DIDA: A curated and annotated digenic diseases database

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D900-D907

  Gazzo, Andrea M ^a,b,c   Daneels, Dorien ^a,c   Cilia, Elisa ^a,b   Bonduelle, Maryse ^c   Abramowicz, Marc ^a,d   Van Dooren, Sonia ^a,c   Smits, Guillaume ^a,d,e   Lenaerts, Tom ^a,b,f  

^a Interuniversity Institute of Bioinformatics in Brussels (IB)2   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c UNIVERSITY HOSPITAL BRUSSELS   (Belgium)

^d ERASME HOSPITAL   (Belgium)

^e HOP UNIV DES ENFANTS REINE FABIOLA   (Belgium)

^f VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; DIGENIC DISEASE; DIGENIC DISEASES DATABASE; FACTUAL DATABASE; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; HUMAN GENOME PROJECT; INHERITANCE; INTERNET; MOLECULAR GENETICS; OLIGOGENIC INHERITANCE; PRIORITY JOURNAL; PUBLICATION; DISEASES; GENE; GENETIC DATABASE; GENETIC VARIATION; GENETICS; MULTIFACTORIAL INHERITANCE;

DATABASES, GENETIC; DISEASE; GENES; GENETIC VARIATION; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MULTIFACTORIAL INHERITANCE;

EID: 84968730568     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1068     Document Type: Article

References (46)

