Linking genes to diseases: it's all in the data.
Genome-wide association analyses on large patient cohorts are generating large sets of candidate disease genes. This is coupled with the availability of ever-increasing genomic databases and a rapidly expanding repository of biomedical literature. Computational approaches to disease-gene association attempt to harness these data sources to identify the most likely disease gene candidates for further empirical analysis by translational researchers, resulting in efficient identification of genes of diagnostic, prognostic and therapeutic value. Existing computational methods analyze gene structure and sequence, functional annotation of candidate genes, characteristics of known disease genes, gene regulatory networks, protein-protein interactions, data from animal models and disease phenotype. To date, a few studies have successfully applied computational analysis of clinical phenotype data for specific diseases and shown genetic associations. In the near future, computational strategies will be facilitated by improved integration of clinical and computational research, and by increased availability of clinical phenotype data in a format accessible to computational approaches.
Tiffin
Nicki
N
MRC/UWC/SANBI Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. nickitiffin@imaginet.co.za.
Andrade-Navarro
Miguel A
MA
Perez-Iratxeta
Carolina
C
Genome Biol. 2003;4(11):R75
14611661
BMC Genomics. 2007 Sep 24;8:333
17892551
J Hum Genet. 2008;53(7):644-655
18463784
BMC Med Genomics. 2009 May 28;2:31
19476647
Brief Bioinform. 2008 Jul;9(4):326-32
18436575
Nat Genet. 2004 Sep;36(9):925-7
15340424
Nat Biotechnol. 2007 Mar;25(3):309-16
17344885
Bioinformatics. 2002;18 Suppl 2:S110-5
12385992
Nucleic Acids Res. 2005 Mar 14;33(5):1544-52
15767279
BMC Bioinformatics. 2007 Oct 16;8:392
17939863
Nat Genet. 2007 Jul;39(7):906-13
17572673
PLoS One. 2008 Aug 06;3(8):e2907
18682798
EMBO Rep. 2007 Dec;8(12):1135-41
18059312
Am J Hum Genet. 2009 Apr;84(4):524-33
19344873
Exp Mol Med. 2008 Oct 31;40(5):523-32
18985010
Am J Hum Genet. 2008 Nov;83(5):610-5
18950739
Hum Mol Genet. 2007 Jan 15;16(2):210-22
17200153
Physiol Genomics. 2008 Sep 17;35(1):55-64
18612082
Trends Genet. 2008 Mar;24(3):133-41
18262675
Am J Hum Genet. 2005 Nov;77(5):795-806
16252239
Cell. 2007 Jan 12;128(1):9-13
17218247
Nucleic Acids Res. 2008 Jan;36(Database issue):D724-8
18158299
Nat Genet. 2002 Jul;31(3):316-9
12006977
PLoS One. 2009 May 28;4(5):e5324
19492091
Pharmacogenomics. 2009 Feb;10(2):191-201
19207020
Nat Genet. 2006 Aug;38(8):879-87
16832355
Nucleic Acids Res. 2006 Jun 06;34(10):3067-81
16757574
BMC Bioinformatics. 2009 Feb 05;10 Suppl 2:S8
19208196
Nat Rev Genet. 2009 Mar;10(3):155-9
19188922
Public Health Genomics. 2010;13(2):72-9
19439916
Nature. 2000 Jun 15;405(6788):847-56
10866211
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W212-6
17478516
Nucleic Acids Res. 2004 Jun 04;32(10):3108-14
15181176
Bioinformatics. 2006 Feb 1;22(3):269-77
16287936
PLoS Genet. 2008 Feb;4(2):e33
18454206
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W758-61
15980578
Neuromuscul Disord. 1996 Dec;6(6):475-82
9027858
Nucleic Acids Res. 2007 Jan;35(Database issue):D658-62
17151068
Nat Genet. 2000 May;25(1):25-9
10802651
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6
14681408
Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
18045790
Bioinformatics. 2008 Feb 1;24(3):428-9
18048394
Trends Biochem Sci. 2004 Feb;29(2):88-94
15102435
Hum Mol Genet. 2007 Apr 15;16 Spec No 1:R88-95
17613553
Science. 2009 May 29;324(5931):1210-3
19478186
BMC Bioinformatics. 2005 Mar 14;6:55
15766383
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62
19420067
Nat Genet. 2007 Jul;39(7):813-5
17597768
Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90
18940857
Nature. 2007 Oct 18;449(7164):851-61
17943122
Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14
18000006
Biotechniques. 2008 Apr;44(5):627-8, 630, 632
18474037
BMC Genomics. 2007 Oct 25;8:389
17961254
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W377-84
18508807
Am J Hum Genet. 2003 Mar;72(3):636-49
12592605
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W717-23
15980570
Nucleic Acids Res. 2009 Jan;37(Database issue):D755-61
18996895
Genome Biol. 2007;8(11):R252
18042286
Eur J Hum Genet. 2006 May;14(5):535-42
16493445
Clin Genet. 2007 Jan;71(1):1-11
17204041
Nucleic Acids Res. 2009 Jan;37(Database issue):D657-60
18984619
Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22
18981052
Genome Biol. 2005;6(1):R7
15642099
Adv Genet. 2008;60:571-601
18358333
J Med Genet. 2006 Aug;43(8):691-8
16611749
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
18940858