An unbiased evaluation of gene prioritization tools

Bioinformatics

Volumn 28, Issue 23, 2012, Pages 3081-3088

  Börnigen, Daniela ^a,b,c   Tranchevent, Léon Charles ^a,b   Bonachela Capdevila, Francisco ^b   Devriendt, Koenraad ^b   De Moor, Bart ^a,b   De Causmaecker, Patrick ^b   Moreau, Yves ^a,b  

^a Katholieke Universiteit Leuven   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE STUDY; GENETIC ASSOCIATION; GENETIC DATABASE; HUMAN; INTERNET; VALIDATION STUDY;

DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; HUMANS; INTERNET;

EID: 84870474023     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts581     Document Type: Article

References (77)

1. Abnet, C.C. et al. (2010) A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma. Nat. Genet., 42, 764-767.
2. Adie, E.A. et al. (2006) SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics, 22, 773-774.
3. Aerts, S. et al. (2006) Gene prioritization through genomic data fusion. Nat. Biotech., 24, 537-544.
4. Aerts, S. et al. (2009) Integrating computational biology and forward genetics in drosophila. PLoS Genet., 5, e1000351.
5. Arrington, C.B. et al. (2010) Haploinsufficiency of the LIM domain containing preferred translocation partner in lipoma (LPP) gene in patients with tetralogy of fallot and VACTERL association. Am. J. Med. Genet. A, 152, 2919-2923.
6. Banka, S. et al. (2010) Mutations in the G6PC3 gene cause Dursun syndrome. Am. J. Med. Genet. A, 152, 2609-2611.
7. Becker, K.G. et al. (2004) The genetic association database. Nat. Genet., 36, 431-432.
8. Bei, J. et al. (2010) A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nat. Genet., 42, 599-603.
9. Briggs, F.B.S. et al. (2010) Evidence for CRHR1 in multiple sclerosis using supervised machine learning and meta-analysis in 12, 566 individuals. Hum. Mol. Genet., 19, 4286-4295.
10. Calvo, S. et al. (2006) Systematic identification of human mitochondrial disease genes through integrative genomics. Nat. Genet., 38, 576-582.
11. Cardoso, C.C. et al. (2010) IFNG +874 TntextgreaterA single nucleotide polymorphism is associated with leprosy among Brazilians. Hum. Genet., 128, 481-490.
12. Chen, J. et al. (2007) Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics, 8, 392.
13. Cheong, H.S. et al. (2011) Association of RANBP1 haplotype with smooth pursuit eye movement abnormality. Am. J. Med. Genet. B, 156, 67-71.
14. Doms, A. and Schroeder, M. (2005) GoPubMed: exploring PubMed with the gene ontology. Nucleic Acids Res., 33, W783-W786.
15. Doncheva, N.T. et al. (2012) Recent approaches to the prioritization of candidate disease genes. WIREs Syst. Biol. Med., 4, 429-442.
16. Elbers, C.C. et al. (2007) A strategy to search for common obesity and type 2 diabetes genes. Trends Endocrinol. Metab., 18, 19-26.
17. Ellinghaus, E. et al. (2010) Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2. Nat. Genet., 42, 991-995.
18. Erlich, Y. et al. (2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res., 21, 558-664.
19. Fransen, K. et al. (2010) Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum. Mol. Genet., 19, 3482-3488.
20. Gimelli, S. et al. (2010) Mutations in SOX17 are associated with congenital anomalies of the kidney and the urinary tract. Hum. Mutat., 31, 1352-1359.
21. Green, E.K. et al. (2010) Variation at the GABAA receptor gene, rho 1 (GABRR1) associated with susceptibility to bipolar schizoaffective disorder. Am. J. Med. Genet. B, 153, 1347-1349.
22. Gretarsdottir, S. et al. (2010) Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm. Nat. Genet., 42, 692-697.
23. Haack, T.B. et al. (2010) Exome sequencing identifies ACAD9 mutations as a cause of complex i deficiency. Nat. Genet., 42, 1131-1134.
