EATRIS Research Quality Work Featured in Nature Biotechnology

Over five years, EATRIS researchers have contributed to the US FDA-led DNA sequencing quality control consortium, SEQC2 (MAQC IV), which is now featured in the September issue of the journal “Nature Biotechnology”. The issue also includes a commentary section from Marc Salit (Stanford University) and Janet Woodcock (Commissioner of the U.S. Food and Drug Administration) as well as an editorial on the work of the SEQC2. You can read it here.

The SEQC2 team also developed the cover image of this Nature Biotechnology Issue, illustrating steps of the workflow from biological samples to statistical analysis.

Nature Biotechnology is one of the world’s leading journals in the science and business of biotechnology. It publishes new concepts in technology/methodology of relevance to the biological, biomedical, agricultural and environmental sciences as well as covers the commercial, political, ethical, legal, and societal aspects of this research.

Andreas Scherer, Board of Directors of MAQC Society, EATRIS Quality Initiative, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, says the following about the SEQC2:

It is fantastic to see that well-organised quality control studies are valued and can be published in top tier journals. It has been a long road for the SEQC2 to reach this point, but thanks to outstanding coordination by the SEQC2 team and the superb contributions and high-quality work of  EATRIS sequencing and bioinformatics teams, we can now see the results. We hope that the reference datasets and recommendations that the SEQC2 produced will be useful for the research community towards assessing the quality of their data for improvement of research output.”

This feature edition in Nature Biotechnology brings the overall contribution of EATRIS researchers to the SEQC2 project to three Nature Biotechnology publications, two in Genome Biology, and one accepted manuscript in Scientific Data. Several analyses and manuscripts with EATRIS contributions are still in process.

The following EATRIS researchers contributed to the respective publications:

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing https://doi.org/10.1038/s41587-021-00994-5

  • Jessica Nordlund & Ulrika Liljedahl (Uppsala University, SciLifeLab, Sweden)
  • Roberta Maestro, Maurizio Polano (Centro di Riferimento Oncologico di Aviano IRCCS, Italy)
  • Jiri Drabek, Petr Vojta, Sulev Kõks (IMTM, Czech Republic)
  • Ene Reimann (Estonian Genome Center, Estonia)
  • Andreas Scherer (Institute for Molecular Medicine Finland, FIMM, Univ. Helsinki, Finland).

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing https://doi.org/10.1038/s41587-021-00993-6

  • Jessica Nordlund & Ulrika Liljedahl (Uppsala University, SciLifeLab, Sweden)
  • Roberta Maestro, Daniela Gasparotto & Maurizio Polano (Centro di Riferimento Oncologico di Aviano IRCCS, Italy)
  • Jiri Drabek & Petr Vojta (IMTM, Czech Republic)
  • Ene Reimann (Estonian Genome Center, Estonia)
  • Sulev Kõks (Perron Institute for Neurological and Translational Science, Australia)
  • Andreas Scherer (Institute for Molecular Medicine Finland, FIMM, Univ. Helsinki, Finland)

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology https://doi.org/10.1038/s41587-021-00857-z

  •  Andreas Scherer (Institute for Molecular Medicine Finland, FIMM, Univ. Helsinki, Finland)

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency https://doi.org/10.1186/s13059-021-02316-z

  • Angela del Pozo and Mario Solis Lopez (Institute of Medical and Molecular Genetics (INGEMM), Spain)
  • Nikola Tom (Center of Molecular Medicine, Masaryk University, Czech Republic)
  • Andreas Scherer (Institute for Molecular Medicine Finland, FIMM, Univ. Helsinki, Finland)  

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions https://doi.org/10.1186/s13059-021-02315-0

  •  Angela del Pozo and Mario Solis Lopez (Institute of Medical and Molecular Genetics (INGEMM), Spain)
  • Nikola Tom and Boris Tichy (Center of Molecular Medicine, Masaryk University, Czech Republic)
  • Andreas Scherer (Institute for Molecular Medicine Finland, FIMM, Univ. Helsinki, Finland)