By GA4GH

Articles written by active GA4GH contributors presenting either a product release or an opinion of GA4GH or one of its teams.

• Dianne Nicol, Lisa Eckstein, Heidi Beate Bentzen, Pascal Borry, Mike Burgess, Wylie Burke, Don Chalmers, Mildred Cho, Edward Dove, Stephanie Fullerton, Ryuchi Ida, Kazuto Kato, Jane Kaye, Barbara Koenig, Spero Manson, Kimberlyn McGrail, Eric Meslin, Kieran O'Doherty, Barbara Prainsack, Mahsa Shabani, Holly Tabor, Adrian Thorogood, Jantina de Vries (2019). Consent insufficient for data release. Science 445-446 doi:10.1126/science.aax0892
• Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S (2019). Federated discovery and sharing of genomic data using Beacons. Nature Biotechnology 220-224 doi:10.1038/s41587-019-0046-x
• Knoppers, Bartha Maria, Adrian Thorogood, and Ma’n H. Zawati (2019). Letter: Relearning the 3 R’s? Reinterpretation, Recontact, and Return of Genetic Variants. Genetics in Medicine doi:10.1038/s41436-019-0494-1
• Minh Thu Nguyen, Jack Goldblatt, Rosario Isasi, Marlene Jagut, Anneliene Hechtelt Jonker, Petra Kaufmann, Laetitia Ouillade, Fruszina Molnar-Gabor, Mahsa Shabani, Eric Sid, Anne Marie Tassé, Durhane Wong-Rieger, Bartha Maria Knoppers & on behalf of the IRDiRC-GA4GH Model Consent Clauses Task Force (2019). Model consent clauses for rare disease research. BMC Medical Ethics doi:10.1186/s12910-019-0390-x
• Stark, Z., Dolman, L., Manolio, T. A., Ozenberger, B., Hill, S. L., Caulfied, M. J.,...North, K. N. (2019). Integrating Genomics into Healthcare: A Global Responsibility. American Journal of Human Genetics 13-20 doi:10.1016/j.ajhg.2018.11.014
• Thorogood, A., Dalpé, G., Knoppers, B. M. (2019). Return of individual genomic research results: are laws and policies keeping step?. European Journal of Human Genetics doi:10.1038/s41431-018-0311-3
• Thorogood, A., Mäki-Petäjä-Leinonen, A., Dalpé, G., Gastmans, C., Gauthier, S. (2019). Openness, inclusion, and respect in dementia research. Lancet Neurology 135-136 doi:10.1016/S1474-4422(18)30445-9
• Baker D, Knoppers BM, Phillips M, van Enckevort D, Kaufmann P, Lochmuller H, Taruscio D (2018). Privacy-Preserving Linkage of Genomic and Clinical Data Sets. IEEE/ACM transactions on computational biology and bioinformatics doi:10.1109/TCBB.2018.2855125
• Cabili, M. N., Carey, K., Dyke, S. O., Brookes, A. J., Fiume, M., Jeanson, F., . . . Pandya, R. (2018). Simplifying research access to genomics and health data with Library Cards. Scientific Data 180039 doi:10.1038/sdata.2018.39
• Cline, M.S., Liao, R. G., Parsons, M. T., Paten, B., Alquaddoomi, F., Antoniou, A.,...Spurdle, A. B. (2018). BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLOS Genetics doi:10.1371/journal.pgen.1007752
• Contreras JL, Knoppers BM (2018). The Genomic Commons. Annual Review of Genomics and Human Genetics 29-453 doi:10.1146/annurev-genom-083117-021552
• Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL (2018). ClinGen advancing genomic data-sharing standards as a GA4GH driver project. Human Mutation 1686-1689 doi:10.1002/humu.23625
• Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P (2018). Registered access: authorizing data access. European Journal of Human Genetics 1721-1731 doi:10.1038/s41431-018-0219-y
• Joly, Y., Knoppers, B. (Eds.) (2018). Genomic Data Sharing [Special issue]. Human Genetics 137(8). doi:10.1007/s00439-018-1923-y
• Kelleher, J., Lin, M., Albach, C., Birney, E., Davies, R., Gourtovaia, M., . . . Keane, T. M. (2018). Htsget: A protocol for securely streaming genomic data. Bioinformatics doi:10.1093/bioinformatics/bty492
• Knoppers, B. (2018). Broaden human-rights focus for health data under GDPR. Nature 189-189 doi:10.1038/d41586-018-05388-3
