Publications

Browse academic papers authored by the GA4GH community.

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Title Year Author(s) Publisher Work Streams Products
Navigating ethical, legal and social implications in genomic newborn screening 2026 Lewis, A.C.F. et al. Lewis, A.C.F., Brown, G., Bombard, Y. NATURE REVIEWS GENETICS Regulatory & Ethics Work Stream (REWS) Genomic sequencing in newborn screening
Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework 2025 Bridges, Y. et al. Bridges, Y., de Souza, V., Cortes, K.G., Haendel, M., Harris, N.L., Korn, D.R., Marinakis, N.M., Matentzoglu, N., McLaughlin, J.A., Mungall, C.J., Odell, A., Robinson, P.N., Smedley, D., Jacobsen, J.O.B. BMC BIOINFORMATICS Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
The International Health Cohorts Consortium (IHCC) advances population health research and genomic discovery 2025 Connolly, J.J et al. Connolly, J.J, Sundseth, S., Wood, G.M., Nwaneri, S., Awadalla, P., Ramsay, M., Keane, T., Goodhand, P., Butterworth, A.S., Hakonarson, H. COMMUNICATIONS MEDICINE
The ICGC ARGO data dictionary for standardizing global cancer clinical data 2025 Nahal-Bose, H.K. et al. Nahal-Bose, H.K., Lichter, P., Weber, U., Stein, L.D., Bajari, R., Xiang, L., Su, E., Eubank, J., Schütte, C., Yung, C.K., Courtot, M. SCIENTIFIC DATA Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data 2025 D’Altri, T. et al. D’Altri, T., Freeberg, M.A., Curwin, A.J., et al. NATURE GENETI Data Use & Researcher Identity (DURI) Work Stream Data Use Ontology (DUO)
The expanding global genomics landscape: Converging priorities from national genomics programs 2025 Howley, C. et al. Howley, C., Haas, M.A., Al Muftah, W.A., Annan, R.B., Green, E.D., Lundgren, B., Scott, R.H., Stark, Z., Tan, P., North, K.N., Boughtwood, T. AMERICAN JOURNAL OF HUMAN GENETICS
Rakeiora Genomics Platform: a pathfinder for genomic medicine research in Aotearoa New Zealand 2025 Wihongi, H. et al. Wihongi, H., Te Aika, B., de Ligt, J., Print, C.G., Tsai, P., Curran, B., Jones, N., Huh, J, Owen Perkins, E., Pestle, M., Zhao, K., Halytskyy, Y., Robertson, S.P., Halliday, B.J., Goodin, E., Markie, D.M., Lamont, A., Wilcox, P. JOURNAL OF THE ROYAL SOCIETY OF NEW ZEALAND Large-Scale Genomics (LSG) Work Stream, Data Security Work Stream, Data Use & Researcher Identity (DURI) Work Stream Passports, htsget
pgxRpi: an R/bioconductor package for user-friendly access to the Beacon v2 API 2025 Zhao, H. et al. Zhao, H., Baudis, M. BIOINFORMATICS ADVANCES Discovery Work Stream Beacon
Multimodal data curation via interoperability: use cases with the Medical Imaging and Data Resource Center 2025 Chen, W. et al. Chen, W., Whitney, H.M., Kahaki, S., Meyer, C., Li, H., Sá, R.C., Lauderdale, D., Napel, S., Gersing, K, Grossman, R.L., Giger, M.L. SCIENTIFIC DATA Federated Analysis Work Stream (formerly Cloud Work Stream) Data Repository Service (DRS)
GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders 2025 Lauren Rekerle, L. et al. Lauren Rekerle, L., Danis, D., Rehburg, F., Graefe, A.S.L., Bily, V., Cacheiro, P.,  Chimirri, L., Chong, J.X., Connelly, E., de Vries, B.B.A., Dingemans, A.J.M., Duyzend, M.H., Freiberger, T., Gehle, P., Groza, T.,  Hansen, P., Jacobsen, J.O.B.,  Klocperk, A., Ladewig. M.S., Love, M.I.,  Mordhorst, A., Munoz-Torres, M.C., Reese, J., Schuetz, C., Smedley, D., Strauss, T., Vladyka, O., Zocche, D.,  Thun, S., Mungall, C.J., Haendel, M.A., Robinson, P.N. THE AMERICAN JOURNAL OF HUMAN GENETICS Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
GA4GH Data Passports: Proposing a New Technical Specification for Data Policy Representation 2025 Lawson, J. et al. Lawson, J., Conner, T. SSRN Data Use & Researcher Identity (DURI) Work Stream, Data Security Work Stream Data Passports
Communicating clearly about data sharing in genomics 2025 Thaler, D. et al. Thaler, D., Uberoi, D., Thorogood, A., Milne, R., Newson A.J., Hall, A., Glazer, D., Esselaar, P., Joly, Y. HUMAN GENOMICS Regulatory & Ethics Work Stream (REWS) Data Sharing Lexicon
An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets 2025 Graefe, A.S.L. et al. Graefe, A.S.L., Hübner, M.R., Rehburg, F., Sander, S., Alkarkoukly, S., Grönke, A., Weyersberg, A., Danis, D., Zschüntzsch, J., Nyoungui, E.F., Wiegand, S., Kühnen, P., Robinson, P.N., Beyan, O., Thun, S. NATURE Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
A call for a global cyberbiosecurity framework in genomics 2025 Joly, Y. et al. Joly, Y., Xue, Y., Huang, J., Uberoi, D. NATURE GENETICS
Use of Beacon v2 for Improving Genomics Based Research in a Clinical Setting 2024 Naro, D. et al. Naro, D., Delgado, J., Llorente, S., Hernaez, M. IOS PRESS Discovery Work Stream Beacon
The Key Features of a Genetic Nondiscrimination Policy: A Delphi Consensus Statement 2024 Uberoi, D. et al. Uberoi, D., Dalpé, G., Cheung, K., Kondrup, E., Palmour, N., Arawi, T., Arych, M., Ayuso, C., Bentzen, H.B., Blizinsky, K., Bombard, Y., Chung, B.H.Y., de Paor, A., Doerr, M., Dove, E.S., Dupras, C., Greenbaum, D., Haidar, H., Ho, C.H., Jamuar, S.S., Kim, H., Lebret, A., Macdonald, A., Minssen, T., Nasir, J., Nicol, D., Nicolás, P., Otlowski, M., Nair, A.P.S.,  Prince, A.E.R., Rothstein, M., Ryan, R., Sillon, G., Singh, K.K., Stedman, I., Tiller, J., Van Hoyweghen, I., Zawati, M.H., Joly, Y. JAMA NETWORK OPEN Regulatory & Ethics Work Stream (REWS) Genetic Discrimination Toolkit, Genetic Discrimination Toolkit
The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution 2024 Kanitz, A. et al. Kanitz, A., McLoughlin, M.H., Beckman, L., Malladi, V.S., Ellrott, K. COMPUTING IN SCIENCE & ENGINEERING Federated Analysis Work Stream (formerly Cloud Work Stream) Task Execution Service (TES)
Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child? 2024 Friedman J.M. et al. Friedman J.M., Bombard Y., Carleton B., Issa A.M., Knoppers B., Plon S.E., Rahimzadeh V., Relling M.V., Williams M.S., van Karnebeek C., Vears D., Cornel M.C. GENETICS IN MEDICINE Regulatory & Ethics Work Stream (REWS)
Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond 2024 Leist, I.C. et al. Leist, I.C., Rivas-Torrubia, M., Barturen, G., Gut, I.G., Rueda, M. BMC BIOINFORMATICS Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Discovery Work Stream Phenopackets, Beacon
Investigating the roles and responsibilities of institutional signing officials after data sharing policy reform for federally funded research in the United States: national survey 2024 Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J. JMIR Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream Data Access Committee Review Standards (DACReS) Toolkit
EpiVar Browser: advanced exploration of epigenomics data under controlled access 2024 Lougheed, D.R. et al. Lougheed, D.R., Liu, H., Aracena, K.A., Grégoire, R., Pacis, A., Pastinen, T., Barreiro, L.B., Joly, Y., Bujold, D., Bourque, G. BIOINFORMATICS Regulatory & Ethics Work Stream (REWS)
Defining and pursuing diversity in human genetic studies 2024 Raven-Adams, M.C. et al. Raven-Adams, M.C., Joly, Y., Knoppers, B.M., Thorogood, A., Kumuthini, J., Ho, C.W.L, Gonzalez, A., Nelson, S.C., Bombard, Y., Thaldar, D., Liu, H., Costa, A., Muralidharan, V., Henriques, S., Nasir, J., Lumaka, A.,  Kaiser, B., Jamuar, S.S., Lewis, A.C.F. NATURE GENETICS Regulatory & Ethics Work Stream (REWS) Diversity in Datasets
Comment Form: WHO Principles for Human Genome Access, Use, and Sharing 2024 Nicol, D. et al. Nicol, D., Uberoi, D. SSRN Regulatory & Ethics Work Stream (REWS)
Achieving procedural parity in managing access to genomic and related health data: a global survey of data access committee members 2024 Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J., Dove, E. BIOPRESERVATION AND BIOBANKING Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream Data Access Committee Review Standards (DACReS) Toolkit
A qualitative interview study to determine barriers and facilitators of implementing automated decision support tools for genomic data access 2024 Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J., Dove, E. BMC MEDICAL ETHICS Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream Data Access Committee Review Standards (DACReS) Toolkit
A proposal for an inclusive working definition of genetic discrimination to promote a more coherent debate 2024 Kaiser, B. et al. Kaiser, B., Uberoi, D., Raven-Adams, M.C., Cheung, K., Bruns, A., Otlowski, M., Prince, A.E.R., Tiller, J., Ahmed, A., Bombard, Y., Dupras, C., Ryan, R.,  Joly, Y. NATURE GENETICS Regulatory & Ethics Work Stream (REWS) Genetic Discrimination Toolkit
A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery 2024 Danis, D. et al. Danis, D., Bamshad M.J., Bridges, Y., Cacheiro, P., Carmody, L.C., Chong, J.X., Coleman, B., Dalgleish, R., Freeman, P.J., Graefe, A.S.L,, Groza, T., Jacobsen. J.O.B., Klocperk, A., Kusters, M., Ladewig, M.S., Marcello, A.J., Mattina, T., Mungall, C.J., Munoz-Torres, M.C., Reese, J.T., Rehburg, F., Reis, B.C.S., Schuetz, C., Smedley, D., Strauss, T., Thun, S., Wissink, K., Wagstaff, J.F., Zocche, D., Haendel, M.A., Robinson, P.N. MEDRXIV Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
A call to action to scale up research and clinical genomic data sharing 2024 Stark, Z. et al. Stark, Z., Glazer, D., Hofmann, O., Rendon, A., Marshall, C.R., Ginsburg, G.S.,  Lunt, C., Allen, N.,  Effingham M.,  Ward, J.H., Hill, S.H., Ali, R.,  Goodhand, P.,  Page, A.,  Rehm, H.L.,  North, K.N.,  Scott, R.H. NATURE REVIEW GENETICS
Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows 2023 Suetake, H. et al. Suetake, H., Fukusato, T., Igarashi, T., Ohta, T. GIGA SCIENCE
Recording the ethical provenance of data and automating data stewardship 2023 Bernier, A. et al. Bernier, A., Raven-Adams, M., Zaccagnini, D., Knoppers, B. M. BIG DATA & SOCIETY Regulatory & Ethics Work Stream (REWS) Ethical Provenance Toolkit
Phenopacket-tools: building and validating GA4GH Phenopackets 2023 Danis, D et al. Danis, D, Jacobsen, JOB, Wagner, AH, Groza, T, Beckwith, MA, Rekerle, L, Carmody, LC, Reese, J, Hegde, H, Ladewig, MS, Seitz, B, Munoz-Torres, M, Harris, NL, Rambla, J, Baudis, M, Mungall, CJ, Haendel, MA, Robinson, PN. PLOS ONE Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
Development and application of a computable genotype model in the GA4GH Variation Representation Specification 2023 Goar, W. et al. Goar, W., Babb, L., Chamala,S., Cline, M., Freimuth, R.R., Hart, R.K., Kuzma, K., Lee, J., Nelson, T., Prlić, A., Riehle, K., Smith, A., Stahl, K., Yates, A.D., Rehm, H.L., Wagner, A.H. PACIFIC SYMPOSIUM ON BIOCOMPUTING Genomic Knowledge Standards (GKS) Work Stream Variation Representation Specification (VRS)