1. Gilissen, C, Hoischen, A., Brunner, HG. and Veltman, J. A. (2012) Disease gene identification strategies for exome sequencing. Eur. J. Hum. Genet., 20, 490-497.
2. Lyon, G. J. and Wang, K. (2012) Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med, 4, 58.
3. MacArthur, D., Manolio, T., Dimmock, D., Rehm, H., Shendure, J., Abecasis, G., Adams, D., Altman, R., Antonarakis, S., Ashley, E. et al. (2014) Guidelines for investigating causality of sequence variants in human disease. Nature, 508, 469-476.
4. Chong, J. X., Buckingham, K. J., Jhangiani, S. N., Boehm, C, Sobreira, N., Smith, J. D., Harrell, T. M., McMillin, M. J., Wiszniewski, W., Gambin, T. et al. (2015) The genetic basis of Mendelian phenotypes: discoveries, challenges, and opportunities. Am. J. Hum. Genet., 97, 199-215.
5. ®), an online catalog of human genes and genetic disorders. Nucleic Acids Res., 43, D789-D798.
6. NCBI, Resource Coordinators. (2015) Database resources of the national center for biotechnology information. Nucleic Acids Res., 43, D6-D17.
7. Fokkema, I. F., Taschner, P. E., Schaafsma, GC, Celli, J., Laros, J. F. and Den Dunnen, J. T. (2011) LOVD v. 2.0: the next generation in gene variant databases. Hum. Mutat., 32, 557-563.
8. Landrum, M. J., Lee, J. M., Riley, GR., Jang, W., Rubinstein, W. S., Church, D. M. and Maglott, D. R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980-D985.
9. Bragin, E., Chatzimichali, E. A., Wright, CF., Hurles, M. E., Firth, H. V, Bevan, A. P. and Swaminathan, GJ. (2014) DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res., 42, D993-D1000.
10. Stenson, P, Mort, M., Ball, E., Shaw, K., Phillips, A. and Cooper, D (2014) The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet., 133, 1-9.
11. Johnston, J. J. and Biesecker, L. G (2013) Databases of genomic variation and phenotypes: existing resources and future needs. Hum. Mol. Genet., 22, R27-R31.
12. Vogel, F. and Motulsky, A. G (2010) Vogel and Motulsky's Human Genetics: Problems and Approaches, Springer, NY.
13. Katsanis, N. (2004) The oligogenic properties of Bardet-Biedl syndrome. Hum. Mol. Genet., 13, R65-R71.
14. Millat, G, Chevalier, P, Restier-Miron, L., Da Costa, A., Bouvagnet, P, Kugener, B., Fayol, L., Gonzalez Armengod, C., Oddou, B., Chanavat, V. et al. (2006) Spectrum of pathogenic mutations and associated polymorphisms in a cohort of 44 unrelated patients with long QT syndrome. Clin. Genet., 70, 214-227.
15. Pitteloud, N., Quinton, R., Pearce, S., Raivio, T, Acierno, J., Dwyer, A., Plummer, L., Hughes, V., Seminara, S., Cheng, Y.-Z. et al. (2007) Digenic mutations account for variable phenotypes in idiopathic hypogonadotropic hypogonadism. J. Clin. Invest., 117, 457-463.
16. Dode, C and Hardelin, J.-P (2009) Kallmann syndrome. Eur. J. Hum. Genet., 17, 139-146.
17. Tam, PK. and Garcia-Barcelo, M. (2009) Genetic basis of Hirschsprung's disease. Pediatr. Surg. Int., 25, 543-558.
18. Quaynor, S. D., Kim, H.-G., Cappello, E. M., Williams, T, Chorich, L. P, Bick, D. P, Sherins, R. J. and Layman, L. C (2011) The prevalence of digenic mutations in patients with normosmic hypogonadotropic hypogonadism and Kallmann syndrome. Fertil. Steril, 96, 1424-1430.
19. Schäffer, A. A. (2013) Digenic inheritance in medical genetics. J. Med. Genet., 50, 641-652.
20. Kagawa, T., Oka, A., Kobayashi, Y., Hiasa, Y., Kitamura, T., Sakugawa, H., Adachi, Y., Anzai, K., Tsuruya, K., Arase, Y. et al. (2015) Recessive inheritance of population-specific intronic LINE-1 insertion causes a rotor syndrome phenotype. Hum. Mutat., 36, 327-332.
21. Mlynarski, E. E., Sheridan, M. B., Xie, M., Guo, T., Racedo, S. E., McDonald-McGinn, D. M., Gai, X., Chow, E. W., Vorstman, J., Swillen, A. et al. (2015) Copy-number variation of the glucose transporter gene SLC2A3 and congenital heart defects in the 22q11.2 deletion syndrome. Am. J. Hum. Genet., 96, 753-764.
22. Lupski, J. R. (2012) Digenic inheritance and Mendelian disease. Nat. Genet., 44, 1291-1292.
23. Riazuddin, S. A., Zaghloul, N. A., Al-Saif, A., Davey, L., Diplas, B. H., Meadows, D. N., Eghrari, A. O., Minear, M. A., Li, Y.-J., Klintworth, G. K. et al. (2010) Missense mutations in TCF8 cause late-onset Fuchs corneal dystrophy and interact with FCD4 on chromosome 9p. Am. J. Hum. Genet., 86, 45-53.
24. Den Dunnen, J. T. and Antonarakis, S. E. (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat., 15, 7-12.
25. Köhler, S., Schulz, M. H., Krawitz, P., Bauer, S., Dölken, S., Ott, C. E., Mundlos, C., Horn, D., Mundlos, S. and Robinson, P. N. (2009) Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am. J. Hum. Genet., 85, 457-464.
26. Köhler, S., Doelken, S. C., Mungall, C. J., Bauer, S., Firth, H. V., Bailleul-Forestier, I., Black, G. C., Brown, D. L., Brudno, M., Campbell, J. et al. (2014) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res., 42, D966-D974.
27. World Health Organization. (1992) The ICD-10 Classification of Mental and Behavioural Disorders: Clinical Descriptions and Diagnostic Guidelines, World Health Organization, Geneva.
28. Orphanet: an online database of rare diseases and orphan drugs. Copyright, INSERM 1997.
29. Gray, K. A., Yates, B., Seal, R. L., Wright, M. W. and Bruford, E. A. (2015) Genenames.org: the HGNC resources in 2015. Nucleic Acids Res., 43, D1079-D1085.
30. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
31. Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R. et al. (2014) The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
32. Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J. et al. (2014) Pfam: the protein families database. Nucleic Acids Res., 42, D222-D230.
33. Mitchell, A., Chang, H. Y., Daugherty, L., Fraser, M., Hunter, S., Lopez, R., McAnulla, C., McMenamin, C., Nuka, G., Pesseat, S. et al. (2015) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res., 43, D213-D221.
34. UniProtConsortium. (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.
35. Orchard, S., Ammari, M., Aranda, B., Breuza, L., Briganti, L., Broackes-Carter, F., Campbell, N. H., Chavali, G., Chen, C., Del Toro, N. et al. (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.
36. Chatr-Aryamontri, A., Breitkreutz, B. J., Heinicke, S., Boucher, L., Winter, A., Stark, C., Nixon, J., Ramage, L., Kolas, N., O'Donnell, L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
37. Kamburov, A., Stelzl, U., Lehrach, H. and Herwig, R. (2013) The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res., 41, D793-D800.
38. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U. S. A., 101, 6062-6067.
39. Huang, N., Lee, I., Marcotte, E. M. and Hurles, M. E. (2010) Characterising and predicting haploinsufficiency in the human genome. PLoS Genet., 6, e1001154.
40. MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J. K., Montgomery, S. B. et al. (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335, 823-828.
41. Georgi, B., Voight, B. F. and Bućan, M. (2013) From mouse to human: evolutionary genomics analysis of human orthologs of essential genes. PLoS Genet., 9, e1003484.
42. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S. and Sunyaev, S. R. (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248-249.
43. Kumar, P., Henikoff, S. and Ng, P. C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073-1081.
44. 1000 Genomes Project Consortium. (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
45. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA.
46. Liu, X., Jian, X. and Boerwinkle, E. (2013) dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat., 34, E2393-E2402.