The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

被引：352

作者：

Philippakis, Anthony A. ^{[1
,2
,3
,4
]}

Azzariti, Danielle R. ^{[5
]}

Beltran, Sergi ^{[6
]}

Brookes, Anthony J. ^{[7
]}

Brownstein, Catherine A. ^{[4
,8
,9
]}

Brudno, Michael ^{[10
,11
,12
]}

Brunner, Han G. ^{[13
,14
]}

Buske, Orion J. ^{[10
,11
,12
]}

Carey, Knox ^{[15
]}

Doll, Cassie ^{[16
]}

Dumitriu, Sergiu ^{[12
]}

Dyke, Stephanie O. M. ^{[17
]}

den Dunnen, Johan T. ^{[18
]}

Firth, Helen V. ^{[19
]}

Gibbs, Richard A. ^{[20
]}

Girdea, Marta ^{[10
,12
]}

Gonzalez, Michael ^{[21
]}

Haendel, Melissa A. ^{[22
]}

Hamosh, Ada ^{[23
]}

Holm, Ingrid A. ^{[4
,8
,9
]}

Huang, Lijia ^{[24
]}

Hurles, Matthew E. ^{[25
]}

Hutton, Ben ^{[25
]}

Krier, Joel B. ^{[4
,26
]}

Misyura, Andriy ^{[12
]}

Mungall, Christopher J. ^{[27
]}

Paschall, Justin ^{[28
]}

Paten, Benedict ^{[29
]}

Robinson, Peter N. ^{[30
,31
,32
,33
]}

Schiettecatte, Francois ^{[34
]}

Sobreira, Nara L. ^{[23
]}

Swaminathan, Ganesh J. ^{[25
,35
]}

Taschner, Peter E. ^{[18
]}

Terry, Sharon F. ^{[36
]}

Washington, Nicole L. ^{[3
]}

Zuechner, Stephan ^{[37
,38
]}

Boycott, Kym M. ^{[39
]}

Rehm, Heidi L. ^{[1
,2
,4
,5
,40
]}

机构：

[1] Harvard Univ, Broad Inst, Cambridge, MA 02138 USA

[2] MIT, Cambridge, MA 02139 USA

[3] Brigham & Womens Hosp, Dept Cardiol, Boston, MA 02115 USA

[4] Harvard Univ, Sch Med, Boston, MA USA

[5] Partners Lab Mol Med, Mol Med Lab, Cambridge, MA 02139 USA

[6] Ctr Nacl Anal Genom, Barcelona, Spain

[7] Univ Leicester, Dept Genet, Leicester LE1 7RH, Leics, England

[8] Boston Childrens Hosp, Div Genet & Genom, Boston, MA USA

[9] Boston Childrens Hosp, Manton Ctr Orphan Dis Res, Boston, MA USA

[10] Univ Toronto, Dept Comp Sci, Toronto, ON, Canada

[11] Hosp Sick Children, Genet & Genome Biol Program, Toronto, ON M5G 1X8, Canada

[12] Hosp Sick Children, Ctr Computat Med, Toronto, ON M5G 1X8, Canada

[13] Radboud Univ Nijmegen, Med Ctr, Dept Human Genet, NL-6500 HB Nijmegen, Netherlands

[14] Maastricht Univ, Med Ctr, Dept Clin Genet, NL-6202 AZ Maastricht, Netherlands

[15] Gene Cloud, Orange, CA USA

[16] Google Inc, Mountain View, CA USA

[17] McGill Univ, Fac Med, Ctr Genom & Policy, Quebec City, PQ, Canada

[18] Leiden Univ, Med Ctr, Human & Clin Genet, Leiden, Netherlands

[19] Cambridge Univ Hosp NHS Fdn Trust, East Anglian Med Genet Serv, Cambridge CB2 0QQ, England

[20] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[21] Genesis Project Inc, Miami, FL USA

[22] Oregon Hlth & Sci Univ, Dept Med Informat & Clin Epidemiol, Portland, OR 97201 USA

[23] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD USA

[24] Eastern Ontario Res Inst, Childrens Hosp, Ottawa, ON, Canada

[25] Wellcome Trust Res Labs, Wellcome Trust Sanger Inst, Hinxton CB10 1SA, England

[26] Brigham & Womens Hosp, Dept Med, Div Genet, Boston, MA 02115 USA

[27] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[28] Wellcome Trust Res Labs, European Bioinformat Inst, European Mol Biol Lab, Hinxton CB10 1SD, Cambs, England

[29] UC Santa Cruz Genom Inst, Santa Cruz, CA USA

[30] Charite, Inst Med Genet & Human Genet, D-13353 Berlin, Germany

[31] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

[32] Free Univ Berlin, Dept Math & Comp Sci, Inst Bioinformat, D-14195 Berlin, Germany