The GA4GH Phenopacket schema defines a computable representation of clinical data 2022 Jacobsen, J. O. et al. Jacobsen, J. O., Baudis, M., Baynam, G. S., Beckmann, J. S., Beltran, S., Buske, O. J., Callahan, T. J., Chute, C. G., Courtot, M., Danis, D., Elemento, O., Essenwanger, A., Freimuth, R. R., Gargano, M. A., Groza, T., Hamosh, A., Harris, N. L., Kaliyaperumal, R., Lloyd, K. C., Robinson, P. N., Khalifa, Aly, Krawitz, Peter M., Köhler, Sebastian, Laraway, Brian J., Matalonga, Leslie, McMurry, Julie A., Ogishima, Soichi, Piscia, Davide, Pontikos, Nikolas, Roos, Marco, Sass, Julian, Schofield, Paul N., Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D., Steinhaus, Robin, Thun, Sylvia, Wagner, Alex H., Warner, Jeremy L., Weiland, Claus NATURE BIOTECHNOLOGY Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
Sapporo: a workflow execution service that encourages the reuse of workflows in various languages in bioinformatics 2022 Suetake, H. et al. Suetake, H., Tanjo, T., Ishii, M,., Kinoshita, B.P., Fujino, T., Hachiya, T., Kodama, Y., Fujisawa, T., Ogasawara, O., Shimizu, A., Arita, M., Fukusato, T., Igarashi, T., Ohta, T. F1000RESEARCH Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
Return of genomic results does not motivate intent to participate in research for all: Perspectives across 22 countries 2022 Richard Milne Richard Milne GENETICS IN MEDICINE Regulatory & Ethics Work Stream (REWS) Policy on Clinically Actionable Genomic Research Results
Leveraging Algorithms to Improve Decision-Making Workflows for Genomic Data Access and Management 2022 Rahimzadeh, V. et al. Rahimzadeh, V., Lawson, J., Rushton, G., Dove, E.S. BIOPRESERVATION AND BIOBANKING Regulatory & Ethics Work Stream (REWS)
Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space 2022 Schatz, M.C. et al. Schatz, M.C., Philippakis, A.A,, Afgan, E., Banks, E., Carey, V.J., Carroll, R.J., Culotti, A., Ellrott, K., Goecks, J., Grossman, R.L., Hall, I.M., Hansen, K.D., Lawson, J., Leek, J.T., Mosher, S., Morgan, M., Nekrutenko, A., O’Connor, B.D., Osborn, K., Paten, B., Patterson, C., Tan, F.J., Waldron, L., Wang, T., Wuichet, K., and AnVIL Team. CELL GENOMICS Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
Genetic discrimination still casts a large shadow in 2022. 2022 Joly, Y. et al. Joly, Y., Dalpe, G. EUR J HUM GENET Regulatory & Ethics Work Stream (REWS)
GA4GH Phenopackets: a practical introduction 2022 Ladewig, Markus S. et al. Ladewig, Markus S., Wagner, Alex H., Danis, Daniel, ElKassaby, Baha, Gargano, Michael, Groza, Tudor, Baudis, Michael, Steinhaus, Robin, Seelow, Dominik, Schofield, Paul N., Elemento, Olivier, Smith, Lindsay, McMurry, Julie A. ADVANCED GENETICS Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Phenopackets
CRAM 3.1: advances in the CRAM file format 2022 Bonfield, J.K. Bonfield, J.K. BIOINFORMATICS Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream CRAM
Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review 2022 McDermott J.H. et al. McDermott J.H., Wright S., Sharma V., Newman W.G., Payne K., Wilson P. FRONT MED Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream Pharmacogenomics Data Standardisation
Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data 2022 Rueda, M. et al. Rueda, M., Ariosa, R., Moldes, M., Rambla, J. BIOINFORMATICS Discovery Work Stream Beacon
Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond 2022 Rambla, J. et al. Rambla, J., Baudis, M., Ariosa, R., Beck, T., Fromont, L. A., Navarro, A., Paloots, R., Rueda, M., Saunders, G., Singh, B., Spalding, J. D., Törnroos, J., Vasallo, C., Veal, C. D., Brookes, A. J. HUMAN MUTATION Discovery Work Stream Beacon
The Data Use Ontology to streamline responsible access to human biomedical datasets 2021 Lawson, J. et al. Lawson, J., Cabili, M.N., Kerry, G., Boughtwood, T., Thorogood, A., Alper, P., Bowers, S.R., Boyles, R.R., Brookes, A.J., Brush, M., Burdett, T., Clissold, H., Donnelly, S., Dyke, S.O.M., Freeberg, M.A., Haendel, M.A., Hata, C., Holub, P., Jeanson, F., Jene, A., Kawashima, M., Kawashima, S., Konopko, M., Kyomugisha, I., Li, H., Linden, M., Rodriguez, L.L., Morita, M., Mulder, N., Muller, J., Nagaie, S., Nasir, J., Ogishima, S., Ota Wang, V., Paglione, L.D., Pandya, R.N., Parkinson, H., Philippakis, A.A., Prasser, F., Rambla, J., Reinold, K., Rushton, G.A., Saltzman, A., Saunders, G., Sofia, H.J., Spalding, J.D., Swertz, M.A., Tulchinsky, I., Varma, S., Voisin, C., Yamamoto, N., Yamasaki, C., Zass, L., Guidry Auvil, J.M., Nyrönen, T.H., Courtot, M. CELL GENOMICS Data Use & Researcher Identity (DURI) Work Stream Data Use Ontology (DUO)
Refget: standardized access to reference sequences 2021 Yates, A.D. et al. Yates, A.D., Adams, J., Chaturvedi, S., Davies, R.M., Laird, M., Leinonen, R., Nag, R., Sheffield, N.C., Hofmann, O., Keane, T.O. BIOINFORMATICS Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream refget Sequences
International federation of genomic medicine databases using GA4GH standards 2021 Thorogood, A. et al. Thorogood, A., Rehm, H.L., Goodhand, P., Page, A.J.H., Joly, Y., Baudis, M., Rambla, J., Navarro, A., Nyronen, T.H., Linden, M., Dove, E.S., Fiume, M., Brudno, M., Cline, M.S., Birney, E. CELL GENOMICS Data Security Work Stream, Data Use & Researcher Identity (DURI) Work Stream, Regulatory & Ethics Work Stream (REWS), Discovery Work Stream Passports, Beacon, Authorisation and Authentication Infrastructure (AAI), Data Connect, Data Use Ontology (DUO), Workflow Execution Service (WES), Task Execution Service (TES), Tool Registry Service (TRS), Data Repository Service (DRS)
I can drive in Iceland: Enabling international joint analyses 2021 Lunt, C. et al. Lunt, C., Denny, J.C. CELL GENOMICS
GA4GH: International policies and standards for data sharing across genomic research and healthcare 2021 Rehm, H. et al. Rehm, H., Goodhand, P., North, K., Birney, E., et al. CELL GENOMICS
GA4GH Passport standard for digital identity and access permissions 2021 Voisin, C. et al. Voisin, C., Linden, M., Dyke, S.O.M., Bowers, S.R., Alper, P., Barkley, M.P., Bernick, D., Chao, J., Courtot, M., Jeanson, F., Konopko, M.A., Kuba, M., Lawson, J., Leinonen, J., Li, S., Ota Wang, V., Philippakis, A.A., Reinold, K., Rushton, G.A., Spalding, J.D., Törnroos, J., Tulchinsky, I., Guidry Auvil, J.M., Nyrönen, T.H. CELL GENOMICS Data Use & Researcher Identity (DURI) Work Stream Passports, Authorisation and Authentication Infrastructure (AAI)
Executing workflows in the cloud with WESkit 2021 Kensche, P.R. et al. Kensche, P.R., Kanitz, A., Topolsky, I., Jablonski, K.P., Mandreoli, P., Twardziok, S. BIOHACKRXIV PREPRINTS Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
Empirical validation of an automated approach to data use oversight 2021 Cabili, M.N. et al. Cabili, M.N., Lawson, J., Saltzman, A., Rushton, G., O’Rourke, P., Wilbanks, J., Rodriguez, L.L., Nyronen, T., Courtot, M., Donnelly, S. MORAN N. CABILI 7 JONATHAN LAWSON 7 ANDREA SALTZMAN GREG RUSHTON PEARL O’ROURKE JOHN WILBANKS LAURA LYMAN RODRIGUEZ TOMMI NYRONEN MéLANIE COURTOT STACEY DONNELLY ANTHONY A. PHILIPPAKIS 8 SHOW LESS SHOW FOOTNOTES OPEN ACCESSDOI:HTTPS://DOI.ORG/10.1016/J.XGEN.2021.100031 PLUMX METRICS PREVIOUS ARTICLETHE DATA USE ONTOLOGY TO STREAMLINE RESPONSIBLE …
Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries 2021 Milne, R. et al. Milne, R., Morley, K.I., Almarri, M.A. GENOME MED Regulatory & Ethics Work Stream (REWS)
CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis 2021 Dursi, L.J et al. Dursi, L.J, Bozoky, Z., de Borja, R., Li, H., Bujold, D, Lipski, A., Rashid, S.F., Sethi, A., Memon, N., Naidoo, N., Coral-Sasso, F., Wong, M,, Quirion, P.O., Lu, Z., Agarwal, S., Pavlov, Y., Ponomarev, A., Husic, M., Pace, K., Palmer, S., Grover, S.A., Hakgor, S., Siu, L.L., Malkin, D., Virtanen, C., Pugh, T.J., Jacques, P.E., Joly, Y., Jones, S.J.M., Bourque, G., Brudno, M. CELL GENOMICS
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers 2021 Bai, J. et al. Bai, J., Bandla, C., Guo, J., Vera Alvarez, R., Bai, M., Vizcaíno, J.A., Moreno, P., Grüning, B., Sallou, O., Perez-Riverol, Y. JOURNAL OF PROTEOME RESEARCH Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
An international policy on returning genomic research results. 2021 Lewis, A.C.F. et al. Lewis, A.C.F., Knoppers, B.M., Green, R.C. GENOME MED Regulatory & Ethics Work Stream (REWS) Policy on Clinically Actionable Genomic Research Results
The GA4GH Variation Representation Specification (VRS): A Computational Framework for the Precise Representation and Federated Identification of Molecular Variation 2020 Wagner, A.H. et al. Wagner, A.H., Babb, L., Alterovitz, G., Baudis, M., Brush, M., Cameron, D.L., Cline, M., Griffith, M., Griffith, O.L., Hunt, S.  CELL GENOMICS Genomic Knowledge Standards (GKS) Work Stream Variation Representation Specification (VRS)
Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases 2020 Corvò, A. et al. Corvò, A., Matalonga, L., Spalding, D., Senf, A., Laurie, S., Picó-Amador, D., Paramonov, I., Foix Romero, A., Garcia-Rios, E., Mohan, A., Thomas, C., Halmagyi, C., Freeberg, M.A., Töpf, A., Horvath, R., Saunders, G., Gut, I., Keane, T., Piscia, D., Beltran, S. CELL GENOMICS Large-Scale Genomics (LSG) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream) htsget
Members of the public in the USA, UK, Canada and Australia expressing genetic exceptionalism say they are more willing to donate genomic data. 2020 Middleton, A. et al. Middleton, A., Milne, R., Howard, H. EUR J HUM GENET Regulatory & Ethics Work Stream (REWS)
How Can We Not Waste Legacy Genomic Research Data? 2020 Wallace, S.E. et al. Wallace, S.E., Kirby, E., Knoppers, B.M. FRONT. GENET. Regulatory & Ethics Work Stream (REWS)
Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data? 2020 Middleton, A. et al. Middleton, A., et al. THE AMERICAN JOURNAL OF HUMAN GENETICS Regulatory & Ethics Work Stream (REWS)
Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale 2020 Carey, V.J. et al. Carey, V.J., Ramos, M., Stubbs, B.J., Oh, S., Turaga, N., Waldron, L., Morgan, M. JCO CLINICAL CANCER INFORMATICS Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia 2019 Milne, R. et al. Milne, R., Morley, K.I., Howard, H., Niemiec, E., Nicol, D., Critchley, C., Prainsack, B., Vears, D., Smith, J., Steed, C., Bevan, P., Atutornu, J., Farley, L., Goodhand, P., Thorogood, A., Kleiderman,E., Middleton, A. HUMAN GENETICS Regulatory & Ethics Work Stream (REWS) Your DNA, Your Say (Participant Values Survey)
Trust in genomic data sharing among members of the general public in the UK 2019 Milne, R. et al. Milne, R., Morley, K.I., Howard, H. CANADA AND AUSTRALIA. HUM GENET Regulatory & Ethics Work Stream (REWS)
Return of individual genomic research results: are laws and policies keeping step? 2019 Thorogood, A. et al. Thorogood, A., Dalpé, G., Knoppers, B.M. EUROPEAN JOURNAL OF HUMAN GENETICS Regulatory & Ethics Work Stream (REWS) Policy on Clinically Actionable Genomic Research Results
Openness, inclusion, and respect in dementia research 2019 Thorogood, A. et al. Thorogood, A., Dalpé, G., Gastmans, C., Gauthier, S. LANCET NEUROLOGY Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Model consent clauses for rare disease research. 2019 Nguyen, M.T. et al. Nguyen, M.T., Goldblatt, J., Isasi, R., et al. BMC MED ETHICS 20 Regulatory & Ethics Work Stream (REWS) Consent Toolkit
