SIB is a new bioinformatics partner of the QCMD (Quality Control for Molecular Diagnostics) organization. The partnership aims to enhance bioinformatics solutions for international molecular external quality assessments. It will initially focus on the development of new computational tools to support nucleic acid sequence data analysis in the context of viral metagenomics and drug resistance.

Pioneering the harmonization of sequencing practices in Switzerland

In 2018, the SIB Clinical Bioinformatics Group launched several nationwide ring trials in virology, bacteriology and oncology. The purpose of a ring trial is to benchmark the practices of different labs in order to contribute to the definition of common best practices and assess harmonization needs. The team did it by building on working groups, already established for several years, with Swiss hospitals and universities. The focus of the trials was on the next-generation sequencing (NGS) techniques employed in these fields, as NGS is increasingly used to support, for instance, viral diagnostics in the case of patient infection, and the choice of therapy in the case of cancer. These were the very first Swiss-wide ring trials and they resulted in a published paper, and two others in preparation, in collaboration with clinical partners.

Expanding bioinformatics expertise for quality assessments

QCMD (Quality Control for Molecular Diagnostics) is one of the main independent international organizations that conducts ISO-certified External Quality Assessments (EQA) for microbiology/virology labs from across the globe. It runs over 100 EQA schemes in more than 160 countries. QCMD and SIB are joining forces to expand the bioinformatics analytical pipeline on the data submitted by international laboratories, notably aiming to participate in certified EQAs as part of their accreditation processes. “The combination of QCMD’s EQA expertise and global network with SIB’s bioinformatics know-how will help shape the future of our quality assessment schemes in this rapidly developing area of molecular diagnostics”, says Elaine McCulloch, Technical Project Manager at QCMD.

Viral metagenomics and resistance as a starter

SIB is currently involved in two External Quality Assessment Programmes. The first one is in viral metagenomics, a promising technique for analysing both the viral DNA and RNA from patient samples, notably to support the diagnosis of viral infections in unknown aetiologies, systemic infections, or for virus discovery. The second one is in viral resistance, to enable the detection of mutations leading to drug resistance in HIV-1 in particular, for both classical Sanger sequencing and NGS. “We are extremely pleased of this partnership, which aligns nicely with our ongoing work on the Swiss level [see box], to ensure high quality practices are developed and adopted across molecular diagnostics actors”, says Aitana Lebrand, Senior Project Manager in the Clinical Bioinformatics Group at SIB, who is spearheading the collaboration.