• Krusche, P., Trigg, L., Boutros, P. C., Mason, C. E., Vega, F. M., Moore, B. L., . . . Zook, J. M. (2018). Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes. BioRxiv doi:10.1101/270157
• Rahimzadeh, V., Schickhardt, C., Knoppers, B. M., Sénécal, K., Vears, D. F., Fernandez, C. V., . . . Friedman, J. M. (2018). Key Implications of Data Sharing in Pediatric Genomics. JAMA 476 doi:10.1001/jamapediatrics.2017.5500
• Thorogood, A., Bobe, J., Prainsack, B., Middleton, A., Scott, E., Nelson, S., . . . Kleiderman, E. (2018). APPLaUD: Access for patients and participants to individual level uninterpreted genomic data. Human Genomics doi:10.1186/s40246-018-0139-5
• Woolley, J. Patrick, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N. Cabili, Gregory Rushton, James G. Hazard, et al (2018). Responsible Sharing of Biomedical Data and Biospecimens via the ‘Automatable Discovery and Access Matrix’ (ADA-M). NPJ Genomic Medicine doi:10.1038/s41525-018-0057-4
• Aziz, M. M., Ghasemi, R., Waliullah, M., & Mohammed, N. (2017). Aftermath of bustamante attack on genomic beacon service. BMC Medical Genomics doi:10.1186/s12920-017-0278-x
• Birney, E., Vamathevan, J., & Goodhand, P. (2017). Genomics in healthcare: GA4GH looks to 2022. BioRxiv doi:10.1101/203554
• Friedman, J. M., Cornel, M. C., Goldenberg, A. J., Lister, K. J., Sénécal, K., & Vears, D. F. (2017). Genomic newborn screening: Public health policy considerations and recommendations. BMC Medical Genomics, 10(1) doi:10.1186/s12920-017-0247-4
• Middleton, A. (2017). Your DNA, Your Say. The New Bioethics 74-80 doi:10.1080/20502877.2017.1314890
• Edward S. Dove1, David Townend, Eric M. Meslin, Martin Bobrow, Katherine Littler, Dianne Nicol, Jantina de Vries, Anne Junker, Chiara Garattini, Jasper Bovenberg, Mahsa Shabani, Emmanuelle Lévesque, Bartha M. Knoppers (2016). Ethics review for international data-intensive research. Science 1399-1400 doi:10.1126/science.aad5269
• Lewin, Jeremy Howard, Daniel J. Vis, Emile E. Voest, Rachel Liao, Petra M. Nederlof, Barbara A. Conley, David B. Solit, et al (2016). Determining Barriers to Effective Data Sharing in Cancer Genomic Sequencing Initiatives: A Global Alliance for Genomics and Health (GA4GH) Survey. Journal of Clinical Oncology doi:10.1200/JCO.2016.34.15_suppl.11502
• Siu, Lillian L., Mark Lawler, David Haussler, Bartha Maria Knoppers, Jeremy Lewin, Daniel J. Vis, Rachel G. Liao, et al (2016). Facilitating a Culture of Responsible and Effective Sharing of Cancer Genome Data. Nature Medicine doi:10.1038/nm.4089
• The Global Alliance for Genomics and Health, (2016). A federated ecosystem for sharing genomic, clinical data. Science 352(6291), 1278-1280 doi:10.1126/science.aaf6162
• Lawler, Mark, Lillian L. Siu, Heidi L. Rehm, Stephen J. Chanock, Gil Alterovitz, John Burn, Fabien Calvo, et al (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health. Cancer Discovery doi:10.1158/2159-8290.CD-15-0821
• Knoppers, B. M. (2014). International ethics harmonization and the global alliance for genomics and health. Genome Medicine doi:10.1186/gm530
• Knoppers, Bartha Maria (2014). Framework for Responsible Sharing of Genomic and Health-Related Data. The HUGO Journal doi:10.1186/s11568-014-0003-1
• Regulatory and Ethics Working Group, Global Alliance for Genomics & Health, & Sugano, S., (2014). International code of conduct for genomic and health-related data sharing. The HUGO Journal 8(1), 1 doi:10.1186/1877-6566-8-1
• Yoshizawa, G., Ho, C. W., Zhu, W., Hu, C., Syukriani, Y., Lee, I., . . . Kato, K. (2014). ELSI practices in genomic research in East Asia: Implications for research collaboration and public participation. Genome Medicine doi:10.1186/gm556

About GA4GH

Articles primarily about GA4GH or one of its products but not presenting a product for the first time and not representing the opinion of GA4GH or one of its teams.