Model consent clauses for rare disease research 2019 Nguyen, M.T. et al. Nguyen, M.T., Goldblatt, J., Isasi, R., Jagut, M., Jonker, A.H., Kaufmann, P., Ouillade, L., Molnar-Gabor, F., Shabani, M., Sid, E., Tassé, A., Wong-Rieger, D., Knoppers, B.M. BMC MEDICAL ETHICS Regulatory & Ethics Work Stream (REWS) Consent Toolkit
Letter: Relearning the 3 R’s? Reinterpretation, Recontact, and Return of Genetic Variants 2019 Knoppers, B.M. et al. Knoppers, B.M., Thorogood, A., Zawati, M.H. GENETICS IN MEDICINE Regulatory & Ethics Work Stream (REWS)
Integrating Genomics into Healthcare: A Global Responsibility 2019 Stark, Z. et al. Stark, Z., Dolman, L., Manolio, T.A., Ozenberger, B., Hill, S.L., Caulfied, M.J., Levy, Y., Glazer, D., Wilson, J., Lawler, M., Boughtwood, T., Braithwaite, J., Goodhand, P., Birney, E., North, K.N. AMERICAN JOURNAL OF HUMAN GENETICS
Federated discovery and sharing of genomic data using Beacons 2019 Fiume, M. et al. Fiume, M., Cupak, M., Keenan, S., Rambla, J., de la Torre, S., Dyke, S.O.M., Brookes, A.J., Carey, K., Lloyd, D., Goodhand, P., Haeussler, M., Baudis, M., Stockinger, H., Dolman, L., Lappalainen, I., Törnroos, J., Linden, M., Spalding, J.D., Ur-Rehman, S., Page, A., Flicek, P., Sherry, S.T., Haussler, D., Varma, S., Saunders, G., Scollen, S. NATURE BIOTECHNOLOGY Discovery Work Stream Beacon, Framework for responsible sharing of genomic and health-related data
End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA 2019 Senf, A. Senf, A. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Data Security Work Stream, Large-Scale Genomics (LSG) Work Stream Genetic Data Encryption (Crypt4GH)
Consent insufficient for data release 2019 Nicol, D. et al. Nicol, D., Eckstein, L., Bentzen, H.B., Borry, P., Burgess, M., Burke, W., Chalmers, D.R., Cho, M., Dove, E.S., Fullerton, S., Ida, R., Kato, K., Kaye, J., Koenig, B., Manson, S., McGrail, K., Meslin, E.M., O'Doherty, K., Prainsack, B., Shabani, M., Tabor, H., Thorogood, A., de Vries, J. SCIENCE Regulatory & Ethics Work Stream (REWS)
Connecting Data and Expertise: A New Alliance for Biodiversity Knowledge. 2019 Hobern, D. et al. Hobern, D., Baptiste, B., Copas, K., Guralnick, R., Hahn, A., van Huis, E., Kim, E. BIODIVERSITY DATA JOURNAL
BioSamples Database: An Updated Sample Metadata Hub. 2019 Courtot, M. et al. Courtot, M., Cherubin, L., Faulconbridge, A., Vaughan, D., Green, M., Richardson, D., Harrison, P., Whetzel, P.L., Parkinson, H., Burdett, T. NUCLEIC ACIDS RESEARCH Data Use & Researcher Identity (DURI) Work Stream Authorisation and Authentication Infrastructure (AAI), Data Use Ontology (DUO)
Best practices for benchmarking germline small-variant calls in human genomes 2019 Krusche, P. et al. Krusche, P., Trigg, L., Boutros, P.C., Mason, C.E., De La Vega, F.M., Moore, B.L., Gonzalez-Porta, M., Eberle, M.A., Tezak, Z., Lababidi, S., Truty, R., Asimenos, G., Funke, B., Fleharty, M., Chapman, B.A., Salit, M., Zook, J.M. NATURE BIOTECHNOLOGY Genomic Knowledge Standards (GKS) Work Stream Variant Benchmarking Tools
The Genomic Commons 2018 Contreras, J.L. et al. Contreras, J.L., Knoppers, B.M. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Simplifying research access to genomics and health data with Library Cards 2018 Cabili, M.N. et al. Cabili, M.N., Carey, K., Dyke, S.O.M., Brookes, A.J., Fiume, M., Jeanson, F., Kerry, G., Lash, A., Sofia, H., Spalding, J.D., Tassé, A., Varma, S., Pandya, R. SCIENTIFIC DATA Data Use & Researcher Identity (DURI) Work Stream Passports, Data Use Ontology (DUO)
Review and comparison of electronic patient-facing family health history tools 2018 Welch, B.M. et al. Welch, B.M., Wiley, K., Pflieger, L., Achiangia, R., Baker, K., Hughes-Halbert, C., Morrison, H., Schiffman, J., Doerr, M. JOURNAL OF GENETIC COUNSELING Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Regulatory & Ethics Work Stream (REWS) Family History Toolkit
Responsible Sharing of Biomedical Data and Biospecimens via the ‘Automatable Discovery and Access Matrix’ (ADA-M) 2018 Woolley, J.P. et al. Woolley, J.P., Kirby, E., Leslie, J., Jeanson, F., Cabili, M.N., Rushton, G., Hazard, J.G. NPJ GENOMIC MEDICINE Regulatory & Ethics Work Stream (REWS)
Registered access: authorizing data access. 2018 Dyke, S.O.M. et al. Dyke, S.O.M., Linden, M., Lappalainen, I., et al. EUR J HUM GENET
Registered access: authorizing data access 2018 Dyke, S.O.M. et al. Dyke, S.O.M., Linden, M., Lappalainen, I., De Argila, J.R., Carey, K., Lloyd, D., Spalding, J.D., Cabili, M.N., Kerry, G., Foreman, J., Cutts, T., Shabani, M., Rodriguez, L.L., Haeussler, M., Walsh, B., Jiang, X., Wang, S., Perrett, D., Boughtwood, T., Matern, A., Brookes, A.J., Cupak, M., Fiume, M., Pandya, R., Tulchinsky, I., Scollen, S., Törnroos, J., Das, S., Evans, A.C., Malin, B.A., Beck, S., Brenner, S.E., Nyrönen, T., Blomberg, N., Firth, H.V., Hurles, M.E., Philippakis, A.A., Rätsch, G., Brudno, M., Boycott, K.M., Rehm, H.L., Baudis, M., Sherry, S.T., Kato, K., Knoppers, B.M., Baker, D., Flicek, P. EUROPEAN JOURNAL OF HUMAN GENETICS Data Use & Researcher Identity (DURI) Work Stream, Regulatory & Ethics Work Stream (REWS) Passports
Privacy-Preserving Linkage of Genomic and Clinical Data Sets 2018 Baker, D. et al. Baker, D., Knoppers, B.M., Phillips, M., van Enckevort, D., Kaufmann, P., Lochmuller, H., Taruscio, D. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Regulatory & Ethics Work Stream (REWS), Data Security Work Stream
Privacy-Preserving Linkage of Genomic and Clinical Data Sets 2018 Baker, D.B. et al. Baker, D.B., Knoppers, B.M., Phillips, M., van Enckevort, D., Kaufmann, P., Lochmuller, H., Taruscio, D. IEEE/ACM TRANS COMPUT BIOL BIOINFORM. Regulatory & Ethics Work Stream (REWS)
Model Framework for Governance of Genomic Research and Biobanking in Africa - a Content Description 2018 Yakubu, A. et al. Yakubu, A., Tindana, P., Matimba, A., Littler, K., Munung, N.S., Madden, E., Staunton, C., de Vries, J. AAS OPEN RESEARCH Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Key Implications of Data Sharing in Pediatric Genomics 2018 Rahimzadeh, V. et al. Rahimzadeh, V., Schickhardt, C., Knoppers, B.M., Sénécal, K., Vears, D.F., Fernandez, C.F., Pfister, S., Plon, S.E., Terry, S.F., Williams, J., Williams, M.S., Cornel, M.C., Friedman, J.M. JAMA Regulatory & Ethics Work Stream (REWS) Consent Toolkit
Key Implications of Data Sharing in Pediatric Genomics 2018 Rahimzadeh, V. et al. Rahimzadeh, V., Schickhardt, C., Knoppers, B.M. JAMA PEDIATR. Regulatory & Ethics Work Stream (REWS)
Htsget: A protocol for securely streaming genomic data 2018 Kelleher, J. et al. Kelleher, J., Lin, M., Albach, C.H., Birney, E., Davies, R., Gourtovaia, M., Glazer, D., Gonzalez, C.Y., Jackson, D.K., Kemp, A., Marshall, J., Nowak, A., Senf, A., Tovar-Corona, J.M., Vikhorev, A., Keane, T.M. BIOINFORMATICS Large-Scale Genomics (LSG) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream) htsget
Genomic Data Sharing [Special issue] 2018 Joly, Y. et al. Joly, Y., Knoppers, B.M. HUMAN GENETICS Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
ClinGen advancing genomic data-sharing standards as a GA4GH driver project 2018 Dolman, L. et al. Dolman, L., Page, A., Babb, L., Freimuth, R.R., Arachchi, H., Bizon, C., Brush, M., Fiume, M., Haendel, M.A., Hansen, D.P., Milosavljevic, A., Patel, R.Y., Pawliczek, P., Yates, A.D., Rehm, H.L. HUMAN MUTATION
Broaden human-rights focus for health data under GDPR 2018 Knoppers, B.M. Knoppers, B.M. NATURE Regulatory & Ethics Work Stream (REWS) Health Data Sharing, Privacy, and Regulatory Forum (formerly GDPR Forum), Framework for responsible sharing of genomic and health-related data
BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2 2018 Cline, M.S. et al. Cline, M.S., Liao, R.G., Parsons, M.T., Paten, B., Alquaddoomi, F., Antoniou, A., Baxter, S., Brody, L., Cook-Deegan, R., Coffin, A., Couch, F.J., Craft, B., Currie, R., Dlott, C.C., Dolman, L., den Dunnen, J.T., Dyke, S.O.M., Domchek, S.M., Easton, D., Fischmann, Z., Foulkes, W.D., Garber, J., Goldgar, D., Goldman, M.J., Goodhand, P., Harrison, S., Haussler, D., Kato, K., Knoppers, B.M., Markello, C., Nussbaum, R., Offit, K., Plon, S.E., Rashbass, J., Rehm, H.L., Robson, M., Rubinstein, W.S., Stoppa-Lyonnet, D., Tavtigian, S., Thorogood, A., Zhang, C. PLOS GENETICS Regulatory & Ethics Work Stream (REWS)
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes 2018 Krusche, P. et al. Krusche, P., Trigg, L., Boutros, P.C., Mason, C.E., De La Vega, F.M., Moore, B.L., Gonzalez-Porta, M., Eberle, M.A., Tezak, Z., Lababidi, S., Truty, R., Asimenos, G., Funke, B., Fleharty, M., Salit, M., Zook, J.M. NATURE BIOTECHNOLOGY Large-Scale Genomics (LSG) Work Stream
Appraisal of the Jordanian Law for Data Sharing in Stem Cell Research: In the Light of the ‘GA4GH Framework’ for Innovative Cancer Care. 2018 Al-Tabba, A. et al. Al-Tabba, A., Al-Omari, A., Al-Hussaini, M. 2018 1ST INTERNATIONAL CONFERENCE ON CANCER CARE INFORMATICS (CCI) Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
APPLaUD: access for patients and participants to individual level uninterpreted genomic data. 2018 Thorogood, A. et al. Thorogood, A., Bobe, J., Prainsack, B. HUM GENOMICS Regulatory & Ethics Work Stream (REWS)
APPLaUD: Access for patients and participants to individual level uninterpreted genomic data 2018 Thorogood, A. et al. Thorogood, A., Bobe, J., Prainsack, B., Middleton, A., Scott, E., Nelson, S., Corpas, M., Bonhomme, N., Rodriguez, L.L., Murtagh, M., Kleiderman, E. HUMAN GENOMICS Regulatory & Ethics Work Stream (REWS)
Your DNA, Your Say 2017 Middleton, A. Middleton, A. THE NEW BIOETHICS Regulatory & Ethics Work Stream (REWS) Your DNA, Your Say (Participant Values Survey)
Using High Performance Computing to Create and Freely Distribute the South Asian Genomic Database, Necessary for Precision Medicine in this Population 2017 Shah, A.H. et al. Shah, A.H., Picker, J.D., Jamuar, S.S. SUPERCOMPUTING FRONTIERS AND INNOVATIONS Beacon
Tools to foster trust in sharing healthcare data: Toward a common language for regulatory metadata 2017 Woolley, J.P. Woolley, J.P. MEDICINE AND LAW Regulatory & Ethics Work Stream (REWS)
The path to reducing duplication of human research ethics review in Australia 2017 Johns, A. et al. Johns, A., Nicol, D., Zeps, N., Chalmers, D.R. MEDICINE AND LAW Regulatory & Ethics Work Stream (REWS)
The Dockstore: Enabling modular, community-focused sharing of Docker-based genomics tools and workflows 2017 O'Connor, B.O. et al. O'Connor, B.O., Yuen, D., Chung, V., Duncan, A.G., Liu, X.K., Patricia, J., Paten, B., Stein, L.D., Ferretti, V. F1000RESEARCH Federated Analysis Work Stream (formerly Cloud Work Stream) Tool Registry Service (TRS)
Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance 2017 Cook-Deegan, R. et al. Cook-Deegan, R., Ankeny, R.A., Jones, K.M. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS Regulatory & Ethics Work Stream (REWS)
Genomics in healthcare: GA4GH looks to 2022 2017 Birney, E. et al. Birney, E., Vamathevan, J., Goodhand, P. BIORXIV
Genomic newborn screening: Public health policy considerations and recommendations 2017 Friedman, J.M. et al. Friedman, J.M., Cornel, M.C., Goldenberg, A.J., Lister, K.J., Sénécal, K., Vears, D.F. BMC MEDICAL GENOMICS, Regulatory & Ethics Work Stream (REWS) Consent Toolkit
