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Title: The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. In conclusion, three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [6] ;  [8] ;  [9] ;  [10] ;  [11] ;  [12] ;  [13] ;  [14] ;  [15] ;  [16] ;  [17] ;  [18] ;  [5] more »;  [19] ;  [20] ;  [20] ;  [21] ;  [10] ;  [22] ;  [23] ;  [24] ;  [25] ;  [26] ;  [18] ;  [27] ;  [28] ;  [29] ;  [22] ;  [30] ;  [31] ;  [32] « less
  1. Broad Inst. of Harvard and MIT, Cambridge, MA (United States); Brigham and Women's Hospital (Harvard Medical School), Boston, MA (United States). Dept. of Cardiology
  2. Partners Personalized Medicine, Boston, MA (United States). Lab. for Molecular Medicine
  3. Centro Nacional de Analisis Genomico, Barcelona (Spain)
  4. Univ. of Leicester (United Kingdom). Dept. of Genetics
  5. Harvard Univ., Boston, MA (United States). Harvard Medical School; Boston Children's Hospital, Boston, MA (United States). Division of Genetics and Genomics and the Manton Center for Orphan Disease Research
  6. Univ. of Toronto, ON (Canada). Dept. of Computer Science; The Hospital for Sick Children, Toronto (Canada). Genetics and Genome Biology Program; The Hospital for Sick Children, Toronto (Canada). Centre for Computational Medicine
  7. Radboud Univ. Medical Center, Nijmegen (The Netherlands). Dept. of Human Genetics; Maastricht Univ. (The Netherlands). Dept. of Clinical Genetics
  8. Gene Cloud, CA (United States)
  9. Google Inc., Mountain View, CA (United States)
  10. The Hospital for Sick Children, Toronto (Canada). Centre for Computational Medicine
  11. McGill Univ., Montreal, QC (Canada). Centre of Genomics and Policy
  12. Leiden Univ. Medical Center, Leiden (The Netherlands)
  13. Cambridge Univ. Hospitals NHS Foundation Trust, Cambridge (United Kingdom). Biomedical Campus, East Anglian Medical Genetics Service
  14. Baylor College of Medicine, Houston, TX (United States). Human Genome Sequencing Center
  15. Univ. of Toronto, ON (Canada). Dept. of Computer Science; The Hospital for Sick Children, Toronto (Canada). Centre for Computational Medicine
  16. Genesis Project Inc, Miami, FL (United States)
  17. Oregon Health & Science Univ., Portland, OR (United States). Dept. of Medical Informatics and Clinical Epidemiology
  18. Johns Hopkins Univ., Baltimore, MD (United States). McKusick-Nathans Inst. of Genetic Medicine
  19. Children's Hospital of Eastern Ontario Research Inst., Ottawa, ON (Canada)
  20. Wellcome Trust Sanger Inst., Hinxton (United Kingdom). Wellcome Trust Genome Campus
  21. Brigham and Women's Hospital, Boston, MA (United States). Division of Genetics, Dept. of Medicine
  22. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
  23. European Molecular Biology Lab. - European Bioinformatics Inst. (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire (United Kingdom)
  24. Univ. of California, Santa Cruz, CA (United States). Genomics Inst.
  25. Charite-Univ., Berlin (Germany); Max Planck Inst. for Molecular Genetics, Berlin (Germany); Freie Univ., Berlin (Germany). Dept. of Mathematics and Computer Science; Berlin Brandenburg Center for Regenerative Therapies, Berlin (Germany)
  26. FS Consulting LLC, Salem, MA (United States)
  27. Wellcome Trust Genome Campus, Hinxton, Cambridgeshire (United Kingdom)
  28. Oregon Health & Science Univ., Portland, OR (United States). Dept. of Medical Informatics and Clinical Epidemiology; Brigham and Women's Hospital, Boston, MA (United States). Division of Genetics, Dept. of Medicine
  29. Genetic Alliance, Washington, DC (United States)
  30. Univ. of Miami, Miami, FL (United States). Dr. John T. Macdonald Foundation Dept. of Human Genetics and John P. Hussman Inst. for Human Genomics
  31. Children's Hospital of Eastern Ontario, Ottawa, ON (Canada). Dept. of Genetics
  32. Broad Inst. of Harvard and MIT, Cambridge, MA (United States); Harvard Univ., Boston, MA (United States). Harvard Medical School; Partners Personalized Medicine, Boston, MA (United States). Lab. for Molecular Medicine; Brigham and Women's Hospital, Boston, MA (United States). Dept. of Pathology
Publication Date:
Grant/Contract Number:
AC02-05CH11231; U41HG006834; U54HG007990; HG007530; HG007690; HD077671; PPRN-1306-04899; 1U54HG006542; N01CO42400-80; WT098051; 305444; U54 HG003273; EP1-120608; EP2-120609
Type:
Accepted Manuscript
Journal Name:
Human Mutation
Additional Journal Information:
Journal Volume: 36; Journal Issue: 10; Journal ID: ISSN 1059-7794
Publisher:
Wiley
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Institutes of Health (NIH); Canadian Institutes of Health Research; Wellcome Trust; European Union (EU)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; matchmaking; rare disease; genomic API; gene discovery; Matchmaker Exchange; GA4GH, IRDiRC
OSTI Identifier:
1377611

Philippakis, Anthony A., Azzariti, Danielle R., Beltran, Sergi, Brookes, Anthony J., Brownstein, Catherine A., Brudno, Michael, Brunner, Han G., Buske, Orion J., Carey, Knox, Doll, Cassie, Dumitriu, Sergiu, Dyke, Stephanie O. M., den Dunnen, Johan T., Firth, Helen V., Gibbs, Richard A., Girdea, Marta, Gonzalez, Michael, Haendel, Melissa A., Hamosh, Ada, Holm, Ingrid A., Huang, Lijia, Hurles, Matthew E., Hutton, Ben, Krier, Joel B., Misyura, Andriy, Mungall, Christopher J., Paschall, Justin, Paten, Benedict, Robinson, Peter N., Schiettecatte, François, Sobreira, Nara L., Swaminathan, Ganesh J., Taschner, Peter E., Terry, Sharon F., Washington, Nicole L., Züchner, Stephan, Boycott, Kym M., and Rehm, Heidi L.. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. United States: N. p., Web. doi:10.1002/humu.22858.