[33] Berlin Brandenburg Ctr Regenerat Therapies, D-13353 Berlin, Germany

[34] FS Consulting LLC, Salem, MA 01970 USA

[35] Univ Appl Sci Leiden, Generade Ctr Expertise Genom, Leiden, Netherlands

[36] Genet Alliance, Washington, DC USA

[37] Univ Miami, Miller Sch Med, Dept Human Genet, Dr John T Macdonald Fdn, Miami, FL 33136 USA

[38] Univ Miami, Miller Sch Med, John P Hussman Inst Human Genom, Miami, FL 33136 USA

[39] Childrens Hosp Eastern Ontario, Dept Genet, Ottawa, ON K1H 8L1, Canada

[40] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

来源：

HUMAN MUTATION | 2015年 / 36卷 / 10期

基金：

加拿大自然科学与工程研究理事会; 加拿大健康研究院; 英国惠康基金;

关键词：

matchmaking; rare disease; genomic API; gene discovery; Matchmaker Exchange; GA4GH; IRDiRC; INTELLECTUAL DISABILITY; IDENTIFICATION; COLLABORATION; GENEMATCHER; VARIANTS; SOFTWARE; GEM.APP; TOOL;

D O I：

10.1002/humu.22858

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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. 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. (C) 2015 Wiley Periodicals, Inc.

引用

页码：915 / 921

页数：7

共 27 条

[1] Mitigating False-Positive Associations in Rare Disease Gene Discovery [J].

Akle, Sebastian ;

Chun, Sung ;

Jordan, Daniel M. ;

Cassa, Christopher A. .

HUMAN MUTATION, 2015, 36 (10) :998-1003

[2] Genetic Mapping in Human Disease [J].

Altshuler, David ;

Daly, Mark J. ;

Lander, Eric S. .

SCIENCE, 2008, 322 (5903) :881-888

[3]

[Anonymous], NCBI HDB

[4] GeneMatcher Aids in the Identification of a New Malformation Syndrome with Intellectual Disability, Unique Facial Dysmorphisms, and Skeletal and Connective Tissue Abnormalities Caused by De Novo Variants in HNRNPK [J].

Au, P. Y. Billie ;

You, Jing ;

Caluseriu, Oana ;

Schwartzentruber, Jeremy ;

Majewski, Jacek ;

Bernier, Francois P. ;

Ferguson, Marcia ;

Valle, David ;

Parboosingh, Jillian S. ;

Sobreira, Nara ;

Innes, A. Micheil ;

Kline, Antonie D. .

HUMAN MUTATION, 2015, 36 (10) :1009-1014

[5] Data Sharing in the Undiagnosed Diseases Network [J].

Brownstein, Catherine A. ;

Holm, Ingrid A. ;

Ramoni, Rachel ;

Goldstein, David B. .

HUMAN MUTATION, 2015, 36 (10) :985-988

[6] PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases [J].

Buske, Orion J. ;

Girdea, Marta ;

Dumitriu, Sergiu ;

Gallinger, Bailey ;

Hartley, Taila ;

Trang, Heather ;

Misyura, Andriy ;

Friedman, Tal ;

Beaulieu, Chandree ;

Bone, William P. ;

Links, Amanda E. ;

Washington, Nicole L. ;

Haendel, Melissa A. ;

Robinson, Peter N. ;

Boerkoel, Cornelius F. ;

Adams, David ;

Gahl, William A. ;

Boycott, Kym M. ;

Brudno, Michael .

HUMAN MUTATION, 2015, 36 (10) :931-940

[7] The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles [J].

Buske, Orion J. ;

Schiettecatte, Francois ;

Hutton, Benjamin ;

Dumitriu, Sergiu ;

Misyura, Andriy ;

Huang, Lijia ;

Hartley, Taila ;

Girdea, Marta ;

Sobreira, Nara ;

Mungall, Chris ;

Brudno, Michael .

HUMAN MUTATION, 2015, 36 (10) :922-927

[8] Facilitating Collaboration in Rare Genetic Disorders Through Effective Matchmaking in DECIPHER [J].

Chatzimichali, Eleni A. ;

Brent, Simon ;

Hutton, Benjamin ;

Perrett, Daniel ;

Wright, Caroline F. ;

Bevan, Andrew P. ;

Hurles, Matthew E. ;

Firth, Helen V. ;

Swaminathan, Ganesh J. .

HUMAN MUTATION, 2015, 36 (10) :941-949

[9] PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations [J].

Denny, Joshua C. ;

Ritchie, Marylyn D. ;

Basford, Melissa A. ;

Pulley, Jill M. ;

Bastarache, Lisa ;

Brown-Gentry, Kristin ;

Wang, Deede ;

Masys, Dan R. ;

Roden, Dan M. ;

Crawford, Dana C. .

BIOINFORMATICS, 2010, 26 (09) :1205-1210

[10] Innovative Genomic Collaboration Using the GENESIS (GEM.app) Platform [J].

Gonzalez, Michael ;

Falk, Marni J. ;

Gai, Xiaowu ;

Postrel, Richard ;

Schuele, Rebecca ;

Zuchner, Stephan .

HUMAN MUTATION, 2015, 36 (10) :950-956

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