From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine 2017 Lawler, M. et al. Lawler, M., Maughan, T. THE NEW BIOETHICS Data Security Work Stream, Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data, Data Security Infrastructure Policy (DSIP)
Ethics and Big Data in health 2017 Knoppers, B.M. et al. Knoppers, B.M., Thorogood, A.M. CURRENT OPINION IN SYSTEMS BIOLOGY Regulatory & Ethics Work Stream (REWS)
Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services 2017 Wan, Z. et al. Wan, Z., Vorobeychik, Y., Kantarcioglu, M., Malin, B.A. BMC MEDICAL GENOMICS Discovery Work Stream Beacon
Consent Processes for Mobile App Mediated Research: Systematic Review 2017 Moore, S. et al. Moore, S., Tassé, A.M., Thorogood, A., Winship, I., Zawati. M., Doerr, M. JMIR MHEALTH UHEALTH Regulatory & Ethics Work Stream (REWS)
Aftermath of bustamante attack on genomic beacon service 2017 Aziz, M.M. et al. Aziz, M.M., Ghasemi, R., Waliullah, M., Mohammed, N. BMC MEDICAL GENOMICS Discovery Work Stream Beacon
Addressing Beacon re-identification attacks: Quantification and mitigation of privacy risks 2017 Raisaro, J.L et al. Raisaro, J.L, Tramèr, F., Ji, Z., Bu, D., Zhao, Y., Carey, K., Lloyd, D., Sofia, H., Baker, D., Flicek, P., Shringarpure, S., Bustamante, C., Wang, S., Jiang, X., Ohno-Machado, L., Tang, H., Wang, X., Hubaux, J.P. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION Discovery Work Stream Beacon
A community effort to protect genomic data sharing, collaboration and outsourcing 2017 Wang, S. et al. Wang, S., Jiang, X., Tang, H., Wang, X., Bu, D., Carey, K., Dyke, S.O.M., Fox, D., Jiang, C., Lauter, K., Malin, B.A., Sofia, H., Telenti, A., Wang, L., Wang, W., Ohno-Machado, L. NPJ GENOMIC MEDICINE Data Security Work Stream, Regulatory & Ethics Work Stream (REWS) Data Privacy and Security Policy, Data Security Infrastructure Policy (DSIP)
 Public variant databases: Liability? 2016 Thorogood, A. et al. Thorogood, A., Cook-Deegan, R., Knoppers, B.M. GENETICS IN MEDICINE Regulatory & Ethics Work Stream (REWS)
The Human Variome Project 2016 Burn, J. et al. Burn, J., Watson, M. HUMAN MUTATION
The discombobulation of de-identification 2016 Phillips, M. et al. Phillips, M., Knoppers, B.M. NATURE BIOTECHNOLOGY Regulatory & Ethics Work Stream (REWS) Data Privacy and Security Policy
Sharing Health-Related Data: A Privacy Test? 2016 Dyke, S.O.M. et al. Dyke, S.O.M., Dove, E.S., Knoppers, B.M. NPJ GENOMIC MEDICINE Regulatory & Ethics Work Stream (REWS) Beacon, Framework for responsible sharing of genomic and health-related data
Registered access: a ‘Triple-A’ approach. 2016 Dyke, S.O.M. et al. Dyke, S.O.M., Kirby, E., Shabani, M. EUR J HUM GENET
RD-Connect: Data Sharing and Analysis for Rare Disease Research within the Integrated Platform and through GA4GH Beacon and Matchmaker Exchange 2016 Roos, A. et al. Roos, A., Beltran, S., Piscia, D., Laurie, S., Protasio, J., Cañada, A., Fernández, J. NEUROMUSCULAR DISORDERS Discovery Work Stream Beacon
IRDIRC and GA4GH: International Efforts to Advance Rare Disease Discovery 2016 Boycott, K.M. Boycott, K.M. PATHOLOGY
Facilitating a Culture of Responsible and Effective Sharing of Cancer Genome Data 2016 Siu, L.L. et al. Siu, L.L., Lawler, M., Haussler, D., Knoppers, B.M., Lewin, J.H., Vis, D.J., Liao, R.G. NATURE MEDICINE Regulatory & Ethics Work Stream (REWS), Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream), Discovery Work Stream Framework for responsible sharing of genomic and health-related data, Consent Policy, Beacon, Data Security Infrastructure Policy (DSIP)
Ethics review for international data-intensive research 2016 Dove, E.S. et al. Dove, E.S., Townend, D., Meslin, E.M., Bobrow, M., Littler, K., Nicol, D., de Vries, J., Junker, A., Garattini, C., Bovenberg, J., Shabani, M., Lévesque, E., Knoppers, B.M. SCIENCE Regulatory & Ethics Work Stream (REWS) Ethics Review Recognition Policy
Ethical issues in consumer genome sequencing: Use of consumers samples and data 2016 Niemiec, E. et al. Niemiec, E., Howard, H. C. APPLIED & TRANSLATIONAL GENOMICS Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Determining Barriers to Effective Data Sharing in Cancer Genomic Sequencing Initiatives: A Global Alliance for Genomics and Health (GA4GH) Survey 2016 Lewin, J.H. et al. Lewin, J.H., Vis, D.J., Voest, E.E., Liao, R.G., Nederlof, P.M., Conley, B.A., Solit, D.B. JOURNAL OF CLINICAL ONCOLOGY
Consent Codes: Upholding Standard Data Use Conditions 2016 Dyke, S.O.M. et al. Dyke, S.O.M., Philippakis, A.A., Paltoo, D.N., Luetkemeier, E.S., Knoppers, B.M., Brookes, A.J., Spalding, J.D., Thompson, M., Roos, M., Boycott, K.M., Brudno, M., Hurles, M., Rehm, H.L., Matern, A., Fiume, M., Sherry, S.T. PLOS GENETICS Regulatory & Ethics Work Stream (REWS)
Beyond Our Borders? Public Resistance to Global Genomic Data Sharing 2016 Majumder, M. A. et al. Majumder, M. A., Cook-Deegan, R., Mcguire, A. L. PLOS BIOLOGY Regulatory & Ethics Work Stream (REWS)
Are Data Sharing and Privacy Protection Mutually Exclusive? 2016 Joly, Y. et al. Joly, Y., Dyke, S.O.M., Knoppers, B.M., Pastinen, T. CELL Regulatory & Ethics Work Stream (REWS)
An International Framework for Data Sharing: Moving Forward with the Global Alliance for Genomics and Health 2016 Rahimzadeh, V. et al. Rahimzadeh, V., Dyke, S.O.M., Knoppers, B.M. BIOPRESERVATION AND BIOBANKING Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
A federated ecosystem for sharing genomic, clinical data 2016 Page, A. et al. Page, A., Baker, D., Bobrow, M., Boycott, K.M., Burn, J., Chanock, S.J., Donnelly, S., Dove, E.S., Durbin, R., Dyke, S.O.M., Fiume, M., Flicek, P., Glazer, D., Goodhand, P., Haussler, D., Kato, K., Keenan, S., Knoppers, B.M., Liao, R.G., Lloyd, D., Mulder, N., Navarro, A., North, K.N., Philippakis, A.A., Rahman, N., Rehm, H.L., Sawyers, C., Thorogood, A., Wilson, J., Altshuler, D., Hudson, T.J. SCIENCE
UK gears up to decode 100 000 genomes from NHS patients 2015 Siva, N. Siva, N. LANCET
The NIH BD2K center for big data in translational genomics 2015 Paten, B. et al. Paten, B., Diekhans, M., Druker, B.J., Friend, S., Guinney, J., Gassner, N., Guttman, M., Kent, W.J., Mantey, P., Margolin, A.A., Massie, M., Novak, A.M., Nothaft, F., Pachter, L., Patterson, D., Smuga-Otto, M., Stuart, J.M., Van't Veer, L., Wold, B., Haussler, D. JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery 2015 Philippakis, A.A. et al. Philippakis, A.A., Azzariti, D.R., Beltran, S., Brookes, A.J., Brownstein, C.A., Brudno, M., Brunner, H.G., Buske, O.J., Carey, K., Doll, C., Dumitriu, S., Dyke, S.O.M., den Dunnen, J.T., Firth, H.V., Gibbs, R.A., Girdea, M., Gonzalez, M., Haendel, M.A., Hamosh, A., Holm, I.A., Huang, L., Hurles, M.E., Hutton, B., Krier, J.B., Misyura, A., Mungall, C.J., Paschall, J ., Paten, B., Robinson, P.N., Schiettecatte, F., Sobreira, N.L., Swaminathan, G.J., Taschner, G.E., Terry, S.F., Washington, N.L., Züchner, S., Boycott, K.M., Rehm, H.L. HUMAN MUTATION
The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles 2015 Buske, O.J. et al. Buske, O.J., Schiettecatte, F., Hutton, B., Dumitriu, S., Misyura, A., Huang, L., Hartley, T., Girdea, M., Sobreira, N.L., Mungall, C.J., Brudno, M. HUMAN MUTATION
The big medical data miss: Challenges in establishing an open medical resource 2015 Topol, E.J. Topol, E.J. NATURE REVIEWS GENETICS
Data sharing in stem cell translational science: Policy statement by the International Stem Cell Forum Ethics Working Party 2015 Bredenoord, A.L. et al. Bredenoord, A.L., Mostert, M., Isasi, R., Knoppers, B.M. REGENERATIVE MEDICINE Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Data analysis: Create a cloud commons 2015 Stein, L.D. et al. Stein, L.D., Knoppers, B.M., Campbell, P., Getz, G., Korbel, J.O. NATURE Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Curating the Way to Better Determinants of Genetic Risk 2015 Phimister, E.G. Phimister, E.G. NEW ENGLAND JOURNAL OF MEDICINE
Building the foundation for genomics in precision medicine 2015 Aronson, S.J. et al. Aronson, S.J., Rehm, H.L. NATURE Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
An ecosystem of cancer cell line factories to support a cancer dependency map 2015 Boehm, J. S. et al. Boehm, J. S., Golub, T. R. NATURE REVIEWS GENETICS
All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health 2015 Lawler, M. et al. Lawler, M., Siu, L.L., Rehm, H.L., Chanock, S.J., Alterovitz, G., Burn, J., Calvo, F. CANCER DISCOVERY Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
To share or not to share is the question 2014 Chalmers, D.R. et al. Chalmers, D.R., Nicol, D., Otlowski, M.F. APPLIED & TRANSLATIONAL GENOMICS Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
The Global Alliance for Genomics & Health 2014 Terry, S.F. Terry, S.F. GENETIC TESTING AND MOLECULAR BIOMARKERS
Redefining Genomic Privacy: Trust and Empowerment 2014 Erlich, Y. et al. Erlich, Y., Williams, J.B., Glazer, D., Yocum, K., Farahany, N., Olson, M., Narayanan, A., Stein, L.D., Witkowski, J.A., Kain, R.C. PLOS BIOLOGY
International ethics harmonization and the global alliance for genomics and health 2014 Knoppers, B.M. Knoppers, B.M. GENOME MEDICINE Regulatory & Ethics Work Stream (REWS) Ethics Review Recognition Policy
International code of conduct for genomic and health-related data sharing 2014 Sugano, S. Sugano, S. THE HUGO JOURNAL Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Framework for responsible sharing of genomic and health-related data. 2014 Knoppers, B.M. Knoppers, B.M. HUGO J Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Framework for Responsible Sharing of Genomic and Health-Related Data 2014 Knoppers, B.M. Knoppers, B.M. THE HUGO JOURNAL Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
ELSI practices in genomic research in East Asia: Implications for research collaboration and public participation 2014 Yoshizawa, G. et al. Yoshizawa, G., Ho, C.W., Zhu, W., Hu, C., Syukriani, Y., Lee, I., Kim, H., Tsai, D.F.C., Minari, J., Kato, K. GENOME MEDICINE Regulatory & Ethics Work Stream (REWS)
Does policy grow on trees? 2014 Knoppers, B.M. Knoppers, B.M. BMC MEDICAL ETHICS Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
Building a Data Sharing Model for Global Genomic Research 2014 Kosseim, P. et al. Kosseim, P., Dove, E.S., Baggaley, C., Meslin, E.M., Cate, F.H., Kaye, J., Harris, J.R., Knoppers, B.M. GENOME BIOLOGY Regulatory & Ethics Work Stream (REWS) Framework for responsible sharing of genomic and health-related data
The variant call format and VCFtools 2011 BIOINFORMATICS Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream Genetic Variation Formats (VCF)
Efficient storage of high throughput DNA sequencing data using reference-based compression 2011 GENOME RESEARCH Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream CRAM
The Sequence Alignment/Map format and SAMtools 2009 Li, H. et al. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. BIOINFORMATICS Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream SAM/BAM

