contain sections for primary and secondary observations, carrier status and risk alleles. Somatic reporting based on ASCO tiering is also available. Build an organisation-specific repository of saved interpretation text to be used in reducing the time needed to report.