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Old and new challenges regarding comparable and viable data sharing in population-scale genomic research

European Journal of Human Genetics volume 31, pages 617–618 (2023)Cite this article

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Large-scale studies derived from genomic and health data repositories are at the forefront of personalized medicine. The US NIH Cancer Genome Atlas Project, for example, has generated maps of genomic changes in a large variety of cancer types and cases to help improve diagnosis and treatment based on the large-scale genome sequencing of patients. Another recent example is polygenic risk scoring (PRS), which, despite criticism that it should be carefully evaluated, will be used by the NHS for risk assessment as part of clinical decision-making, including access to screening. PRS, too, has become more widely available due to the development of population-level genetic studies, particularly genome-wide association studies (GWAS). Both cancer genomics and PRS demonstrate the need for and challenges involved in comparable and viable data sharing in population-scale genomic research. Here, we focus on genomic repositories sharing data among themselves, with researchers, and with donors. Despite the rapid expansion of large-scale national genomic repositories and efforts to create diverse datasets, genomic diversity, which is crucial in comparative research, is not easily attainable. Many barriers to sharing genomic data have already been identified, including the interrelated challenges of comparability, confidentiality, and viability.

First, let us consider comparability. While the research community has agreed that many more samples and genomic data are required, the diversity and limited availability of genomic data often create challenges in terms of comparability. As previous studies have shown by comparing biobank data from the UK, Japan, and Taiwan, PRS’s prediction accuracy based on UK data was far lower in non-European populations. Indeed, it was 2.5-fold lower in East Asians and 4.9-fold lower in Africans, on average [1]. Similarly, the differences in accessible genomic data between populations have led, for example, to the development of Japanese oncogenetic panels for the Japanese population [2]. Transforming genomic data into scientific insights and knowledge requires appropriate quantifications and annotations from medical and clinical perspectives. Particularly when researchers use decentralized datasets internationally, while the processing of genomic data must be standardized, direct access to raw data is often avoided due to privacy concerns. However, these data repositories are still thought of as local and separate datasets [3]. In this regard, one of the key tasks is harmonizing the interpretation and reporting of disease-associated markers detected during sequencing, for example, cancer germline/somatic mutations and their various categories of variants [4]. Moreover, there is an on-going struggle to integrate other health data from separate labs or hospitals with genomic data.

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Funding

Funding

AR and JM are grateful for the funding provided by the JSPS – ISF Joint Program, grant 62/22, “Biobanks for genomic medicine in Israel and Japan: An analysis of ethics and policy”.

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Authors and Affiliations

  1. Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beer-Sheba, Israel

    Aviad Raz & Yael Hashiloni-Dolev

  2. Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan

    Jusaku Minari, Kayo Takashima & Hristina Gaydarska

  3. The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford, Oxford, UK

    Ruth Horn

  4. Ethics of Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany

    Ruth Horn

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  1. Aviad Raz
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  5. Yael Hashiloni-Dolev
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Contributions

Original draft preparation: AR; conceptualization: JM and AR; review and editing of the draft: AR, JM, KT, HG, YH, RH; All authors have read and agreed to the published version of the manuscript.

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Correspondence to Aviad Raz.

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Raz, A., Minari, J., Takashima, K. et al. Old and new challenges regarding comparable and viable data sharing in population-scale genomic research. Eur J Hum Genet 31, 617–618 (2023). https://doi.org/10.1038/s41431-023-01355-3

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