24. Haider, S. et al. (2009) BioMart central portal-unified access to biological data. Nucleic Acids Res., 37, W23-W27.
25. Hardy, J. and Singleton, A. (2009) Genomewide association studies and human disease. N. Engl. J. Med., 360, 1759-1768.
26. Hirschfield, G.M. et al. (2010) Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis. Nat. Genet., 42, 655-657.
27. Huffmeier, U. et al. (2010) Common variants at TRAF3IP2 are associated with susceptibility to psoriatic arthritis and psoriasis. Nat. Genet., 42, 996-999.
28. Hutz, J.E. et al. (2008) CANDID: a flexible method for prioritizing candidate genes for complex human traits. Genet. Epidemiol., 32, 779-790.
29. Kantarci, S. et al. (2010) Characterization of the chromosome 1q41q42.12 region, and the candidate gene DISP1, in patients with CDH. Am. J. Med. Genet. A, 152, 2493-2504.
30. Kohler, S. et al. (2008) Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet., 82, 949-958.
31. Letra, A. et al. (2010) Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Am. J. Med. Genet. A, 152, 1701-1710.
32. Linghu, B. et al. (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol., 10, R91.
33. Liu, X. et al. (2010) Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat. Genet., 42, 658-660.
34. Lupski, J.R. et al. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med., 362, 1181-1191.
35. McDonald-McGinn, D.M. et al. (2010) Metopic craniosynostosis due to mutations in GLI3: a novel association. Am. J. Med. Genet. A, 152, 1654-1660.
36. McGovern, D.P.B. et al. (2010) Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. Hum. Mol. Genet., 19, 3468-3476.
37. McKusick, V.A. (1998) Mendelian Inheritance in Man: A Catalog of Human Genes and Genetic Disorders. 12th edn. The Johns Hopkins University Press, Baltimore, Maryland, USA.
38. Mefford, H.C. et al. (2010) Copy number variation analysis in single-suture cranio-synostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis. Am. J. Med. Genet. A, 152, 2203-2210.
39. Miki, D. et al. (2010) Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations. Nat. Genet., 42, 893-896.
40. Miyake, N. et al. (2010) Loss-of-function mutations of CHST14 in a new type of Ehlers-Danlos syndrome. Hum. Mutat., 31, 966-974.
41. Mizuki, N. et al. (2010) Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behcet's disease susceptibility loci. Nat. Genet., 42, 703-706.
42. Moreau, Y. et al. (2012) Computational tools for prioritizing candidate genes: boosting disease gene discover. Nat. Rev. Genet., 13, 523-536.
43. Nicholas, A.K. et al. (2010) WDR62 is associated with the spindle pole and is mutated in human microcephaly. Nat. Genet., 42, 1010-1014.
44. Nikoloski, G. et al. (2010) Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat. Genet., 42, 665-667.
45. Nitsch, D. et al. (2010) Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics, 11, 460.
46. Oti, M. (2011) Web tools for the prioritization of candidate disease genes. Methods Mol. Biol., 760, 189-206.
47. Otto, E.A. et al. (2010) Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat. Genet., 42, 840-850.
48. Piro, R.M. et al. (2012) Computational approaches to disease-gene prediction: rationale, classification and successes. FEBS J., 279, 678-696.
49. Qidwai, K. et al. (2010) Deletions of Xp provide evidence for the role of holocyto-chrome c-type synthase (HCCS) in congenital diaphragmatic hernia. Am. J. Med. Genet. A, 152, 1588-1590.
50. Quadros, E.V. et al. (2010) Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin b(12). Hum. Mutat., 31, 924-929.
51. Radio, F.C. et al. (2010) TBX2 gene duplication associated with complex heart defect and skeletal malformations. Am. J. Med. Genet. A, 152, 2061-2066.
52. Rajab, A. et al. (2010) Fatal cardiac arrhythmia and long-QT syndrome in a new form of congenital generalized lipodystrophy with muscle rippling (CGL4) due to PTRF-CAVIN mutations. PLoS Genet., 6, e1000874.