Philippakis, Anthony A., Azzariti, Danielle R., Beltran, Sergi, Brookes, Anthony J., Brownstein, Catherine A., Brudno, Michael, Brunner, Han G., Buske, Orion J., Carey, Knox, Doll, Cassie, Dumitriu, Sergiu, Dyke, Stephanie O. M., den Dunnen, Johan T., Firth, Helen V., Gibbs, Richard A., Girdea, Marta, Gonzalez, Michael, Haendel, Melissa A., Hamosh, Ada, Holm, Ingrid A., Huang, Lijia, Hurles, Matthew E., Hutton, Ben, Krier, Joel B., Misyura, Andriy, Mungall, Christopher J., Paschall, Justin, Paten, Benedict, Robinson, Peter N., Schiettecatte, François, Sobreira, Nara L., Swaminathan, Ganesh J., Taschner, Peter E., Terry, Sharon F., Washington, Nicole L., Züchner, Stephan, Boycott, Kym M., & Rehm, Heidi L.. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. United States. doi:10.1002/humu.22858.
Philippakis, Anthony A., Azzariti, Danielle R., Beltran, Sergi, Brookes, Anthony J., Brownstein, Catherine A., Brudno, Michael, Brunner, Han G., Buske, Orion J., Carey, Knox, Doll, Cassie, Dumitriu, Sergiu, Dyke, Stephanie O. M., den Dunnen, Johan T., Firth, Helen V., Gibbs, Richard A., Girdea, Marta, Gonzalez, Michael, Haendel, Melissa A., Hamosh, Ada, Holm, Ingrid A., Huang, Lijia, Hurles, Matthew E., Hutton, Ben, Krier, Joel B., Misyura, Andriy, Mungall, Christopher J., Paschall, Justin, Paten, Benedict, Robinson, Peter N., Schiettecatte, François, Sobreira, Nara L., Swaminathan, Ganesh J., Taschner, Peter E., Terry, Sharon F., Washington, Nicole L., Züchner, Stephan, Boycott, Kym M., and Rehm, Heidi L.. 2015. "The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery". United States. doi:10.1002/humu.22858. https://www.osti.gov/servlets/purl/1377611.
@article{osti_1377611,
title = {The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery},
author = {Philippakis, Anthony A. and Azzariti, Danielle R. and Beltran, Sergi and Brookes, Anthony J. and Brownstein, Catherine A. and Brudno, Michael and Brunner, Han G. and Buske, Orion J. and Carey, Knox and Doll, Cassie and Dumitriu, Sergiu and Dyke, Stephanie O. M. and den Dunnen, Johan T. and Firth, Helen V. and Gibbs, Richard A. and Girdea, Marta and Gonzalez, Michael and Haendel, Melissa A. and Hamosh, Ada and Holm, Ingrid A. and Huang, Lijia and Hurles, Matthew E. and Hutton, Ben and Krier, Joel B. and Misyura, Andriy and Mungall, Christopher J. and Paschall, Justin and Paten, Benedict and Robinson, Peter N. and Schiettecatte, François and Sobreira, Nara L. and Swaminathan, Ganesh J. and Taschner, Peter E. and Terry, Sharon F. and Washington, Nicole L. and Züchner, Stephan and Boycott, Kym M. and Rehm, Heidi L.},
abstractNote = {There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. In conclusion, three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.},
doi = {10.1002/humu.22858},
journal = {Human Mutation},
number = 10,
volume = 36,
place = {United States},
year = {2015},
month = {9}
}