DECIPHER: Database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Bragin, Eugene ^a   Chatzimichali, Eleni A ^a   Wright, Caroline F ^a   Hurles, Matthew E ^a   Firth, Helen V ^a,b   Bevan, A Paul ^a   Swaminathan, G Jawahar ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLINICAL DATA REPOSITORY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COPY NUMBER VARIATION; DECIPHER DATABASE; DEVELOPMENTAL DISORDER; GENETIC DATABASE; GENETIC VARIABILITY; GENOTYPE; INFORMATION DISSEMINATION; INFORMATION RETRIEVAL; INFORMATION STORAGE; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; WEB BROWSER; GENETICS; HUMAN; HUMAN GENOME; INTERNET; NUCLEIC ACID DATABASE; RARE DISEASE; ACCESS TO INFORMATION; BIOINFORMATICS; GENETIC DISORDER; INFORMATION PROCESSING; NONHUMAN; ONLINE SYSTEM; PHENOTYPIC VARIATION;

DATABASES, NUCLEIC ACID; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; GENOTYPE; HUMANS; INTERNET; PHENOTYPE; RARE DISEASES;

EID: 84891779149     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt937     Document Type: Article

References (31)

1. Swaminathan, G.J., Bragin, E., Chatzimichali, E.A., Corpas, M., Bevan, A.P., Wright, C.F., Carter, N.P., Hurles, M.E. and Firth, H.V. (2012) DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet., 21, R37-R44.
2. Roizen, N.J. and Patterson, D. (2003) Down's syndrome. Lancet, 361, 1281-1289.
3. Shaw-Smith, C., Redon, R., Rickman, L., Rio, M., Willatt, L., Fiegler, H., Firth, H., Sanlaville, D., Winter, R., Colleaux, L. et al. (2004) Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J. Med. Genet., 41, 241-248.
4. Stankiewicz, P. and Beaudet, A.L. (2007) Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr. Opin. Genet. Dev., 17, 182-192.
5. Ng, S.B., Nickerson, D.A., Bamshad, M.J. and Shendure, J. (2010) Massively parallel sequencing and rare disease. Hum. Mol. Genet., 19, R119-R124.
6. Firth, H.V. and Wright, C.F. (2011) The Deciphering Developmental Disorders (DDD) study. Dev. Med. Child Neurol., 53, 702-703.
7. Firth, H.V., Richards, S.M., Bevan, A.P., Clayton, S., Corpas, M., Rajan, D., Van Vooren, S., Moreau, Y., Pettett, R.M. and Carter, N.P. (2009) DECIPHER: database of chromosomal imbalance and phenotype in humans using Ensembl eesources. Am. J. Hum. Genet., 84, 524-533.
8. Barge-Schaapveld, D.Q., Maas, S.M., Polstra, A., Knegt, L.C. and Hennekam, R.C. (2011) The atypical 16p11.2 deletion: a not so atypical microdeletion syndrome? Am. J. Med. Genet. A, 155A, 1066-1072.
9. Engels, H., Wohlleber, E., Zink, A., Hoyer, J., Ludwig, K.U., Brockschmidt, F.F., Wieczorek, D., Moog, U., Hellmann-Mersch, B., Weber, R.G. et al. (2009) A novel microdeletion syndrome involving 5q14.3-q15: clinical and molecular cytogenetic characterization of three patients. Eur. J. Hum. Genet., 17, 1592-1599.
10. Malan, V., Raoul, O., Firth, H.V., Royer, G., Turleau, C., Bernheim, A., Willatt, L., Munnich, A., Vekemans, M., Lyonnet, S. et al. (2009) 19q13.11 deletion syndrome: a novel clinically recognisable genetic condition identified by array comparative genomic hybridisation. J. Med. Genet., 46, 635-640.
11. Molin, A.M., Andrieux, J., Koolen, D.A., Malan, V., Carella, M., Colleaux, L., Cormier-Daire, V., David, A., de Leeuw, N., Delobel, B. et al. (2012) A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic facial features. J. Med. Genet., 49, 104-109.
12. Shaw-Smith, C., Pittman, A.M., Willatt, L., Martin, H., Rickman, L., Gribble, S., Curley, R., Cumming, S., Dunn, C., Kalaitzopoulos, D. et al. (2006) Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat. Genet., 38, 1032-1037.
13. Thevenon, J., Callier, P., Andrieux, J., Delobel, B., David, A., Sukno, S., Minot, D., Mosca Anne, L., Marle, N., Sanlaville, D. et al. (2012) 12p13.33 microdeletion including ELKS/ERC1, a new locus associated with childhood apraxia of speech. Eur. J. Hum. Genet., 21, 82-88.
14. Zahir, F., Firth, H.V., Baross, A., Delaney, A.D., Eydoux, P., Gibson, W.T., Langlois, S., Martin, H., Willatt, L., Marra, M.A. et al. (2007) Novel deletions of 14q11.2 associated with developmental delay, cognitive impairment and similar minor anomalies in three children. J. Med. Genet., 44, 556-561.
15. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
16. Kuhn, R.M., Haussler, D. and Kent, W.J. (2012) The UCSC genome browser and associated tools. Brief. Bioinform., 14, 144-161.
17. Riggs, E.R., Jackson, L., Miller, D.T. and Van Vooren, S. (2012) Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience. Hum. Mutat., 33, 787-796.
18. Huang, N., Lee, I., Marcotte, E.M. and Hurles, M.E. (2010) Characterising and predicting haploinsufficiency in the human genome. PLoS Genet., 6, e1001154.
19. Robinson, P.N. and Mundlos, S. (2010) The human phenotype ontology. Clin. Genet., 77, 525-534.
20. Klopocki, E., Schulze, H., Strauss, G., Ott, C.E., Hall, J., Trotier, F., Fleischhauer, S., Greenhalgh, L., Newbury-Ecob, R.A., Neumann, L.M. et al. (2007) Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. Am. J. Hum. Genet., 80, 232-240.
21. 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.
22. 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.
23. McLaren, W., Pritchard, B., Rios, D., Chen, Y., Flicek, P. and Cunningham, F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics, 26, 2069-2070.
24. Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R. and Ashburner, M. (2005) The sequence ontology: a tool for the unification of genome annotations. Genome Biol., 6, R44.
25. 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.
26. Fokkema, I.F., Taschner, P.E., Schaafsma, G.C., 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.
27. Stenson, P.D., Ball, E.V., Howells, K., Phillips, A.D., Mort, M. and Cooper, D.N. (2009) The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum. Genomics, 4, 69-72.
28. Celli, J., Dalgleish, R., Vihinen, M., Taschner, P.E. and den Dunnen, J.T. (2012) Curating gene variant databases (LSDBs): toward a universal standard. Hum. Mutat., 33, 291-297.
29. Baraitser, M. and Winter, R. (1991) Update on the London Dysmorphology database. Cleft Palate. Craniofac. J., 28, 318.
30. Boulding, H. and Webber, C. (2012) Large-scale objective association of mouse phenotypes with human symptoms through structural variation identified in patients with developmental disorders. Hum. Mutat., 33, 874-883.
31. Johansson, A.C. and Feuk, L. (2011) Characterization of copy number-stable regions in the human genome. Hum. Mutat., 32, 947-955.