VARSTATION: A CLOUD-BASED PLATFORM FOR THE COMPLETE FLOW OF NEXT GENERATION SEQUENCING DATA ANALYSIS AND INTERPRETATION FOR CLINICAL DIAGNOSIS

Rodrigo S. Reis; Marcel Pinheiro Caraciolo; Diego Colombo; Felipe Val; Carolina Nakamura; Michel Chieregato; Pedro Lui Nigro Chazanas; Murilo C. Cervato

Paper Title

Authors

Rodrigo S. Reis
Marcel Pinheiro Caraciolo
Diego Colombo
Felipe Val
Carolina Nakamura
Michel Chieregato
Pedro Lui Nigro Chazanas
Murilo C. Cervato

Modality

Xpress presentation

Subject area

Database and Software Development

Publishing Date

26/04/2022

Country of Publishing

Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeetingxp2021/419209-varstation--a-cloud-based-platform-for-the-complete-flow-of-next-generation-sequencing-data-analysis-and-interpre

ISBN

978-65-5941-645-5

Keywords

next-generation sequencing, sequence variants, bioinformatics

Summary

A wide variety of Next Generation Sequencing (NGS) applications are becoming routine and are continually replacing other molecular techniques for screening, diagnosing and prognosing genetic diseases in clinical settings. Consequently, analysis and interpretation increase in complexity with advanced bioinformatics pipelines that include processes from demultiplexing unique molecular identifiers to calling structural variants. In addition, recommended laboratory standards for clinical accreditation require rigorous test validation to ensure accuracy and reproducibility, extensive quality control and assurance, and traceable clinical interpretation of sequence variants. Existing software do not support peer review capabilities according to compliance guidelines such those from the College of American Pathologists (CAP) and usually do not offer the possibility to analyze data from different library preparation kits and platforms, it is normally necessary to use many independent software. In this work, we present Varstation®, a clinical cloud-based bioinformatics platform for processing and analysis of human sequence variants obtained by NGS. Bioinformatics pipelines for different purposes can be created or customized using Workflow Description Language (WDL) which is orchestrated by a Cromwell server at the AWS cloud infrastructure. Files can be uploaded to the application either by a command-line interface, a web browser or Illumina’s Basespace integration. Once data is uploaded, users can select a workflow from a list of clinically validated pipelines to be executed for samples at the run. Also, a pipeline can be created by filling simple information such as the sequencing platform, library preparation kit, region or genes of interest, desired reference genome build and expected quality control metrics. After saving the run, the workflow tasks for each sample will be executed in parallel until its completion. Quality control metrics will be available for user inspection, if necessary, samples can be reproved. A tab where users can navigate between a table of small variants, copy number variants or structural variants will be available for clinical interpretation and validation. For clinical interpretation support, more than 40 genetic databases are annotated and variants are automatically pre-classified according to recommendations and guidelines of the American College of Medical Genetics and Genomics (ACMG), the Association of Molecular Pathology (AMP) and CAP. Dynamic filters can be created based on pre-set scenarios, shared with all users from an organization and used by selecting any combination of them during filtration and prioritization. For each type of variant, an interactive and pre-configured display of the genomic data is accessible for visual examination. The platform provides the ideal analysis flow for accredited laboratories where two independent analyses are required for compliance. During interpretation, variants can be selected to generate reports and to integrate a customized organization’s database of curated variants. Varstation is freely available for academic and non-profit users at https://varsomics.com/varstation/.

Title of the Event: X-Meeting XPerience 2021
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

REIS, Rodrigo S. et al.. VARSTATION: A CLOUD-BASED PLATFORM FOR THE COMPLETE FLOW OF NEXT GENERATION SEQUENCING DATA ANALYSIS AND INTERPRETATION FOR CLINICAL DIAGNOSIS.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/419209-VARSTATION--A-CLOUD-BASED-PLATFORM-FOR-THE-COMPLETE-FLOW-OF-NEXT-GENERATION-SEQUENCING-DATA-ANALYSIS-AND-INTERPRE. Access in: 11/05/2025