Disease insights through cross-species phenotype comparisons

Mammalian Genome

Volumn 26, Issue 9-10, 2015, Pages 548-555

  Haendel, Melissa A ^a   Vasilevsky, Nicole ^a   Brush, Matthew ^a   Hochheiser, Harry S ^b   Jacobsen, Julius ^c   Oellrich, Anika ^c   Mungall, Christopher J ^d   Washington, Nicole ^d   Köhler, Sebastian ^e   Lewis, Suzanna E ^d   Robinson, Peter N ^e   Smedley, Damian ^c  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CRANIOFACIAL SYNOSTOSIS; EXOME; GENE DISRUPTION; GENE MUTATION; GENETIC ASSOCIATION; GENOME; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INCIDENCE; NONHUMAN; PATHOGENICITY; PHENOTYPE; QUANTITATIVE ASSAY; RARE DISEASE; REVIEW; SPECIES COMPARISON; ANIMAL; BIOLOGY; DISEASE MODEL; GENETIC DATABASE; GENETIC DISORDER; GENETICS; GENOMICS; MOUSE; MUTATION;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DISEASE MODELS, ANIMAL; EXOME; GENETIC DISEASES, INBORN; GENOMICS; HUMANS; MICE; MUTATION; PHENOTYPE;

EID: 84943813608     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-015-9577-8     Document Type: Review

References (33)

1. Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res 43:D789–D798
2. Ayme S (2003) Orphanet, an information site on rare diseases. Soins; la revue de reference infirmiere 672:46–47
3. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE (2013) Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 14:681–691
4. Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, Swaminathan GJ (2014) DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res 42:D993–D1000
5. Chen CK, Mungall CJ, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield PN, Smedley D (2012) MouseFinder: candidate disease genes from mouse phenotype data. Hum Mutat 33:858–866
6. Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE (2013) Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech 6:358–372
7. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 43:D726–D736
8. Gahl WA, Markello TC, Toro C, Fajardo KF, Sincan M, Gill F, Carlson-Donohoe H, Gropman A, Pierson TM, Golas G, Wolfe L, Groden C, Godfrey R, Nehrebecky M, Wahl C, Landis DM, Yang S, Madeo A, Mullikin JC, Boerkoel CF, Tifft CJ, Adams D (2012) The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases. Genet Med 14:51–59
9. Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chenier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M (2013) PhenoTips: patient phenotyping software for clinical and research use. Hum Mutat 34:1057–1065
10. Gkoutos GV, Schofield PN, Hoehndorf R (2012) Computational tools for comparative phenomics: the role and promise of ontologies. Mamm Genome 23:669–679
11. GO Consortium (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049–D1056
12. Haendel M, Balhoff J, Bastian F, Blackburn D, Blake J, Bradford Y, Comte A, Dahdul W, Dececchi T, Druzinsky R, Hayamizu T, Ibrahim N, Lewis S, Mabee P, Niknejad A, Robinson-Rechavi M, Sereno P, Mungall C (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 5:21
13. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41:D456–D463
14. Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res 39:e119
15. Javed A, Agrawal S, Ng PC (2014) Phen-Gen: combining phenotype and genotype to analyze rare disorders. Nat Methods 11:935–937
16. Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ (2013) Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res 2:30
17. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jahn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN (2014a) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 42:D966–D974
18. Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN (2014b) Clinical interpretation of CNVs with cross-species phenotype data. J Med Genet 51:766–772
19. Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H (2014) The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res 42:D802–D809
20. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335:823–828
21. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M (2010) Integrating phenotype ontologies across multiple species. Genome Biol 11:R2
22. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA (2012) Uberon, an integrative multi-species anatomy ontology. Genome Biol 13:R5
23. Oellrich A, Koehler S, Washington N, Mungall C, Lewis S, Haendel M, Robinson PN, Smedley D (2014) The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics 5:S4
24. Pesquita C, Faria D, Falcao AO, Lord P, Couto FM (2009) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5:e1000443
25. Robinson PN, Webber C (2014) Phenotype ontologies and cross-species analysis for translational research. PLoS Genet 10:e1004268
26. Robinson PN, Köhler S, Oellrich A, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D (2014) Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res 24:340–348
27. Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, Sakai R, Konings P, Vermeesch JR, Aerts J, De Moor B, Moreau Y (2013) eXtasy: variant prioritization by genomic data fusion. Nat Methods 10:1083–1084
28. Smedley D, Oellrich A, Köhler S, Ruef B, Sanger Mouse Genetics P, Westerfield M, Robinson P, Lewis S, Mungall C (2013) PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database 2013:bat025
29. Smith CL, Eppig JT (2012) The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 23:653–668
30. Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ 1:e148
31. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 7:e1000247
32. Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D (2010) EMMA—mouse mutant resources for the international scientific community. Nucleic Acids Res 38:D570–D576
33. Zemojtel T, Köhler S, Mackenroth L, Jager M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Kruger U, Frommer G, Fischer B, Kornak U, Flottmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN (2014) Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med 6:252ra123