matchbox: An open-source tool for patient matching via the Matchmaker Exchange

Human Mutation

Volumn 39, Issue 12, 2018, Pages 1827-1834

  Arachchi, Harindra ^a   Wojcik, Monica H ^a,b   Weisburd, Benjamin ^a   Jacobsen, Julius O B ^c   Valkanas, Elise ^a   Baxter, Samantha ^a   Byrne, Alicia B ^a,d,e   O'Donnell Luria, Anne H ^a,b   Haendel, Melissa ^f,g   Smedley, Damian ^c   MacArthur, Daniel G ^a,h   Philippakis, Anthony A ^a   Rehm, Heidi L ^a,h  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^d Centre for Cancer Biology and Department of Haematology   (Australia)

^e UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

^f OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^g OREGON STATE UNIVERSITY   (United States)

^h MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

matchbox; Matchmaker Exchange; novel gene; open source; rare disease

Indexed keywords

ARTICLE; GENETIC ALGORITHM; HUMAN; MATCHMAKER EXCHANGE; PHENOTYPE; PRIORITY JOURNAL; RARE DISEASE; ACCESS TO INFORMATION; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENETICS; INFORMATION DISSEMINATION; INFORMATION RETRIEVAL; PATIENT SELECTION; PROCEDURES; SOFTWARE; WEB BROWSER;

ACCESS TO INFORMATION; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INFORMATION DISSEMINATION; INFORMATION STORAGE AND RETRIEVAL; PATIENT SELECTION; PHENOTYPE; RARE DISEASES; SOFTWARE; WEB BROWSER;

EID: 85054362005     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.23655     Document Type: Article

References (20)

1. Bone, W. P., Washington, N. L., Buske, O. J., Adams, D. R., Davis, J., Draper, D., … Smedley, D. (2016). Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genetics in Medicine, 18(6), 608–617. https://doi.org/10.1038/gim.2015.137
2. 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, 36(10), 922–927. https://doi.org/10.1002/humu.22850
3. Firth, H. V., Richards, S. M., Bevan, A. P., Clayton, S., Corpas, M., Rajan, D., … Carter, N. P. (2009). DECIPHER: Database of chromosomal imbalance and phenotype in humans using ensembl resources. American Journal of Human Genetics, 84(4), 524–533. https://doi.org/10.1016/j.ajhg.2009.03.010
4. Girdea, M., Dumitriu, S., Fiume, M., Bowdin, S., Boycott, K. M., Chenier, S., … Brudno, M. (2013). PhenoTips: Patient phenotyping software for clinical and research use. Human Mutation, 34(8), 1057–1065. https://doi.org/10.1002/humu.22347
5. Guissart, C., Latypova, X., Rollier, P., Khan, T. N., Stamberger, H., McWalter, K., … Küry, S. (2018). Dual molecular effects of dominant RORA mutations cause two variants of syndromic intellectual disability with either autism or cerebellar ataxia. The American Journal of Human Genetics, 102(5), 744–759. 10.1016/j.ajhg.2018.02.021. Retrieved from https://www.cell.com/ajhg/abstract/S0002-9297(18)30089-2
6. Hamdan, F. F., Myers, C. T., Cossette, P., Lemay, P., Spiegelman, D., Laporte, A. D., … Michaud, J. L. (2017). High rate of recurrent de novo mutations in developmental and epileptic encephalopathies. American Journal of Human Genetics, 101(5), 664–685. S0002-9297(17)30377-4 [pii]
7. Kohler, S., Vasilevsky, N. A., Engelstad, M., Foster, E., McMurry, J., Ayme, S., … Robinson, P. N. (2017). The human phenotype ontology in 2017. Nucleic Acids Research, 45(D1), D876. https://doi.org/10.1093/nar/gkw1039
8. Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T. … Exome Aggregation Consortium.(2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285–291. https://doi.org/10.1038/nature19057
9. Mungall, C. J., McMurry, J. A., Kohler, S., Balhoff, J. P., Borromeo, C., Brush, M., … Haendel, M. A. (2017). The monarch initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research, 45(D1), D722. https://doi.org/10.1093/nar/gkw1128
10. 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, 36(10), 915–921. https://doi.org/10.1002/humu.22858
11. Robinson, P. N., Kohler, S., Oellrich, A., Sanger Mouse Genetics Project, Wang, K., Mungall, C. J., … Smedley, D. (2014) Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Research, 24(2), 340–348. https://doi.org/10.1101/gr.160325.113
12. Smedley, D., Jacobsen, J. O., Jager, M., Kohler, S., Holtgrewe, M., Schubach, M., … Robinson, P. N. (2015). Next-generation diagnostics and disease-gene discovery with the exomiser. Nature Protocols, 10(12), 2004–2015. https://doi.org/10.1038/nprot.2015.124
13. Smedley, D., Kohler, S., Czeschik, J. C., Amberger, J., Bocchini, C., Hamosh, A., … Robinson, P. N. (2014). Walking the interactome for candidate prioritization in exome sequencing studies of mendelian diseases. Bioinformatics, 30(22), 3215–3222. https://doi.org/10.1093/bioinformatics/btu508
14. Smedley, D., Oellrich, A., Kohler, S., Ruef, B., Sanger Mouse Genetics Project, Westerfield, M., … Mungall, C. (2013). PhenoDigm: Analyzing curated annotations to associate animal models with human diseases. Database, 2013, bat025. https://doi.org/10.1093/database/bat025
15. Smedley, D., Schubach, M., Jacobsen, J. O. B., Kohler, S., Zemojtel, T., Spielmann, M., … Robinson, P. N. (2016). A whole-genome analysis framework for effective identification of pathogenic regulatory variants in mendelian disease. American Journal of Human Genetics, 99(3), 595–606. S0002-9297(16)30278-6 [pii]
16. Sobreira, N. L. M., Arachchi, H., Buske, O. J., Chong, J. X., Hutton, B., Foreman, J. … Matchmaker Exchange Consortium.(2017) Matchmaker exchange. Current Protocols in Human Genetics, 95, 9.31.15. https://doi.org/10.1002/cphg.50
17. Sobreira, N., Schiettecatte, F., Boehm, C., Valle, D., & Hamosh, A. (2015). New tools for mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Human Mutation, 36(4), 425–431. https://doi.org/10.1002/humu.22769
18. Sobreira, N., Schiettecatte, F., Valle, D., & Hamosh, A. (2015). GeneMatcher: A matching tool for connecting investigators with an interest in the same gene. Human Mutation, 36(10), 928–930. https://doi.org/10.1002/humu.22844
19. Yates, T. M., Vasudevan, P. C., Chandler, K. E., Donnelly, D. E., Stark, Z., Sadedin, S., … Balasubramanian, M. (2017). De novo mutations in HNRNPU result in a neurodevelopmental syndrome. American Journal of Medical Genetics. Part A, 173(11), 3003–3012. https://doi.org/10.1002/ajmg.a.38492
20. Zemojtel, T., Kohler, S., Mackenroth, L., Jager, M., Hecht, J., Krawitz, P., … Robinson, P. N. (2014). Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Science Translational Medicine, 6(252), 252ra123. https://doi.org/10.1126/scitranslmed.3009262