News SeqOne users

Get actionable insights from your tumor samples with TheraOne

28 December 2021

By deploying the new TheraOne view, SeqOne sets the objective of accelerating the identification and provision of a treatment adapted to each patient according to the genomic profile of their tumor.

TheraOne will support you in identifying actionable biomarkers from  both DNA and RNA analyses in order to offer a personalized therapeutic solution to your patients.

December 2021 Newsletter

Introduction

The comprehensive characterization of a tumor’s unique genomic landscape is a challenging undertaking that is made accessible by providing the right bioinformatic tools. However improving patient outcomes doesn’t end with the sole detection of mutations and other genomic events. A greater challenge lies in evaluating the real contribution of each genetic variant to a patient’s cancer, and their clinical implications.

Too often, it is still up to oncologists and pathologists to search through various resources in order to identify treatments that would fit the unique genomic profile of a patient’s tumor.  

With TheraOne, we address this issue and aim at establishing a cartography of potentially actionable genomic events for each patient according to their type of cancer, in order to identify a personalized treatment strategy, or to direct them towards relevant clinical trials.

This new module takes advantage of SeqOne’s powerful bioinformatic pipelines for both DNA and RNA assays, and aggregates all their outputs into a single patient-centric dashboard to quickly identify actionable biomarkers.

Patients and samples

TheraOne opens a new ‘Patients’ section on the SeqOne dashboard, that lists all patients available on the account.

Simply put, a patient can be seen as a collection of samples and their associated analyses on SeqOne. One or more samples, of the same or different nature (DNA, RNA) can thus be associated with the same patient, and the variants originating from the different somatic pipelines (SomaVar, SomaCNVCapture, SomaMSI, SomaRNA) will be accessible from this view.

A new patient can be created:

  • When uploading a new sample to the platform,
  • From the “Create Patient” icon in the upper right corner of the user dashboard.

All variants relevant to the patient’s cancer type

The new Cancer ROI viewer groups together the variants detected through the various analyses carried out on the samples attached to the patient: variants, CNVs, fusions and splices. It lists the associations that exist between specific genomic regions and each type of variant (SNV, CNV, fusions or splices) on the one hand, and the patient’s cancer type on the other hand.

This association is based on a database, built in particular from the COSMIC gene census and COSMIC mutation census. 

SeqOne Cancer ROI database

The SeqOne Cancer ROI DB identifies cancer genes/exons/codons for which a cancer driver mutation is known for the patient disease.

For each gene, the mutation type (point mutations, deletion, amplification, fusions or splice) and cancer function (tumor suppressor or oncogene) is identified using the COSMIC gene census and a manually curated internal database.

– For tumor suppressor genes, all exons are added to the database. 
– For oncogenes, all exons with a tier 1 to 3 mutation from COSMIC mutation, and codons with a tier 1 mutation are added.

Additional predictive biomarkers

Both microsatellite instability (MSI) and tumor mutational burden (TMB), used as predictive biomarkers for immunotherapy in cancer treatment, can be visualized from the Signature tab. 

MSI

Microsatellite status is assessed in a cohort-based fashion. Not only looking at a set of predefined regions, our tool identifies any microsatellite region within the targeted genomic regions in order to increase the resolution of the assay, and generates a panel of controls from the sample cohort directly in order to identify unstable microsatellites.

For more information on the SomaMSI workset, you can read our dedicated blog post.

TMB

When performing a SomaVar analysis on a large panel, missense somatic mutations are used in order to compute a Mut/Mb score for each tumoral sample. This raw score is further interpreted based on an organ specific regression model built from the TCGA (The Cancer Genome Atlas) exome dataset.

Prioritized actionable information 

TheraOne matches the genomic profile of your patient’s tumor with actionable information on available drugs and ongoing clinical trials.

Through the Actionability tab, you can access:

  • a list of prioritized FDA-approved treatments for which actionable variants have been identified in the patient. Each variant – drug association in this list comes with their respective AMP/ASCO classification, type of response and specificity.
  • Phase I to IV clinical trials matching the tumor’s genomic profile, with ongoing recruitment near the user’s geographic location.

Reporting

A comprehensive report can be generated and exported in both an editable or a pdf format, including:

  • Patient and sample metadata,
  • Identified genomic alterations and biomarkers,
  • Actionability and available FDA approved drugs,
  • Recruiting clinical trials in the user’s geographic area.

How to get access to TheraOne on SeqOne?

If you are interested in this new module, contact our Customer Support service at support@seqone.com.

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