Bioinformatics pipelines

Understanding the underlying genetic code causing disease is key to precision medicine, be it personal genomes, cancer genomes or microbial genomes. With improved availability and affordability of genomic sequencing in the last decade, the challenge has shifted towards efficient and effective bioinformatics analysis of the output of genomic sequencing.

The bioinformatics pipelines currently in use vary greatly from site to site. There is urgent need for standardization of reporting and use of pipeline components, to ensure equal quality of input to genetic clinical decision support systems. Toward this end, BigMed is developing current OUS pipelines, and mapping and benchmarking these to other pipelines, while tackling quality control issues along the entire pipelines, from initial sample to clinical report.

Activities and deliverables are described below.

Somatic sequencing analysis pipelines

Gene panel DNA sequencing
Whole exome DNA sequencing
Somatic RNA-seq analysis pipeline
Germ-line whole genome sequencing

Quality control

Benchmarking of pipelines
Report: Mapping of regulatory frameworks and quality assurance for NGS-based diagnostics
Report: Framework for quality in NGS
Report: Mapping of best practice molecular diagnostics in clinical oncology

Clinical reporting

Genomics-based reports for use with clinical systems.
Clinical decision support module for tumor board meeting dashboard

Partners: OUS Dept of Medical Genomics, OUS Dept of Tumor Biology, DNV GL, PubGene.

Eivind Hovig

Professor and Manager

OUS - Dept. of Tumor Biology and UiO - Dept. of informatics

Relevant Projects

Comprehensive clinical report from molecular diagnostics in cancer

Comprehensive clinical report from molecular diagnostics in cancer

Cancer is a genetic disease, as DNA is altered in each tumor. The changes differ greatly between different tumors and over time in a tumor. Many changes can occur in each tumor, and these changes may represent targets for therapy, or serve

Close up photo of test equipment in a lab

Benchmarking as a tool for quality in genetic testing

Ensuring accuracy in genomic medicineModern medical tests based on DNA and RNA sequencing are composed of a pipeline of numerous hardware systems, complex proprietary and open-source software, custom-built scripts, and manual,

Boy - with simplified mesh of his face illustrated.

Big data management for the precise treatment of three patient groups

This report is produced as part of the BigMed project to document and distribute knowledge accumulated in the first phase of the project, identifying the challenges and obstacles the project aims to address.

Clinical reporting of genomics – best practices

Clinical reporting of genomics – best practices

Next-generation sequencing (NGS) is transitioning from the research environment to clinical diagnostics in a process which has proven difficult, and exome and whole genome sequencing are at the early stages of implementation in Nordic

Consent Management for Genomics

Consent Management for Genomics

With the increased utilization of genomic sequencing in the clinical context in Norway, practical and ethical issues in the development of the content and process of informed consent (IC) are emerging. Challenges exist in bridging the

Regulation of CDS Software

Regulation of CDS Software

The amount of health data used in patients’ diagnosis or treatment is growing beyond a manageable level for individual clinicians. Clinical decision support (CDS) software can help to access and analyse these data and thereby assist

Newborn baby holding parents hands

Variant eXchange - sharing of genomic variants classification between trusted partners

Improving genetic variant interpretation through data sharing with trusted partners of choice.

Regulatory frameworks and quality assurance for NGS-based diagnostics

Regulatory frameworks and quality assurance for NGS-based diagnostics

As patients, we trust that medical diagnostics are reliable and accurate, but how can clinical genomics labs ensure the quality of tests based on new technologies?