53. Remmers, E.F. et al. (2010) Genome-wide association study identifies variants in the MHC class i, IL10, and IL23R-IL12RB2 regions associated with Behcet's disease. Nat. Genet., 42, 698-702.
54. Safran, M. et al. (2010) GeneCards version 3: the human gene integrator. Database, 2010: article ID baq020; doi:10.1093/database/baq020.
55. Sampson, M.G. et al. (2010) Evidence for a recurrent microdeletion at chromosome 16p11.2 associated with congenital anomalies of the kidney and urinary tract (CAKUT) and hirschsprung disease. Am. J. Med. Genet. A, 152, 2618-2622.
56. Schuster, S.C. (2008) Next-generation sequencing transforms today's biology. Nat. Methods, 5, 16-18.
57. Seelow, D. et al. (2008) GeneDistiller-distilling candidate genes from linkage intervals. PLoS One, 3, e3874.
58. Sheen, V.L. et al. (2010) Mutation in PQBP1 is associated with periventricular het-erotopia. Am. J. Med. Genet. A, 152, 2888-2890.
59. Shin, E.K. et al. (2010) Association between colony-stimulating factor 1 receptor gene polymorphisms and asthma risk. Hum. Genet., 128, 293-302.
60. Tabet, A. et al. (2010) Molecular characterization of a de novo 6q24.2q25.3 duplication interrupting UTRN in a patient with arthrogryposis. Am. J. Med. Genet. A, 152, 1781-1788.
61. Teber, E.T. et al. (2009) Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. BMC Bioinformatics, 10 (Suppl. 1), S69.
62. Tesli, M. et al. (2010) Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a Scandinavian case-control sample. Am. J. Med. Genet. B, 153, 1276-1282.
63. Thienpont, B. et al. (2010) Haploinsufficiency of TAB2 causes congenital heart defects in humans. Am. J. Hum. Genet., 86, 839-849.
64. Thornblad, T.A. et al. (2007) Prioritization of positional candidate genes using multiple web-based software tools. Twin Res. Hum. Genet., 10, 861-870.
65. Tiffin, N. (2011) Conceptual thinking for in silico prioritization of candidate disease genes. Methods Mol. Biol., 760, 175-187.
66. Tiffin, N. et al. (2006) Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res., 34, 3067-3081.
67. Tiffin, N. et al. (2009) Linking genes to diseases: it's all in the data. Genome Med., 1, 77.
68. Tranchevent, L. et al. (2010) A guide to web tools to prioritize candidate genes. Brief. Bioinformatics, 12, 22-32.
69. Turnbull, C. et al. (2010) Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer. Nat. Genet., 42, 604-607.
70. van Driel, M.A. et al. (2006) A text-mining analysis of the human phenome. Eur. J. Hum. Genet., 14, 535-542.
71. Vliet-Ostaptchouk, J.V. et al. (2008) HHEX gene polymorphisms are associated with type 2 diabetes in the Dutch Breda cohort. Eur. J. Hum. Genet., 16, 652-656.
72. Wang, L. et al. (2010) Genome-wide association study of esophageal squamous cell carcinoma in Chinese subjects identifies susceptibility loci at PLCE1 and c20orf54. Nat. Genet., 42, 759-763.
73. Yamauchi, T. et al. (2010) A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4AC2CD4B. Nat. Genet., 42, 864-868.
74. Yoshida, Y. et al. (2009) PosMed (Positional medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Res., 37 (Web Server issue), W147-W152.
75. Yu, T.W. et al. (2010) Mutations in WDR62, encoding a centrosome-associated protein, cause microcephaly with simplified gyri and abnormal cortical architecture. Nat. Genet., 42, 1015-1020.
76. Zlojutro, M. et al. (2010) Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence. Am. J. Med. Genet. B, 156, 44-58.
77. Zucchelli, S. et al. (2010) TRAF6 promotes atypical ubiquitination of mutant DJ-1 and alpha-synuclein and is localized to Lewy bodies in sporadic Parkinson's disease brains. Hum. Mol. Genet., 19, 3759-3770.