Scientific publishing in genetic medicine

scientific publishing road blocksThe TGMI is committed to maximising opportunities for genetic research to impact on medical care as rapidly as possible. To achieve this, not only do we need to develop validated tools and resources with utility in genetic medicine, we have to ensure that the tools and any underlying data, evidence and implementation information is readily available. The accepted way of providing this information is through scientific publication, which provides independent peer review of the output and a citable reference that can be included in protocols and other publications.


Challenges in scientific publishing

Anyone with an interest in science and reading scientific literature will know the ongoing turmoil in the area of publishing research outputs – laborious, time-consuming submission and review processes,  massive publication charges, paywall vs open access, journal impact factors etc. So many academic and clinical researchers are frustrated at not being able to share their research outputs quickly and effectively.

It is not the intention of this post to rehash the arguments around all these issues, but we thought it might be of interest to share our recent experience of publishing a resource developed as part of the TGMI aspiration to generate outputs that can be useful to people delivering genetic medicine.


Wellcome Open Research

We wanted to inform the genetic community of the ICR96 exon CNV validation series that can be used for orthogonal assessment of exon copy number variant analysis.  Detecting these kinds of variants is particularly challenging and this dataset offers a resource – freely and openly available to any genetics laboratory – for assessment and validation of the methodology they are using. We submitted a scientific paper to the Wellcome Open Research (WOR) platform that included the description of the dataset, the rationale for its creation and its potential utility. The WOR platform makes all articles open for anyone to read, and accepts submissions from Wellcome-funded researchers.

The manuscript was submitted on 17th May 2017, and accepted, copy edited and published online on 26th May. Acceptance is based on a review by the Wellcome Open Research editorial team who check that the research meets scientific and data accessibility standards, not on whether the research is novel enough or interesting enough.


Post-publication peer review

Simple processes that allow rapid publication of useful research outputs are essential in the fast-moving field of genetic medicine.

Unlike most scientific publishers, Wellcome Open Research publishes articles before the peer review step. In part so that the paper is available to readers as soon as possible and in part because they consider the peer review step to be an important integral part of the process; the peer reviews are published alongside the paper and have their own citable doi. Once two reviews approving the paper are received a WOR paper is treated in the same way as any other published scientific paper, for example it is included in PubMed. The peer review process for our paper was very quick – completed by 13th June. Moreover, one of the reviewers had downloaded the ICR96 dataset and had ran it against their method and they included their experience in their open review.

Within a 3 week period, we submitted the paper, it was published, reviewed, approved and we had already received requests to access the data from four different countries.


Traditional publishing reduces research output

We have previously published similar tools and resources through more traditional publications. The road from submission to publication in these cases has typically taken much longer.  For example, the publication of our software tool, OpEx, took 10 months, and included considerable wranglings, of various types, with editors and reviewers. This length of time is by no means exceptional, as many researchers will attest to.

The challenges faced in achieving publication included opaque editorial selection processes resulting in successive resubmissions to three journals; pre-publication review taking a long time (quite understandable given that reviewers are providing this service for free, in their own time!); reviewers’ interests not always overlapping with the original intention of the paper’s authors requiring reconstructions of essentially the same information.

These types of diversions on the road to publication are daunting and time consuming, and it is highly probable that many researchers focus their energies on publishing only a limited amount of their research output. This means that much useful research data is never seen by anyone else – a huge loss to the scientific and medical communities and society as a whole.


Rapid publication of useful information

Simple processes that allow rapid publication of useful research outputs are essential in the fast-moving field of genetic medicine. These need to have the rigor of traditional scientific publishing but they must also allow researchers to make useful information openly available, easily and quickly. TGMI is committed to supporting the use of platforms like Wellcome Open Research platform in this regard.