Navigating ethical, legal and social implications in genomic newborn screening

2026
NATURE REVIEWS GENETICS
Regulatory & Ethics Work Stream (REWS)
Genomic sequencing in newborn screening
Lewis, A.C.F. et al. Lewis, A.C.F., Brown, G., Bombard, Y.

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

2025
BMC BIOINFORMATICS
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Bridges, Y. et al. Bridges, Y., de Souza, V., Cortes, K.G., Haendel, M., Harris, N.L., Korn, D.R., Marinakis, N.M., Matentzoglu, N., McLaughlin, J.A., Mungall, C.J., Odell, A., Robinson, P.N., Smedley, D., Jacobsen, J.O.B.

The International Health Cohorts Consortium (IHCC) advances population health research and genomic discovery

2025
COMMUNICATIONS MEDICINE
Connolly, J.J et al. Connolly, J.J, Sundseth, S., Wood, G.M., Nwaneri, S., Awadalla, P., Ramsay, M., Keane, T., Goodhand, P., Butterworth, A.S., Hakonarson, H.

The ICGC ARGO data dictionary for standardizing global cancer clinical data

2025
SCIENTIFIC DATA
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Nahal-Bose, H.K. et al. Nahal-Bose, H.K., Lichter, P., Weber, U., Stein, L.D., Bajari, R., Xiang, L., Su, E., Eubank, J., Schütte, C., Yung, C.K., Courtot, M.

The Federated European Genome–Phenome Archive as a global network for sharing human genomics data

2025
NATURE GENETI
Data Use & Researcher Identity (DURI) Work Stream
Data Use Ontology (DUO)
D’Altri, T. et al. D’Altri, T., Freeberg, M.A., Curwin, A.J., et al.

The expanding global genomics landscape: Converging priorities from national genomics programs

2025
AMERICAN JOURNAL OF HUMAN GENETICS
Howley, C. et al. Howley, C., Haas, M.A., Al Muftah, W.A., Annan, R.B., Green, E.D., Lundgren, B., Scott, R.H., Stark, Z., Tan, P., North, K.N., Boughtwood, T.

Rakeiora Genomics Platform: a pathfinder for genomic medicine research in Aotearoa New Zealand

2025
JOURNAL OF THE ROYAL SOCIETY OF NEW ZEALAND
Large-Scale Genomics (LSG) Work Stream, Data Security Work Stream, Data Use & Researcher Identity (DURI) Work Stream
Passports, htsget
Wihongi, H. et al. Wihongi, H., Te Aika, B., de Ligt, J., Print, C.G., Tsai, P., Curran, B., Jones, N., Huh, J, Owen Perkins, E., Pestle, M., Zhao, K., Halytskyy, Y., Robertson, S.P., Halliday, B.J., Goodin, E., Markie, D.M., Lamont, A., Wilcox, P.

pgxRpi: an R/bioconductor package for user-friendly access to the Beacon v2 API

2025
BIOINFORMATICS ADVANCES
Discovery Work Stream
Beacon
Zhao, H. et al. Zhao, H., Baudis, M.

Multimodal data curation via interoperability: use cases with the Medical Imaging and Data Resource Center

2025
SCIENTIFIC DATA
Federated Analysis Work Stream (formerly Cloud Work Stream)
Data Repository Service (DRS)
Chen, W. et al. Chen, W., Whitney, H.M., Kahaki, S., Meyer, C., Li, H., Sá, R.C., Lauderdale, D., Napel, S., Gersing, K, Grossman, R.L., Giger, M.L.

GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders

2025
THE AMERICAN JOURNAL OF HUMAN GENETICS
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Lauren Rekerle, L. et al. Lauren Rekerle, L., Danis, D., Rehburg, F., Graefe, A.S.L., Bily, V., Cacheiro, P.,  Chimirri, L., Chong, J.X., Connelly, E., de Vries, B.B.A., Dingemans, A.J.M., Duyzend, M.H., Freiberger, T., Gehle, P., Groza, T.,  Hansen, P., Jacobsen, J.O.B.,  Klocperk, A., Ladewig. M.S., Love, M.I.,  Mordhorst, A., Munoz-Torres, M.C., Reese, J., Schuetz, C., Smedley, D., Strauss, T., Vladyka, O., Zocche, D.,  Thun, S., Mungall, C.J., Haendel, M.A., Robinson, P.N.

GA4GH Data Passports: Proposing a New Technical Specification for Data Policy Representation

2025
SSRN
Data Use & Researcher Identity (DURI) Work Stream, Data Security Work Stream
Data Passports
Lawson, J. et al. Lawson, J., Conner, T.

Communicating clearly about data sharing in genomics

2025
HUMAN GENOMICS
Regulatory & Ethics Work Stream (REWS)
Data Sharing Lexicon
Thaler, D. et al. Thaler, D., Uberoi, D., Thorogood, A., Milne, R., Newson A.J., Hall, A., Glazer, D., Esselaar, P., Joly, Y.

An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets

2025
NATURE
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Graefe, A.S.L. et al. Graefe, A.S.L., Hübner, M.R., Rehburg, F., Sander, S., Alkarkoukly, S., Grönke, A., Weyersberg, A., Danis, D., Zschüntzsch, J., Nyoungui, E.F., Wiegand, S., Kühnen, P., Robinson, P.N., Beyan, O., Thun, S.

A call for a global cyberbiosecurity framework in genomics

2025
NATURE GENETICS
Joly, Y. et al. Joly, Y., Xue, Y., Huang, J., Uberoi, D.

Use of Beacon v2 for Improving Genomics Based Research in a Clinical Setting

2024
IOS PRESS
Discovery Work Stream
Beacon
Naro, D. et al. Naro, D., Delgado, J., Llorente, S., Hernaez, M.

The Key Features of a Genetic Nondiscrimination Policy: A Delphi Consensus Statement

2024
JAMA NETWORK OPEN
Regulatory & Ethics Work Stream (REWS)
Genetic Discrimination Toolkit, Genetic Discrimination Toolkit
Uberoi, D. et al. Uberoi, D., Dalpé, G., Cheung, K., Kondrup, E., Palmour, N., Arawi, T., Arych, M., Ayuso, C., Bentzen, H.B., Blizinsky, K., Bombard, Y., Chung, B.H.Y., de Paor, A., Doerr, M., Dove, E.S., Dupras, C., Greenbaum, D., Haidar, H., Ho, C.H., Jamuar, S.S., Kim, H., Lebret, A., Macdonald, A., Minssen, T., Nasir, J., Nicol, D., Nicolás, P., Otlowski, M., Nair, A.P.S.,  Prince, A.E.R., Rothstein, M., Ryan, R., Sillon, G., Singh, K.K., Stedman, I., Tiller, J., Van Hoyweghen, I., Zawati, M.H., Joly, Y.

The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution

2024
COMPUTING IN SCIENCE & ENGINEERING
Federated Analysis Work Stream (formerly Cloud Work Stream)
Task Execution Service (TES)
Kanitz, A. et al. Kanitz, A., McLoughlin, M.H., Beckman, L., Malladi, V.S., Ellrott, K.

Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child?

2024
GENETICS IN MEDICINE
Regulatory & Ethics Work Stream (REWS)
Friedman J.M. et al. Friedman J.M., Bombard Y., Carleton B., Issa A.M., Knoppers B., Plon S.E., Rahimzadeh V., Relling M.V., Williams M.S., van Karnebeek C., Vears D., Cornel M.C.

Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond

2024
BMC BIOINFORMATICS
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Discovery Work Stream
Phenopackets, Beacon
Leist, I.C. et al. Leist, I.C., Rivas-Torrubia, M., Barturen, G., Gut, I.G., Rueda, M.

Investigating the roles and responsibilities of institutional signing officials after data sharing policy reform for federally funded research in the United States: national survey

2024
JMIR
Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream
Data Access Committee Review Standards (DACReS) Toolkit
Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J.

EpiVar Browser: advanced exploration of epigenomics data under controlled access

2024
BIOINFORMATICS
Regulatory & Ethics Work Stream (REWS)
Lougheed, D.R. et al. Lougheed, D.R., Liu, H., Aracena, K.A., Grégoire, R., Pacis, A., Pastinen, T., Barreiro, L.B., Joly, Y., Bujold, D., Bourque, G.

Defining and pursuing diversity in human genetic studies

2024
NATURE GENETICS
Regulatory & Ethics Work Stream (REWS)
Diversity in Datasets
Raven-Adams, M.C. et al. Raven-Adams, M.C., Joly, Y., Knoppers, B.M., Thorogood, A., Kumuthini, J., Ho, C.W.L, Gonzalez, A., Nelson, S.C., Bombard, Y., Thaldar, D., Liu, H., Costa, A., Muralidharan, V., Henriques, S., Nasir, J., Lumaka, A.,  Kaiser, B., Jamuar, S.S., Lewis, A.C.F.

Comment Form: WHO Principles for Human Genome Access, Use, and Sharing

2024
SSRN
Regulatory & Ethics Work Stream (REWS)
Nicol, D. et al. Nicol, D., Uberoi, D.

Achieving procedural parity in managing access to genomic and related health data: a global survey of data access committee members

2024
BIOPRESERVATION AND BIOBANKING
Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream
Data Access Committee Review Standards (DACReS) Toolkit
Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J., Dove, E.

A qualitative interview study to determine barriers and facilitators of implementing automated decision support tools for genomic data access

2024
BMC MEDICAL ETHICS
Regulatory & Ethics Work Stream (REWS), Data Use & Researcher Identity (DURI) Work Stream
Data Access Committee Review Standards (DACReS) Toolkit
Rahimzadeh, V. et al. Rahimzadeh, V., Baek, J., Lawson, J., Dove, E.

A proposal for an inclusive working definition of genetic discrimination to promote a more coherent debate

2024
NATURE GENETICS
Regulatory & Ethics Work Stream (REWS)
Genetic Discrimination Toolkit
Kaiser, B. et al. Kaiser, B., Uberoi, D., Raven-Adams, M.C., Cheung, K., Bruns, A., Otlowski, M., Prince, A.E.R., Tiller, J., Ahmed, A., Bombard, Y., Dupras, C., Ryan, R.,  Joly, Y.

A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery

2024
MEDRXIV
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Danis, D. et al. Danis, D., Bamshad M.J., Bridges, Y., Cacheiro, P., Carmody, L.C., Chong, J.X., Coleman, B., Dalgleish, R., Freeman, P.J., Graefe, A.S.L,, Groza, T., Jacobsen. J.O.B., Klocperk, A., Kusters, M., Ladewig, M.S., Marcello, A.J., Mattina, T., Mungall, C.J., Munoz-Torres, M.C., Reese, J.T., Rehburg, F., Reis, B.C.S., Schuetz, C., Smedley, D., Strauss, T., Thun, S., Wissink, K., Wagstaff, J.F., Zocche, D., Haendel, M.A., Robinson, P.N.

A call to action to scale up research and clinical genomic data sharing

2024
NATURE REVIEW GENETICS
Stark, Z. et al. Stark, Z., Glazer, D., Hofmann, O., Rendon, A., Marshall, C.R., Ginsburg, G.S.,  Lunt, C., Allen, N.,  Effingham M.,  Ward, J.H., Hill, S.H., Ali, R.,  Goodhand, P.,  Page, A.,  Rehm, H.L.,  North, K.N.,  Scott, R.H.

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows

2023
GIGA SCIENCE
Suetake, H. et al. Suetake, H., Fukusato, T., Igarashi, T., Ohta, T.

Recording the ethical provenance of data and automating data stewardship

2023
BIG DATA & SOCIETY
Regulatory & Ethics Work Stream (REWS)
Ethical Provenance Toolkit
Bernier, A. et al. Bernier, A., Raven-Adams, M., Zaccagnini, D., Knoppers, B. M.

Phenopacket-tools: building and validating GA4GH Phenopackets

2023
PLOS ONE
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Danis, D et al. Danis, D, Jacobsen, JOB, Wagner, AH, Groza, T, Beckwith, MA, Rekerle, L, Carmody, LC, Reese, J, Hegde, H, Ladewig, MS, Seitz, B, Munoz-Torres, M, Harris, NL, Rambla, J, Baudis, M, Mungall, CJ, Haendel, MA, Robinson, PN.

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

2023
PACIFIC SYMPOSIUM ON BIOCOMPUTING
Genomic Knowledge Standards (GKS) Work Stream
Variation Representation Specification (VRS)
Goar, W. et al. Goar, W., Babb, L., Chamala,S., Cline, M., Freimuth, R.R., Hart, R.K., Kuzma, K., Lee, J., Nelson, T., Prlić, A., Riehle, K., Smith, A., Stahl, K., Yates, A.D., Rehm, H.L., Wagner, A.H.

The GA4GH Phenopacket schema defines a computable representation of clinical data

2022
NATURE BIOTECHNOLOGY
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Jacobsen, J. O. et al. Jacobsen, J. O., Baudis, M., Baynam, G. S., Beckmann, J. S., Beltran, S., Buske, O. J., Callahan, T. J., Chute, C. G., Courtot, M., Danis, D., Elemento, O., Essenwanger, A., Freimuth, R. R., Gargano, M. A., Groza, T., Hamosh, A., Harris, N. L., Kaliyaperumal, R., Lloyd, K. C., Robinson, P. N., Khalifa, Aly, Krawitz, Peter M., Köhler, Sebastian, Laraway, Brian J., Matalonga, Leslie, McMurry, Julie A., Ogishima, Soichi, Piscia, Davide, Pontikos, Nikolas, Roos, Marco, Sass, Julian, Schofield, Paul N., Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D., Steinhaus, Robin, Thun, Sylvia, Wagner, Alex H., Warner, Jeremy L., Weiland, Claus

Sapporo: a workflow execution service that encourages the reuse of workflows in various languages in bioinformatics

2022
F1000RESEARCH
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
Suetake, H. et al. Suetake, H., Tanjo, T., Ishii, M,., Kinoshita, B.P., Fujino, T., Hachiya, T., Kodama, Y., Fujisawa, T., Ogasawara, O., Shimizu, A., Arita, M., Fukusato, T., Igarashi, T., Ohta, T.

