Genetic variations and diseases in UniProtKB/Swiss-Prot: The ins and outs of expert manual curation

Human Mutation

Volumn 35, Issue 8, 2014, Pages 927-935

  Famiglietti, Maria Livia ^a   Estreicher, Anne ^a   Gos, Arnaud ^a   Bolleman, Jerven ^a   Géhant, Sébastien ^a   Breuza, Lionel ^a   Bridge, Alan ^a   Poux, Sylvain ^a   Redaschi, Nicole ^a   Bougueleret, Lydie ^a   Xenarios, Ioannis ^a,b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Controlled vocabulary; Database; Disease; Functional annotation; Genetic variants; Manual curation; UniProtKB Swiss Prot

Indexed keywords

PROTEOME;

AMINO ACID SEQUENCE; COMPUTER PROGRAM; GENETIC ASSOCIATION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; INTERNET; KNOWLEDGE BASE; MEDICAL GENETICS; MOLECULAR GENETICS; NOMENCLATURE; PROTEIN DATABASE; STATISTICS AND NUMERICAL DATA; UTILIZATION;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; GENETIC ASSOCIATION STUDIES; GENETIC VARIATION; GENETICS, MEDICAL; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; KNOWLEDGE BASES; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PROTEOME; SOFTWARE; TERMINOLOGY AS TOPIC;

EID: 84904406947     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22594     Document Type: Article

References (30)

1. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
2. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.
3. Barabási AL, Gulbahce N, Loscalzo J. 2011. Network medicine: a network-based approach to human disease. Nat Rev Genet 12:56-68.
4. Beales PL, Badano JL, Ross AJ, Ansley SJ, Hoskins BE, Kirsten B, Mein CA, Froguel P, Scambler PJ, Lewis RA, Lupski JR, Katsanis N. 2003. Genetic interaction of BBS1 mutations with alleles at other BBS loci can result in non-Mendelian Bardet-Biedl syndrome. Am J Hum Genet 72:1187-1199.
5. Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R. 2013. WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics 14(Suppl 3):S6.
6. Care MA, Needham CJ, Bulpitt AJ, Westhead DR. 2007. Deleterious SNP prediction: be mindful of your training data. Bioinformatics 23:664-672.
7. Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. 2013. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 132:1077-1130.
8. Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, et al. 2010. Locus reference genomic sequences: an improved basis for describing human DNA variants. Genome Med 2:24.
9. Das JK, Ingles J, Bagnall RD, Semsarian C. 2014. Determining pathogenicity of genetic variants in hypertrophic cardiomyopathy: importance of periodic reassessment. Genet Med 16:286-293.
10. Davies WIL, Downes SM, Fu JK, Shanks ME, Copley RR, Lise S, Ramsden SC, Black GCM, Gibson K, Foster RG, Hankins MW, Németh AH. 2012. Next-generation sequencing in health-care delivery: lessons from the functional analysis of rhodopsin. Genet Med 14:891-899.
11. Davis EE, Zhang Q, Liu Q, Diplas BH, Davey LM, Hartley J, Stoetzel C, Szymanska K, Ramaswami G, Logan CV, Muzny DM, Young AC, et al. 2011. TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. Nat Genet 43:189-196.
12. Furlong LI. 2013. Human diseases through the lens of network biology. Trends Genet 29:150-159.
13. Kenna KP, McLaughlin RL, Hardiman O, Bradley DG. 2013. Using reference databases of genetic variation to evaluate the potential pathogenicity of candidate disease variants. Hum Mutat 34:836-841.
14. Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, et al. 2009. A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet 41:739-745.
15. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, et al. 2014. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 42:D966-D974.
16. Macarthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F. 2014. Locus reference genomic: reference sequences for the reporting of clinically relevant sequence variants. Nucleic Acids Res 42:D873-D878.
17. Piton A, Redin C, Mandel JL. 2013. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Am J Hum Genet 93:368-383.
18. Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium. 2014. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database.
19. Rath A, Olry A, Dhombres F, Brandt MM, Urbero B, Ayme S. 2012. Representation of rare diseases in health information systems: the Orphanet approach to serve a wide range of end users. Hum Mutat 33:803-808.
20. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145.
21. Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. 2013. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 34:57-65.
22. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, et al. 2012. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69.
23. Thusberg J, Olatubosun A, Vihinen M. 2011. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat 32:358-368.
24. Vihinen M. 2014. Variation ontology for annotation of variation effects and mechanisms. Genome Res 24:356-364.
25. Waters AM, Beales PL. 2011. Ciliopathies: an expanding disease spectrum. Pediatr Nephrol 26:1039-1056.
26. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PEM. 2008. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat 29:6-13.
27. Yates CM, Sternberg MJE. 2013. Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs). J Mol Biol 425:1274-1286.
28. Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. 2004. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat 23:464-470.
29. Yuan S, Sun Z. 2013. Expanding horizons: ciliary proteins reach beyond cilia. Annu Rev Genet 47:353-376.
30. Zhang Q, Yu D, Seo S, Stone EM, Sheffield VC. 2012. Intrinsic protein-protein interaction-mediated and chaperonin-assisted sequential assembly of stable Bardet-Biedl syndrome protein complex, the BBSome. J Biol Chem 287:20625-20635.