• Al-Tabba, Amal, Amal Al-Omari, and Maysa Al-Hussaini (2018). Appraisal of the Jordanian Law for Data Sharing in Stem Cell Research: In the Light of the ‘GA4GH Framework’ for Innovative Cancer Care.. 2018 1st International Conference on Cancer Care Informatics (CCI) doi:10.1109/cancercare.2018.8618158
• Cook-Deegan, R., Ankeny, R. A., & Jones, K. M. (2017). Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance. Annual Review of Genomics and Human Genetics 389-415 doi:10.1146/annurev-genom-083115-022515
• Lawler, M., & Maughan, T. (2017). From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine. The New Bioethics 64-73 doi:10.1080/20502877.2017.1314883
• Oconnor, B. D., Yuen, D., Chung, V., Duncan, A. G., Liu, X. K., Patricia, J., . . . Ferretti, V. (2017). The Dockstore: Enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Research doi:10.12688/f1000research.10137.1
• Raisaro, J. L., Tramèr, F., Ji, Z., Bu, D., Zhao, Y., Carey, K., . . . Hubaux, J. (2017). Addressing Beacon re-identification attacks: Quantification and mitigation of privacy risks. Journal of the American Medical Informatics Association 799-805 doi:10.1093/jamia/ocw167
• Wan, Z., Vorobeychik, Y., Kantarcioglu, M., & Malin, B. (2017). Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services. BMC Medical Genomics doi:10.1186/s12920-017-0282-1
• Wang, S., Jiang, X., Tang, H., Wang, X., Bu, D., Carey, K., . . . Ohno-Machado, L. (2017). A community effort to protect genomic data sharing, collaboration and outsourcing. Npj Genomic Medicine doi:10.1038/s41525-017-0036-1
• Woolley, J. (2017). Tools to foster trust in sharing healthcare data: Toward a common language for regulatory metadata. Medicine and Law 25-50 doi:
• Boycott, Kym (2016). IRDIRC and GA4GH: International Efforts to Advance Rare Disease Discovery. Pathology doi:10.1016/j.pathol.2015.12.080
• Roos, A., S. Beltran, D. Piscia, S. Laurie, J. Protasio, A. Cañada, J. Fernández, et al (2016). RD-Connect: Data Sharing and Analysis for Rare Disease Research within the Integrated Platform and through GA4GH Beacon and Matchmaker Exchange. Neuromuscular Disorders doi:10.1016/j.nmd.2016.06.272
• Bredenoord, A. L., Mostert, M., Isasi, R., & Knoppers, B. M. (2015). Data sharing in stem cell translational science: Policy statement by the International Stem Cell Forum Ethics Working Party. Regenerative Medicine 857-861 doi:10.2217/rme.15.42
• Chalmers, D. R., Nicol, D., & Otlowski, M. F. (2014). To share or not to share is the question. Applied & Translational Genomics 116-119 doi:10.1016/j.atg.2014.09.011
• Knoppers, B. M. (2014). Does policy grow on trees?. BMC Medical Ethics doi:10.1186/1472-6939-15-87
• Kosseim, Patricia, Edward S. Dove, Carman Baggaley, Eric M. Meslin, Fred H. Cate, Jane Kaye, Jennifer R. Harris, and Bartha M. Knoppers (2014). Building a Data Sharing Model for Global Genomic Research. Genome Biology doi:10.1186/s13059-014-0430-2
• Terry, S. F. (2014). The Global Alliance for Genomics & Health. Genetic Testing and Molecular Biomarkers 375-376 doi:10.1089/gtmb.2014.1555

GA4GH mentions

Articles primarily about other initiatives or topics that mention GA4GH once or several times.