Return of genomic results does not motivate intent to participate in research for all: Perspectives across 22 countries

2022
GENETICS IN MEDICINE
Regulatory & Ethics Work Stream (REWS)
Policy on Clinically Actionable Genomic Research Results
Richard Milne Richard Milne

Leveraging Algorithms to Improve Decision-Making Workflows for Genomic Data Access and Management

2022
BIOPRESERVATION AND BIOBANKING
Regulatory & Ethics Work Stream (REWS)
Rahimzadeh, V. et al. Rahimzadeh, V., Lawson, J., Rushton, G., Dove, E.S.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

2022
CELL GENOMICS
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
Schatz, M.C. et al. Schatz, M.C., Philippakis, A.A,, Afgan, E., Banks, E., Carey, V.J., Carroll, R.J., Culotti, A., Ellrott, K., Goecks, J., Grossman, R.L., Hall, I.M., Hansen, K.D., Lawson, J., Leek, J.T., Mosher, S., Morgan, M., Nekrutenko, A., O’Connor, B.D., Osborn, K., Paten, B., Patterson, C., Tan, F.J., Waldron, L., Wang, T., Wuichet, K., and AnVIL Team.

Genetic discrimination still casts a large shadow in 2022.

2022
EUR J HUM GENET
Regulatory & Ethics Work Stream (REWS)
Joly, Y. et al. Joly, Y., Dalpe, G.

GA4GH Phenopackets: a practical introduction

2022
ADVANCED GENETICS
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Phenopackets
Ladewig, Markus S. et al. Ladewig, Markus S., Wagner, Alex H., Danis, Daniel, ElKassaby, Baha, Gargano, Michael, Groza, Tudor, Baudis, Michael, Steinhaus, Robin, Seelow, Dominik, Schofield, Paul N., Elemento, Olivier, Smith, Lindsay, McMurry, Julie A.

CRAM 3.1: advances in the CRAM file format

2022
BIOINFORMATICS
Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream
CRAM
Bonfield, J.K. Bonfield, J.K.

Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review

2022
FRONT MED
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream
Pharmacogenomics Data Standardisation
McDermott J.H. et al. McDermott J.H., Wright S., Sharma V., Newman W.G., Payne K., Wilson P.

Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data

2022
BIOINFORMATICS
Discovery Work Stream
Beacon
Rueda, M. et al. Rueda, M., Ariosa, R., Moldes, M., Rambla, J.

Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond

2022
HUMAN MUTATION
Discovery Work Stream
Beacon
Rambla, J. et al. Rambla, J., Baudis, M., Ariosa, R., Beck, T., Fromont, L. A., Navarro, A., Paloots, R., Rueda, M., Saunders, G., Singh, B., Spalding, J. D., Törnroos, J., Vasallo, C., Veal, C. D., Brookes, A. J.

The Data Use Ontology to streamline responsible access to human biomedical datasets

2021
CELL GENOMICS
Data Use & Researcher Identity (DURI) Work Stream
Data Use Ontology (DUO)
Lawson, J. et al. Lawson, J., Cabili, M.N., Kerry, G., Boughtwood, T., Thorogood, A., Alper, P., Bowers, S.R., Boyles, R.R., Brookes, A.J., Brush, M., Burdett, T., Clissold, H., Donnelly, S., Dyke, S.O.M., Freeberg, M.A., Haendel, M.A., Hata, C., Holub, P., Jeanson, F., Jene, A., Kawashima, M., Kawashima, S., Konopko, M., Kyomugisha, I., Li, H., Linden, M., Rodriguez, L.L., Morita, M., Mulder, N., Muller, J., Nagaie, S., Nasir, J., Ogishima, S., Ota Wang, V., Paglione, L.D., Pandya, R.N., Parkinson, H., Philippakis, A.A., Prasser, F., Rambla, J., Reinold, K., Rushton, G.A., Saltzman, A., Saunders, G., Sofia, H.J., Spalding, J.D., Swertz, M.A., Tulchinsky, I., Varma, S., Voisin, C., Yamamoto, N., Yamasaki, C., Zass, L., Guidry Auvil, J.M., Nyrönen, T.H., Courtot, M.

Refget: standardized access to reference sequences

2021
BIOINFORMATICS
Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream
refget Sequences
Yates, A.D. et al. Yates, A.D., Adams, J., Chaturvedi, S., Davies, R.M., Laird, M., Leinonen, R., Nag, R., Sheffield, N.C., Hofmann, O., Keane, T.O.

International federation of genomic medicine databases using GA4GH standards

2021
CELL GENOMICS
Data Security Work Stream, Data Use & Researcher Identity (DURI) Work Stream, Regulatory & Ethics Work Stream (REWS), Discovery Work Stream
Passports, Beacon, Authorisation and Authentication Infrastructure (AAI), Data Connect, Data Use Ontology (DUO), Workflow Execution Service (WES), Task Execution Service (TES), Tool Registry Service (TRS), Data Repository Service (DRS)
Thorogood, A. et al. Thorogood, A., Rehm, H.L., Goodhand, P., Page, A.J.H., Joly, Y., Baudis, M., Rambla, J., Navarro, A., Nyronen, T.H., Linden, M., Dove, E.S., Fiume, M., Brudno, M., Cline, M.S., Birney, E.

I can drive in Iceland: Enabling international joint analyses

2021
CELL GENOMICS
Lunt, C. et al. Lunt, C., Denny, J.C.

GA4GH: International policies and standards for data sharing across genomic research and healthcare

2021
CELL GENOMICS
Rehm, H. et al. Rehm, H., Goodhand, P., North, K., Birney, E., et al.

GA4GH Passport standard for digital identity and access permissions

2021
CELL GENOMICS
Data Use & Researcher Identity (DURI) Work Stream
Passports, Authorisation and Authentication Infrastructure (AAI)
Voisin, C. et al. Voisin, C., Linden, M., Dyke, S.O.M., Bowers, S.R., Alper, P., Barkley, M.P., Bernick, D., Chao, J., Courtot, M., Jeanson, F., Konopko, M.A., Kuba, M., Lawson, J., Leinonen, J., Li, S., Ota Wang, V., Philippakis, A.A., Reinold, K., Rushton, G.A., Spalding, J.D., Törnroos, J., Tulchinsky, I., Guidry Auvil, J.M., Nyrönen, T.H.

Executing workflows in the cloud with WESkit

2021
BIOHACKRXIV PREPRINTS
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
Kensche, P.R. et al. Kensche, P.R., Kanitz, A., Topolsky, I., Jablonski, K.P., Mandreoli, P., Twardziok, S.

Empirical validation of an automated approach to data use oversight

2021
MORAN N. CABILI 7 JONATHAN LAWSON 7 ANDREA SALTZMAN GREG RUSHTON PEARL O’ROURKE JOHN WILBANKS LAURA LYMAN RODRIGUEZ TOMMI NYRONEN MéLANIE COURTOT STACEY DONNELLY ANTHONY A. PHILIPPAKIS 8 SHOW LESS SHOW FOOTNOTES OPEN ACCESSDOI:HTTPS://DOI.ORG/10.1016/J.XGEN.2021.100031 PLUMX METRICS PREVIOUS ARTICLETHE DATA USE ONTOLOGY TO STREAMLINE RESPONSIBLE …
Cabili, M.N. et al. Cabili, M.N., Lawson, J., Saltzman, A., Rushton, G., O’Rourke, P., Wilbanks, J., Rodriguez, L.L., Nyronen, T., Courtot, M., Donnelly, S.

Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries

2021
GENOME MED
Regulatory & Ethics Work Stream (REWS)
Milne, R. et al. Milne, R., Morley, K.I., Almarri, M.A.

CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis

2021
CELL GENOMICS
Dursi, L.J et al. Dursi, L.J, Bozoky, Z., de Borja, R., Li, H., Bujold, D, Lipski, A., Rashid, S.F., Sethi, A., Memon, N., Naidoo, N., Coral-Sasso, F., Wong, M,, Quirion, P.O., Lu, Z., Agarwal, S., Pavlov, Y., Ponomarev, A., Husic, M., Pace, K., Palmer, S., Grover, S.A., Hakgor, S., Siu, L.L., Malkin, D., Virtanen, C., Pugh, T.J., Jacques, P.E., Joly, Y., Jones, S.J.M., Bourque, G., Brudno, M.

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

2021
JOURNAL OF PROTEOME RESEARCH
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
Bai, J. et al. Bai, J., Bandla, C., Guo, J., Vera Alvarez, R., Bai, M., Vizcaíno, J.A., Moreno, P., Grüning, B., Sallou, O., Perez-Riverol, Y.

An international policy on returning genomic research results.

2021
GENOME MED
Regulatory & Ethics Work Stream (REWS)
Policy on Clinically Actionable Genomic Research Results
Lewis, A.C.F. et al. Lewis, A.C.F., Knoppers, B.M., Green, R.C.

The GA4GH Variation Representation Specification (VRS): A Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

2020
CELL GENOMICS
Genomic Knowledge Standards (GKS) Work Stream
Variation Representation Specification (VRS)
Wagner, A.H. et al. Wagner, A.H., Babb, L., Alterovitz, G., Baudis, M., Brush, M., Cameron, D.L., Cline, M., Griffith, M., Griffith, O.L., Hunt, S. 

Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases

2020
CELL GENOMICS
Large-Scale Genomics (LSG) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream)
htsget
Corvò, A. et al. Corvò, A., Matalonga, L., Spalding, D., Senf, A., Laurie, S., Picó-Amador, D., Paramonov, I., Foix Romero, A., Garcia-Rios, E., Mohan, A., Thomas, C., Halmagyi, C., Freeberg, M.A., Töpf, A., Horvath, R., Saunders, G., Gut, I., Keane, T., Piscia, D., Beltran, S.

Members of the public in the USA, UK, Canada and Australia expressing genetic exceptionalism say they are more willing to donate genomic data.

2020
EUR J HUM GENET
Regulatory & Ethics Work Stream (REWS)
Middleton, A. et al. Middleton, A., Milne, R., Howard, H.

How Can We Not Waste Legacy Genomic Research Data?

2020
FRONT. GENET.
Regulatory & Ethics Work Stream (REWS)
Wallace, S.E. et al. Wallace, S.E., Kirby, E., Knoppers, B.M.

Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data?

2020
THE AMERICAN JOURNAL OF HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Middleton, A. et al. Middleton, A., et al.

Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale

2020
JCO CLINICAL CANCER INFORMATICS
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
Carey, V.J. et al. Carey, V.J., Ramos, M., Stubbs, B.J., Oh, S., Turaga, N., Waldron, L., Morgan, M.

Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia

2019
HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Your DNA, Your Say (Participant Values Survey)
Milne, R. et al. Milne, R., Morley, K.I., Howard, H., Niemiec, E., Nicol, D., Critchley, C., Prainsack, B., Vears, D., Smith, J., Steed, C., Bevan, P., Atutornu, J., Farley, L., Goodhand, P., Thorogood, A., Kleiderman,E., Middleton, A.

Trust in genomic data sharing among members of the general public in the UK

2019
CANADA AND AUSTRALIA. HUM GENET
Regulatory & Ethics Work Stream (REWS)
Milne, R. et al. Milne, R., Morley, K.I., Howard, H.

Return of individual genomic research results: are laws and policies keeping step?

2019
EUROPEAN JOURNAL OF HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Policy on Clinically Actionable Genomic Research Results
Thorogood, A. et al. Thorogood, A., Dalpé, G., Knoppers, B.M.

Openness, inclusion, and respect in dementia research

2019
LANCET NEUROLOGY
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Thorogood, A. et al. Thorogood, A., Dalpé, G., Gastmans, C., Gauthier, S.

Model consent clauses for rare disease research.

2019
BMC MED ETHICS 20
Regulatory & Ethics Work Stream (REWS)
Consent Toolkit
Nguyen, M.T. et al. Nguyen, M.T., Goldblatt, J., Isasi, R., et al.

Model consent clauses for rare disease research

2019
BMC MEDICAL ETHICS
Regulatory & Ethics Work Stream (REWS)
Consent Toolkit
Nguyen, M.T. et al. Nguyen, M.T., Goldblatt, J., Isasi, R., Jagut, M., Jonker, A.H., Kaufmann, P., Ouillade, L., Molnar-Gabor, F., Shabani, M., Sid, E., Tassé, A., Wong-Rieger, D., Knoppers, B.M.

Letter: Relearning the 3 R’s? Reinterpretation, Recontact, and Return of Genetic Variants

2019
GENETICS IN MEDICINE
Regulatory & Ethics Work Stream (REWS)
Knoppers, B.M. et al. Knoppers, B.M., Thorogood, A., Zawati, M.H.

