30 April 2020

Insight into Making Scientific Findings Publicly Available

By 2020, 100% of scientific publications funded with public money must be published in Open Access (OA) format. In the last 3 years, 70% of Oncode Investigators’ research has been published OA. This is a significantly higher percentage than the one of all Dutch Universities, which in 2018 had increased to 54% OA publications.

Bianca-Olivia Nita

Preprint servers like BioRxiv or MedRxiv are tools that can be combined with traditional peer reviewed journals to increase impact and visibility. Until 2019, only around 5% of publications by Oncode Investigators were shared via a preprint server before being published in a peer reviewed journal, whether OA or subscription. We spoke to Oncode Investigator Lude Franke (UMCG) about how publishing on BioRxiv strongly impacted his research.

What can you tell us about your recent work?

In the last few years, my research group has focused on large-scale functional genomics analyses, ascertaining how germline genetic variation is impacting gene expression and methylation levels. One of the things we observed was that such knowledge was helpful to many scientists for better interpreting their genome-wide association studies. In order to accommodate that, we initiated an international consortium (eQTLGen.org) to determine the effects of disease-associated genetic variants on gene expression levels, comprising in total 37 cohorts and 31,684 samples.

What happened next?

Once we completed the manuscript at the end of 2018, we submitted it to a journal and also put it online, at the same time, as a preprint on BioRXiv. But most importantly, we made all results, including all non-significant findings, publicly available. This made it possible for other geneticists to immediately start using these results, with the understanding that it could well be that there were still some issues with the results we obtained, since the paper had not yet gone through peer review.

Did you see any risks in taking this decision?

We thought that although it could be that other researchers would start using this data in projects that we had also had in mind, we already had more than enough to do, and this would not be a bad thing.

What was the outcome of making your manuscript publicly available?

Our experience turned out quite positive: two of the reviewers of the journal where we submitted our manuscript credited us explicitly for making all results publicly available and emphasised this dataset to be of relevance to our community. I believe this might have been one of the reasons why we could revise our manuscript for this journal.

In what stage is the peer review process now?

We will turn in the revised manuscript and as such, we do not yet know whether the paper will be accepted. However, what we do know is that the preprint has already been cited over 100 times: our results and data have already been used in many papers and the data has been incorporated in various methods that aim to better understand genome-wide association studies. Besides this, we believe these efforts also helped convince 21 groups to join our new single-cell consortium, and we expect results in a year from now, which we will disseminate in the same way as mentioned above. Sharing scientific results using public preprint repositories (open access) and also making the data publicly available (open data|) therefore really works for us: by sharing both our scientific insights and data we benefit the society and at the same time get credit by getting cited for our work, a win win for everyone!

Oncode’s Open Science programme

Oncode strongly encourages the widespread access to its cutting-edge research and knowledge to enable researchers, scholars, clinicians, policymakers, private and not-for-profit organizations, as well as the public, to use and build on this knowledge. In addition to more traditional technology transfer models, Oncode supports open science practices of open data, open access (publications) and open source (software).

The importance of making publications in scholarly journals related to Oncode Research accessible to the public through an open access journal publication as quickly as possible is emphasised in Oncode’s Open Access Publishing Policy.

Please contact the Open Science team if you’d like to receive more information about the Open Science and FAIR data programme.

Inga Tharun Programme Manager

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