Search

CINECA aims to support the federated queries and analyses of distributed cohorts across continents. A vital component of this work is building a machine readable catalogue of cohorts and sites that support the efforts of Work Package 1 discovery and analysis APIs, which can be programmatically queried so that API calls can be made to relevant sites and results gathered and presented to the researcher. Deliverable D1.1, Discovery Service Catalogue, supports the work of dependent work packages by implementing and demonstrating an open-source extended implementation of the Service Registry standard of the Global Alliance for Genomics and Health (GA4GH) for WP1’s discovery queries, the GA4GH Beacon queries. The Service Registry standard is now supported by the ELIXIR Beacon Network that CINECA WP1 uses to federate discovery queries across cohorts, and this demonstrator deliverable demonstrates the use of the service registry and its open source implementation.

TrypanoGEN Research Group., H3Africa Consortium., The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health., We thank the members of the wider H3Africa Consortium (www.h3africa.org). WGS in H3Africa cohorts was supported by a grant from the National Human Genome Research Institute, National Institutes of Health (NIH/NHGRI) U54HG003273. The African Collaborative Center for Microbiome and Genomics Research (ACCME) is funded by NIH/NHGRI grant U54HG006947. The AWI-Gen Collaborative Centre is funded by NIH grant U54HG006938. The Exploring Perspectives on Genomics and Sickle Cell Public Health Interventions was funded by NHGRI/NIH grant U01HG007459. The Clinical and Genetic Studies of Hereditary Neurological Disorders in Mali study was funded by the NHGRI/NIH grant U01HG007044. The Collaborative African Genomics Network (CAfGEN) is funded by the National Institute of Allergy and Infectious Diseases (NIAID) of NIH and the NHGRI of the NIH (U54AI110398). ‘TrypanoGEN: an integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasis’, was funded by the Wellcome Trust (099310/Z/12/Z). L.R.B. was supported by the CERCA Programme/Generalitat de Catalunya and by the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533). N.M. (principal investigator), S.A., G.B., G.W., J.K., Y.J.F., T.O., O.F., E.A., S.H., G. Mazandu, M. Mbiyvanga, A.B., S.K.K., E.R.C. and A. Moussa are funded by the NIH H3ABioNet grant under award number U24HG006941.

In this deliverable document, we report on the activities in task 6.1 - Stakeholder analysis, with the outreach and dissemination plan, as well as the training plan presented in this report, we have completed this task. We have used a combination of surveys and face-to-face meetings to verify and extend or identify key stakeholder groups, understand their interest in the project, and identify bottlenecks that can be addressed by outreach and training. Outreach activities will be accomplished by task 6.2 and training by task 6.3. The stakeholder survey was developed and distributed within the CINECA stakeholder community; a total of 54 responses were received. While the response rate was on the low side, it is sufficient for the initial analysis, which is presented below. A CINECA competency framework was developed and validated through the survey. The competency framework has four areas of competence (generating data, finding and accessing data, analysis and clinical interpretation of data and sharing data), reflecting the research lifecycle. A total of 17 competencies have been defined. We consider both the stakeholder analysis and the competency profile to be living documents that will evolve over the course of the project. We plan to obtain additional feedback on both the competency profile as well as update the stakeholder analysis throughout the project through a range of methods, these could include interviews, discussion groups, conference workshops. A dissemination strategy was created aimed at the effective communication of CINECA activities and outcomes to all relevant partners and stakeholders. To this end, a range of dissemination channels have been set up, including a CINECA project webpage, various social media channels, a newsletter, and physical materials such as flyers and brochures. Furthermore, a set of conferences and events have been identified at which a CINECA presence (e.g. workshop, booth, talk) could benefit stakeholder engagement. Consistent branding across these different dissemination channels is achieved through the development of a logo, colour scheme, and the creation of templates for materials such as brochures, posters and slides. Furthermore, a number of CINECA areas of research and expertise have been identified that may be suitable for publication as peer-reviewed articles. A training plan was developed covering a variety of learning interventions, including webinars, staff visits, workshops and hackathons. In the early phase of the project (first ~18 months), training activities will be focused primarily on internal CINECA knowledge exchanges to allow work package interdepencies to be resolved. To this end, a regular webinar series has been started to inform CINECA project members and other interested parties of the various CINECA activities and outcomes. Furthermore, a staff exchange program was set up to allow knowledge exchanges between different interdependent work packages. CINECA members may submit staff visit requests via an online form, and after the visit a blog post about the outcomes will be posted on the CINECA website. As the project progresses, the focus of training activities will gradually shift to dissemination to a wider audience and will consist primarily of workshops (face-to-face or online) and hackathons.