• Courtot, Mélanie, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter Harrison, Patricia L. Whetzel, Helen Parkinson, and Tony Burdett (2019). BioSamples Database: An Updated Sample Metadata Hub.. Nucleic Acids Research D1172–78 doi:10.1093/nar/gky1061
• Hobern, Donald, Brigitte Baptiste, Kyle Copas, Robert Guralnick, Andrea Hahn, Edwin van Huis, Eun-Shik Kim, et al (2019). Connecting Data and Expertise: A New Alliance for Biodiversity Knowledge.. Biodiversity Data Journal doi:10.3897/BDJ.7.e33679
• Sempéré, Guilhem, Adrien Pétel, Mathieu Rouard, Julien Frouin, Yann Hueber, Fabien De Bellis, and Pierre Larmande (2019). Gigwa v2-Extended and Improved Genotype Investigator. GigaScience doi:10.1093/gigascience/giz051
• Senf, Alexander (2019). End-to-End Security for Local and Remote Human Genetic Data Applications at the EGA. IEEE/ACM Transactions on Computational Biology and Bioinformatics doi:10.1109/TCBB.2019.2916810
• Yakubu, Aminu, Paulina Tindana, Alice Matimba, Katherine Littler, Nchangwi Syntia Munung, Ebony Madden, Ciara Staunton, and Jantina De Vries (2018). Model Framework for Governance of Genomic Research and Biobanking in Africa - a Content Description. AAS Open Research doi:10.12688/aasopenres.12844.1
• Johns, A., Nicol, D., Zeps, N., & Chalmers, D. (2017). The path to reducing duplication of human research ethics review in Australia. Medicine and Law 7-24 doi:
• Shah, A. H., Picker, J. D., & Jamuar, S. S. (2017). Using High Performance Computing to Create and Freely Distribute the South Asian Genomic Database, Necessary for Precision Medicine in this Population. Supercomputing Frontiers and Innovations doi:10.14529/jsfi170201
• Burn, J., & Watson, M. (2016). The Human Variome Project. Human Mutation 505-507 doi:10.1002/humu.22986
• Joly, Y., Dyke, S. O., Knoppers, B. M., & Pastinen, T. (2016). Are Data Sharing and Privacy Protection Mutually Exclusive?. Cell 1150-1154 doi:10.1016/j.cell.2016.11.004
• Majumder, M. A., Cook-Deegan, R., & Mcguire, A. L. (2016). Beyond Our Borders? Public Resistance to Global Genomic Data Sharing. PLOS Biology doi:10.1371/journal.pbio.2000206
• Niemiec, E., & Howard, H. C. (2016). Ethical issues in consumer genome sequencing: Use of consumers samples and data. Applied & Translational Genomics 23-30 doi:10.1016/j.atg.2016.01.005
• Phillips, M., & Knoppers, B. M. (2016). The discombobulation of de-identification. Nature Biotechnology 1102-1103 doi:10.1038/nbt.3696
• Thorogood, A., Cook-Deegan, R., & Knoppers, B. M. (2016).  Public variant databases: Liability?. Genetics in Medicine 838-841 doi:10.1038/gim.2016.189
• Aronson, S. J., & Rehm, H. L. (2015). Building the foundation for genomics in precision medicine. Nature 336-342 doi:10.1038/nature15816
• Boehm, J. S., & Golub, T. R. (2015). An ecosystem of cancer cell line factories to support a cancer dependency map. Nature Reviews Genetics 373-374 doi:10.1038/nrg3967
• Buske, O. J., Schiettecatte, F., Hutton, B., Dumitriu, S., Misyura, A., Huang, L., . . . Brudno, M. (2015). The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles. Human Mutation 922-927 doi:10.1002/humu.22850
• Paten, B., Diekhans, M., Druker, B. J., Friend, S., Guinney, J., Gassner, N., . . . Haussler, D. (2015). The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association doi:8. 10.1093/jamia/ocv047
• Philippakis, A. A., Azzariti, D. R., Beltran, S., Brookes, A. J., Brownstein, C. A., Brudno, M., . . . Rehm, H. L. (2015). The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Human Mutation 915-921 doi:9. 10.1002/humu.22858
• Phimister, E. G. (2015). Curating the Way to Better Determinants of Genetic Risk. New England Journal of Medicine 2227-2228 doi:10.1056/nejme1506276
• Siva, N. (2015). UK gears up to decode 100 000 genomes from NHS patients. Lancet 103-104 doi:11. 10.1016/s0140-6736(14)62453-3
• Stein, L. D., Knoppers, B. M., Campbell, P., Getz, G., & Korbel, J. O. (2015). Data analysis: Create a cloud commons. Nature 149-151 doi:12. 10.1038/523149a
• Topol, E. J. (2015). The big medical data miss: Challenges in establishing an open medical resource. Nature Reviews Genetics 253-254 doi:13. 10.1038/nrg3943
• Erlich, Y., Williams, J. B., Glazer, D., Yocum, K., Farahany, N., Olson, M., . . . Kain, R. (2014). Redefining Genomic Privacy: Trust and Empowerment. PLoS Biology doi:10.1371/journal.pbio.1001983