Integrating Genomics into Healthcare: A Global Responsibility

2019
AMERICAN JOURNAL OF HUMAN GENETICS
Stark, Z. et al. Stark, Z., Dolman, L., Manolio, T.A., Ozenberger, B., Hill, S.L., Caulfied, M.J., Levy, Y., Glazer, D., Wilson, J., Lawler, M., Boughtwood, T., Braithwaite, J., Goodhand, P., Birney, E., North, K.N.

Federated discovery and sharing of genomic data using Beacons

2019
NATURE BIOTECHNOLOGY
Discovery Work Stream
Beacon, Framework for responsible sharing of genomic and health-related data
Fiume, M. et al. Fiume, M., Cupak, M., Keenan, S., Rambla, J., de la Torre, S., Dyke, S.O.M., Brookes, A.J., Carey, K., Lloyd, D., Goodhand, P., Haeussler, M., Baudis, M., Stockinger, H., Dolman, L., Lappalainen, I., Törnroos, J., Linden, M., Spalding, J.D., Ur-Rehman, S., Page, A., Flicek, P., Sherry, S.T., Haussler, D., Varma, S., Saunders, G., Scollen, S.

End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA

2019
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Data Security Work Stream, Large-Scale Genomics (LSG) Work Stream
Genetic Data Encryption (Crypt4GH)
Senf, A. Senf, A.

Consent insufficient for data release

2019
SCIENCE
Regulatory & Ethics Work Stream (REWS)
Nicol, D. et al. Nicol, D., Eckstein, L., Bentzen, H.B., Borry, P., Burgess, M., Burke, W., Chalmers, D.R., Cho, M., Dove, E.S., Fullerton, S., Ida, R., Kato, K., Kaye, J., Koenig, B., Manson, S., McGrail, K., Meslin, E.M., O'Doherty, K., Prainsack, B., Shabani, M., Tabor, H., Thorogood, A., de Vries, J.

Connecting Data and Expertise: A New Alliance for Biodiversity Knowledge.

2019
BIODIVERSITY DATA JOURNAL
Hobern, D. et al. Hobern, D., Baptiste, B., Copas, K., Guralnick, R., Hahn, A., van Huis, E., Kim, E.

BioSamples Database: An Updated Sample Metadata Hub.

2019
NUCLEIC ACIDS RESEARCH
Data Use & Researcher Identity (DURI) Work Stream
Authorisation and Authentication Infrastructure (AAI), Data Use Ontology (DUO)
Courtot, M. et al. Courtot, M., Cherubin, L., Faulconbridge, A., Vaughan, D., Green, M., Richardson, D., Harrison, P., Whetzel, P.L., Parkinson, H., Burdett, T.

Best practices for benchmarking germline small-variant calls in human genomes

2019
NATURE BIOTECHNOLOGY
Genomic Knowledge Standards (GKS) Work Stream
Variant Benchmarking Tools
Krusche, P. et al. Krusche, P., Trigg, L., Boutros, P.C., Mason, C.E., De La Vega, F.M., Moore, B.L., Gonzalez-Porta, M., Eberle, M.A., Tezak, Z., Lababidi, S., Truty, R., Asimenos, G., Funke, B., Fleharty, M., Chapman, B.A., Salit, M., Zook, J.M.

The Genomic Commons

2018
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Contreras, J.L. et al. Contreras, J.L., Knoppers, B.M.

Simplifying research access to genomics and health data with Library Cards

2018
SCIENTIFIC DATA
Data Use & Researcher Identity (DURI) Work Stream
Passports, Data Use Ontology (DUO)
Cabili, M.N. et al. Cabili, M.N., Carey, K., Dyke, S.O.M., Brookes, A.J., Fiume, M., Jeanson, F., Kerry, G., Lash, A., Sofia, H., Spalding, J.D., Tassé, A., Varma, S., Pandya, R.

Review and comparison of electronic patient-facing family health history tools

2018
JOURNAL OF GENETIC COUNSELING
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Regulatory & Ethics Work Stream (REWS)
Family History Toolkit
Welch, B.M. et al. Welch, B.M., Wiley, K., Pflieger, L., Achiangia, R., Baker, K., Hughes-Halbert, C., Morrison, H., Schiffman, J., Doerr, M.

Responsible Sharing of Biomedical Data and Biospecimens via the ‘Automatable Discovery and Access Matrix’ (ADA-M)

2018
NPJ GENOMIC MEDICINE
Regulatory & Ethics Work Stream (REWS)
Woolley, J.P. et al. Woolley, J.P., Kirby, E., Leslie, J., Jeanson, F., Cabili, M.N., Rushton, G., Hazard, J.G.

Registered access: authorizing data access.

2018
EUR J HUM GENET
Dyke, S.O.M. et al. Dyke, S.O.M., Linden, M., Lappalainen, I., et al.

Registered access: authorizing data access

2018
EUROPEAN JOURNAL OF HUMAN GENETICS
Data Use & Researcher Identity (DURI) Work Stream, Regulatory & Ethics Work Stream (REWS)
Passports
Dyke, S.O.M. et al. Dyke, S.O.M., Linden, M., Lappalainen, I., De Argila, J.R., Carey, K., Lloyd, D., Spalding, J.D., Cabili, M.N., Kerry, G., Foreman, J., Cutts, T., Shabani, M., Rodriguez, L.L., Haeussler, M., Walsh, B., Jiang, X., Wang, S., Perrett, D., Boughtwood, T., Matern, A., Brookes, A.J., Cupak, M., Fiume, M., Pandya, R., Tulchinsky, I., Scollen, S., Törnroos, J., Das, S., Evans, A.C., Malin, B.A., Beck, S., Brenner, S.E., Nyrönen, T., Blomberg, N., Firth, H.V., Hurles, M.E., Philippakis, A.A., Rätsch, G., Brudno, M., Boycott, K.M., Rehm, H.L., Baudis, M., Sherry, S.T., Kato, K., Knoppers, B.M., Baker, D., Flicek, P.

Privacy-Preserving Linkage of Genomic and Clinical Data Sets

2018
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Regulatory & Ethics Work Stream (REWS), Data Security Work Stream
Baker, D. et al. Baker, D., Knoppers, B.M., Phillips, M., van Enckevort, D., Kaufmann, P., Lochmuller, H., Taruscio, D.

Privacy-Preserving Linkage of Genomic and Clinical Data Sets

2018
IEEE/ACM TRANS COMPUT BIOL BIOINFORM.
Regulatory & Ethics Work Stream (REWS)
Baker, D.B. et al. Baker, D.B., Knoppers, B.M., Phillips, M., van Enckevort, D., Kaufmann, P., Lochmuller, H., Taruscio, D.

Model Framework for Governance of Genomic Research and Biobanking in Africa - a Content Description

2018
AAS OPEN RESEARCH
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Yakubu, A. et al. Yakubu, A., Tindana, P., Matimba, A., Littler, K., Munung, N.S., Madden, E., Staunton, C., de Vries, J.

Key Implications of Data Sharing in Pediatric Genomics

2018
JAMA
Regulatory & Ethics Work Stream (REWS)
Consent Toolkit
Rahimzadeh, V. et al. Rahimzadeh, V., Schickhardt, C., Knoppers, B.M., Sénécal, K., Vears, D.F., Fernandez, C.F., Pfister, S., Plon, S.E., Terry, S.F., Williams, J., Williams, M.S., Cornel, M.C., Friedman, J.M.

Key Implications of Data Sharing in Pediatric Genomics

2018
JAMA PEDIATR.
Regulatory & Ethics Work Stream (REWS)
Rahimzadeh, V. et al. Rahimzadeh, V., Schickhardt, C., Knoppers, B.M.

Htsget: A protocol for securely streaming genomic data

2018
BIOINFORMATICS
Large-Scale Genomics (LSG) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream)
htsget
Kelleher, J. et al. Kelleher, J., Lin, M., Albach, C.H., Birney, E., Davies, R., Gourtovaia, M., Glazer, D., Gonzalez, C.Y., Jackson, D.K., Kemp, A., Marshall, J., Nowak, A., Senf, A., Tovar-Corona, J.M., Vikhorev, A., Keane, T.M.

Genomic Data Sharing [Special issue]

2018
HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Joly, Y. et al. Joly, Y., Knoppers, B.M.

ClinGen advancing genomic data-sharing standards as a GA4GH driver project

2018
HUMAN MUTATION
Dolman, L. et al. Dolman, L., Page, A., Babb, L., Freimuth, R.R., Arachchi, H., Bizon, C., Brush, M., Fiume, M., Haendel, M.A., Hansen, D.P., Milosavljevic, A., Patel, R.Y., Pawliczek, P., Yates, A.D., Rehm, H.L.

Broaden human-rights focus for health data under GDPR

2018
NATURE
Regulatory & Ethics Work Stream (REWS)
Health Data Sharing, Privacy, and Regulatory Forum (formerly GDPR Forum), Framework for responsible sharing of genomic and health-related data
Knoppers, B.M. Knoppers, B.M.

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

2018
PLOS GENETICS
Regulatory & Ethics Work Stream (REWS)
Cline, M.S. et al. Cline, M.S., Liao, R.G., Parsons, M.T., Paten, B., Alquaddoomi, F., Antoniou, A., Baxter, S., Brody, L., Cook-Deegan, R., Coffin, A., Couch, F.J., Craft, B., Currie, R., Dlott, C.C., Dolman, L., den Dunnen, J.T., Dyke, S.O.M., Domchek, S.M., Easton, D., Fischmann, Z., Foulkes, W.D., Garber, J., Goldgar, D., Goldman, M.J., Goodhand, P., Harrison, S., Haussler, D., Kato, K., Knoppers, B.M., Markello, C., Nussbaum, R., Offit, K., Plon, S.E., Rashbass, J., Rehm, H.L., Robson, M., Rubinstein, W.S., Stoppa-Lyonnet, D., Tavtigian, S., Thorogood, A., Zhang, C.

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes

2018
NATURE BIOTECHNOLOGY
Large-Scale Genomics (LSG) Work Stream
Krusche, P. et al. Krusche, P., Trigg, L., Boutros, P.C., Mason, C.E., De La Vega, F.M., Moore, B.L., Gonzalez-Porta, M., Eberle, M.A., Tezak, Z., Lababidi, S., Truty, R., Asimenos, G., Funke, B., Fleharty, M., Salit, M., Zook, J.M.

Appraisal of the Jordanian Law for Data Sharing in Stem Cell Research: In the Light of the ‘GA4GH Framework’ for Innovative Cancer Care.

2018
2018 1ST INTERNATIONAL CONFERENCE ON CANCER CARE INFORMATICS (CCI)
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Al-Tabba, A. et al. Al-Tabba, A., Al-Omari, A., Al-Hussaini, M.

APPLaUD: access for patients and participants to individual level uninterpreted genomic data.

2018
HUM GENOMICS
Regulatory & Ethics Work Stream (REWS)
Thorogood, A. et al. Thorogood, A., Bobe, J., Prainsack, B.

APPLaUD: Access for patients and participants to individual level uninterpreted genomic data

2018
HUMAN GENOMICS
Regulatory & Ethics Work Stream (REWS)
Thorogood, A. et al. Thorogood, A., Bobe, J., Prainsack, B., Middleton, A., Scott, E., Nelson, S., Corpas, M., Bonhomme, N., Rodriguez, L.L., Murtagh, M., Kleiderman, E.

Your DNA, Your Say

2017
THE NEW BIOETHICS
Regulatory & Ethics Work Stream (REWS)
Your DNA, Your Say (Participant Values Survey)
Middleton, A. Middleton, A.

Using High Performance Computing to Create and Freely Distribute the South Asian Genomic Database, Necessary for Precision Medicine in this Population

2017
SUPERCOMPUTING FRONTIERS AND INNOVATIONS
Beacon
Shah, A.H. et al. Shah, A.H., Picker, J.D., Jamuar, S.S.

Tools to foster trust in sharing healthcare data: Toward a common language for regulatory metadata

2017
MEDICINE AND LAW
Regulatory & Ethics Work Stream (REWS)
Woolley, J.P. Woolley, J.P.

The path to reducing duplication of human research ethics review in Australia

2017
MEDICINE AND LAW
Regulatory & Ethics Work Stream (REWS)
Johns, A. et al. Johns, A., Nicol, D., Zeps, N., Chalmers, D.R.

The Dockstore: Enabling modular, community-focused sharing of Docker-based genomics tools and workflows

2017
F1000RESEARCH
Federated Analysis Work Stream (formerly Cloud Work Stream)
Tool Registry Service (TRS)
O'Connor, B.O. et al. O'Connor, B.O., Yuen, D., Chung, V., Duncan, A.G., Liu, X.K., Patricia, J., Paten, B., Stein, L.D., Ferretti, V.

Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance

2017
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
Regulatory & Ethics Work Stream (REWS)
Cook-Deegan, R. et al. Cook-Deegan, R., Ankeny, R.A., Jones, K.M.

Genomics in healthcare: GA4GH looks to 2022

2017
BIORXIV
Birney, E. et al. Birney, E., Vamathevan, J., Goodhand, P.

Genomic newborn screening: Public health policy considerations and recommendations

2017
BMC MEDICAL GENOMICS,
Regulatory & Ethics Work Stream (REWS)
Consent Toolkit
Friedman, J.M. et al. Friedman, J.M., Cornel, M.C., Goldenberg, A.J., Lister, K.J., Sénécal, K., Vears, D.F.

From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine

2017
THE NEW BIOETHICS
Data Security Work Stream, Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data, Data Security Infrastructure Policy (DSIP)
Lawler, M. et al. Lawler, M., Maughan, T.

Ethics and Big Data in health

2017
CURRENT OPINION IN SYSTEMS BIOLOGY
Regulatory & Ethics Work Stream (REWS)
Knoppers, B.M. et al. Knoppers, B.M., Thorogood, A.M.

Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services

2017
BMC MEDICAL GENOMICS
Discovery Work Stream
Beacon
Wan, Z. et al. Wan, Z., Vorobeychik, Y., Kantarcioglu, M., Malin, B.A.

Consent Processes for Mobile App Mediated Research: Systematic Review

2017
JMIR MHEALTH UHEALTH
Regulatory & Ethics Work Stream (REWS)
Moore, S. et al. Moore, S., Tassé, A.M., Thorogood, A., Winship, I., Zawati. M., Doerr, M.

Aftermath of bustamante attack on genomic beacon service

2017
BMC MEDICAL GENOMICS
Discovery Work Stream
Beacon
Aziz, M.M. et al. Aziz, M.M., Ghasemi, R., Waliullah, M., Mohammed, N.

Addressing Beacon re-identification attacks: Quantification and mitigation of privacy risks

2017
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
Discovery Work Stream
Beacon
Raisaro, J.L et al. Raisaro, J.L, Tramèr, F., Ji, Z., Bu, D., Zhao, Y., Carey, K., Lloyd, D., Sofia, H., Baker, D., Flicek, P., Shringarpure, S., Bustamante, C., Wang, S., Jiang, X., Ohno-Machado, L., Tang, H., Wang, X., Hubaux, J.P.

A community effort to protect genomic data sharing, collaboration and outsourcing

2017
NPJ GENOMIC MEDICINE
Data Security Work Stream, Regulatory & Ethics Work Stream (REWS)
Data Privacy and Security Policy, Data Security Infrastructure Policy (DSIP)
Wang, S. et al. Wang, S., Jiang, X., Tang, H., Wang, X., Bu, D., Carey, K., Dyke, S.O.M., Fox, D., Jiang, C., Lauter, K., Malin, B.A., Sofia, H., Telenti, A., Wang, L., Wang, W., Ohno-Machado, L.

 Public variant databases: Liability?

2016
GENETICS IN MEDICINE
Regulatory & Ethics Work Stream (REWS)
Thorogood, A. et al. Thorogood, A., Cook-Deegan, R., Knoppers, B.M.

The Human Variome Project

2016
HUMAN MUTATION
Burn, J. et al. Burn, J., Watson, M.

The discombobulation of de-identification

2016
NATURE BIOTECHNOLOGY
Regulatory & Ethics Work Stream (REWS)
Data Privacy and Security Policy
Phillips, M. et al. Phillips, M., Knoppers, B.M.

Sharing Health-Related Data: A Privacy Test?

2016
NPJ GENOMIC MEDICINE
Regulatory & Ethics Work Stream (REWS)
Beacon, Framework for responsible sharing of genomic and health-related data
Dyke, S.O.M. et al. Dyke, S.O.M., Dove, E.S., Knoppers, B.M.

Registered access: a ‘Triple-A’ approach.

2016
EUR J HUM GENET
Dyke, S.O.M. et al. Dyke, S.O.M., Kirby, E., Shabani, M.

RD-Connect: Data Sharing and Analysis for Rare Disease Research within the Integrated Platform and through GA4GH Beacon and Matchmaker Exchange

2016
NEUROMUSCULAR DISORDERS
Discovery Work Stream
Beacon
Roos, A. et al. Roos, A., Beltran, S., Piscia, D., Laurie, S., Protasio, J., Cañada, A., Fernández, J.

IRDIRC and GA4GH: International Efforts to Advance Rare Disease Discovery

2016
PATHOLOGY
Boycott, K.M. Boycott, K.M.

Facilitating a Culture of Responsible and Effective Sharing of Cancer Genome Data

2016
NATURE MEDICINE
Regulatory & Ethics Work Stream (REWS), Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Federated Analysis Work Stream (formerly Cloud Work Stream), Discovery Work Stream
Framework for responsible sharing of genomic and health-related data, Consent Policy, Beacon, Data Security Infrastructure Policy (DSIP)
Siu, L.L. et al. Siu, L.L., Lawler, M., Haussler, D., Knoppers, B.M., Lewin, J.H., Vis, D.J., Liao, R.G.

Ethics review for international data-intensive research

2016
SCIENCE
Regulatory & Ethics Work Stream (REWS)
Ethics Review Recognition Policy
Dove, E.S. et al. Dove, E.S., Townend, D., Meslin, E.M., Bobrow, M., Littler, K., Nicol, D., de Vries, J., Junker, A., Garattini, C., Bovenberg, J., Shabani, M., Lévesque, E., Knoppers, B.M.

Ethical issues in consumer genome sequencing: Use of consumers samples and data

2016
APPLIED & TRANSLATIONAL GENOMICS
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Niemiec, E. et al. Niemiec, E., Howard, H. C.

Determining Barriers to Effective Data Sharing in Cancer Genomic Sequencing Initiatives: A Global Alliance for Genomics and Health (GA4GH) Survey

2016
JOURNAL OF CLINICAL ONCOLOGY
Lewin, J.H. et al. Lewin, J.H., Vis, D.J., Voest, E.E., Liao, R.G., Nederlof, P.M., Conley, B.A., Solit, D.B.

Consent Codes: Upholding Standard Data Use Conditions

2016
PLOS GENETICS
Regulatory & Ethics Work Stream (REWS)
Dyke, S.O.M. et al. Dyke, S.O.M., Philippakis, A.A., Paltoo, D.N., Luetkemeier, E.S., Knoppers, B.M., Brookes, A.J., Spalding, J.D., Thompson, M., Roos, M., Boycott, K.M., Brudno, M., Hurles, M., Rehm, H.L., Matern, A., Fiume, M., Sherry, S.T.

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing

2016
PLOS BIOLOGY
Regulatory & Ethics Work Stream (REWS)
Majumder, M. A. et al. Majumder, M. A., Cook-Deegan, R., Mcguire, A. L.

Are Data Sharing and Privacy Protection Mutually Exclusive?

2016
CELL
Regulatory & Ethics Work Stream (REWS)
Joly, Y. et al. Joly, Y., Dyke, S.O.M., Knoppers, B.M., Pastinen, T.

An International Framework for Data Sharing: Moving Forward with the Global Alliance for Genomics and Health

2016
BIOPRESERVATION AND BIOBANKING
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Rahimzadeh, V. et al. Rahimzadeh, V., Dyke, S.O.M., Knoppers, B.M.

A federated ecosystem for sharing genomic, clinical data

2016
SCIENCE
Page, A. et al. Page, A., Baker, D., Bobrow, M., Boycott, K.M., Burn, J., Chanock, S.J., Donnelly, S., Dove, E.S., Durbin, R., Dyke, S.O.M., Fiume, M., Flicek, P., Glazer, D., Goodhand, P., Haussler, D., Kato, K., Keenan, S., Knoppers, B.M., Liao, R.G., Lloyd, D., Mulder, N., Navarro, A., North, K.N., Philippakis, A.A., Rahman, N., Rehm, H.L., Sawyers, C., Thorogood, A., Wilson, J., Altshuler, D., Hudson, T.J.

UK gears up to decode 100 000 genomes from NHS patients

2015
LANCET
Siva, N. Siva, N.

The NIH BD2K center for big data in translational genomics

2015
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
Paten, B. et al. Paten, B., Diekhans, M., Druker, B.J., Friend, S., Guinney, J., Gassner, N., Guttman, M., Kent, W.J., Mantey, P., Margolin, A.A., Massie, M., Novak, A.M., Nothaft, F., Pachter, L., Patterson, D., Smuga-Otto, M., Stuart, J.M., Van't Veer, L., Wold, B., Haussler, D.

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

2015
HUMAN MUTATION
Philippakis, A.A. et al. Philippakis, A.A., Azzariti, D.R., Beltran, S., Brookes, A.J., Brownstein, C.A., Brudno, M., Brunner, H.G., Buske, O.J., Carey, K., Doll, C., Dumitriu, S., Dyke, S.O.M., den Dunnen, J.T., Firth, H.V., Gibbs, R.A., Girdea, M., Gonzalez, M., Haendel, M.A., Hamosh, A., Holm, I.A., Huang, L., Hurles, M.E., Hutton, B., Krier, J.B., Misyura, A., Mungall, C.J., Paschall, J ., Paten, B., Robinson, P.N., Schiettecatte, F., Sobreira, N.L., Swaminathan, G.J., Taschner, G.E., Terry, S.F., Washington, N.L., Züchner, S., Boycott, K.M., Rehm, H.L.

The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles

2015
HUMAN MUTATION
Buske, O.J. et al. Buske, O.J., Schiettecatte, F., Hutton, B., Dumitriu, S., Misyura, A., Huang, L., Hartley, T., Girdea, M., Sobreira, N.L., Mungall, C.J., Brudno, M.

The big medical data miss: Challenges in establishing an open medical resource

2015
NATURE REVIEWS GENETICS
Topol, E.J. Topol, E.J.

Data sharing in stem cell translational science: Policy statement by the International Stem Cell Forum Ethics Working Party

2015
REGENERATIVE MEDICINE
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Bredenoord, A.L. et al. Bredenoord, A.L., Mostert, M., Isasi, R., Knoppers, B.M.

Data analysis: Create a cloud commons

2015
NATURE
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Stein, L.D. et al. Stein, L.D., Knoppers, B.M., Campbell, P., Getz, G., Korbel, J.O.

Curating the Way to Better Determinants of Genetic Risk

2015
NEW ENGLAND JOURNAL OF MEDICINE
Phimister, E.G. Phimister, E.G.

Building the foundation for genomics in precision medicine

2015
NATURE
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Aronson, S.J. et al. Aronson, S.J., Rehm, H.L.

An ecosystem of cancer cell line factories to support a cancer dependency map

2015
NATURE REVIEWS GENETICS
Boehm, J. S. et al. Boehm, J. S., Golub, T. R.

All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health

2015
CANCER DISCOVERY
Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Lawler, M. et al. Lawler, M., Siu, L.L., Rehm, H.L., Chanock, S.J., Alterovitz, G., Burn, J., Calvo, F.

To share or not to share is the question

2014
APPLIED & TRANSLATIONAL GENOMICS
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Chalmers, D.R. et al. Chalmers, D.R., Nicol, D., Otlowski, M.F.

The Global Alliance for Genomics & Health

2014
GENETIC TESTING AND MOLECULAR BIOMARKERS
Terry, S.F. Terry, S.F.

Redefining Genomic Privacy: Trust and Empowerment

2014
PLOS BIOLOGY
Erlich, Y. et al. Erlich, Y., Williams, J.B., Glazer, D., Yocum, K., Farahany, N., Olson, M., Narayanan, A., Stein, L.D., Witkowski, J.A., Kain, R.C.

International ethics harmonization and the global alliance for genomics and health

2014
GENOME MEDICINE
Regulatory & Ethics Work Stream (REWS)
Ethics Review Recognition Policy
Knoppers, B.M. Knoppers, B.M.

International code of conduct for genomic and health-related data sharing

2014
THE HUGO JOURNAL
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Sugano, S. Sugano, S.

Framework for responsible sharing of genomic and health-related data.

2014
HUGO J
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Knoppers, B.M. Knoppers, B.M.

Framework for Responsible Sharing of Genomic and Health-Related Data

2014
THE HUGO JOURNAL
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Knoppers, B.M. Knoppers, B.M.

ELSI practices in genomic research in East Asia: Implications for research collaboration and public participation

2014
GENOME MEDICINE
Regulatory & Ethics Work Stream (REWS)
Yoshizawa, G. et al. Yoshizawa, G., Ho, C.W., Zhu, W., Hu, C., Syukriani, Y., Lee, I., Kim, H., Tsai, D.F.C., Minari, J., Kato, K.

Does policy grow on trees?

2014
BMC MEDICAL ETHICS
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Knoppers, B.M. Knoppers, B.M.

Building a Data Sharing Model for Global Genomic Research

2014
GENOME BIOLOGY
Regulatory & Ethics Work Stream (REWS)
Framework for responsible sharing of genomic and health-related data
Kosseim, P. et al. Kosseim, P., Dove, E.S., Baggaley, C., Meslin, E.M., Cate, F.H., Kaye, J., Harris, J.R., Knoppers, B.M.

The variant call format and VCFtools

2011
BIOINFORMATICS
Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream
Genetic Variation Formats (VCF)

Efficient storage of high throughput DNA sequencing data using reference-based compression

2011
GENOME RESEARCH
Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream
CRAM

The Sequence Alignment/Map format and SAMtools

2009
BIOINFORMATICS
Large-Scale Genomics (LSG) Work Stream, Genomic Knowledge Standards (GKS) Work Stream
SAM/BAM
Li, H. et al. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R.