Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy

Human Genetics

Volumn 135, Issue 1, 2016, Pages 31-40

  Backes, Christina ^a   Meder, Benjamin ^b,c,d   Lai, Alan ^b,c   Stoll, Monika ^e   Rühle, Frank ^e   Katus, Hugo A ^b,c,d   Keller, Andreas ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^c DZHK GERMAN CENTRE FOR CARDIOVASCULAR RESEARCH   (Germany)

^d Klaus Tschira Institute for Integrative Computational Cardiology   (Germany)

^e UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CONTRACTILE PROTEIN; HLA D ANTIGEN; HLA DQA1 ANTIGEN; HLA DQA2 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; UNCLASSIFIED DRUG;

ARTICLE; CHROMOSOME 6; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; EXCISION REPAIR; GENE FREQUENCY; GENE MUTATION; GENETIC ASSOCIATION; GENETIC BACKGROUND; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC TRAIT; GENETIC VARIABILITY; HEART MUSCLE CELL; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; SMOOTH MUSCLE CONTRACTION; VASCULAR SMOOTH MUSCLE; GENETICS; GENOME-WIDE ASSOCIATION STUDY;

CARDIOMYOPATHY, DILATED; GENOME-WIDE ASSOCIATION STUDY; HUMANS;

EID: 84952717040     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-015-1609-7     Document Type: Article

References (33)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25–29
2. Backes C, Ruhle F, Stoll M, Haas J, Frese K, Franke A, Lieb W, Wichmann HE, Weis T, Kloos W et al (2014) Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. BMC Genom 15:622
3. Braun R, Buetow K (2011) Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data. PLoS Genet 7(6):e1002101
4. Communal C, Sumandea M, de Tombe P, Narula J, Solaro RJ, Hajjar RJ (2002) Functional consequences of caspase activation in cardiac myocytes. Proc Natl Acad Sci USA 99(9):6252–6256
5. da Huang W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1–13
6. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55(4):997–1004
7. Dhandapany PS, Razzaque MA, Muthusami U, Kunnoth S, Edwards JJ, Mulero-Navarro S, Riess I, Pardo S, Sheng J, Rani DS et al (2014) RAF1 mutations in childhood-onset dilated cardiomyopathy. Nat Genet 46(6):635–639
8. Gui H, Li M, Sham PC, Cherny SS (2011) Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn’s disease dataset. BMC Res Notes 4:386
9. Haas J, Frese KS, Peil B, Kloos W, Keller A, Nietsch R, Feng Z, Muller S, Kayvanpour E, Vogel B et al (2015) Atlas of the clinical genetics of human dilated cardiomyopathy. Eur Heart J 36(18):1123a–1135a
10. Haines JL, Hauser MA, Schmidt S, Scott WK, Olson LM, Gallins P, Spencer KL, Kwan SY, Noureddine M, Gilbert JR et al (2005) Complement factor H variant increases the risk of age-related macular degeneration. Science 308(5720):419–421
11. Hershberger RE, Norton N, Morales A, Li D, Siegfried JD, Gonzalez-Quintana J (2010) Coding sequence rare variants identified in MYBPC3, MYH6, TPM1, TNNC1, and TNNI3 from 312 patients with familial or idiopathic dilated cardiomyopathy. Circ Cardiovasc Genet 3(2):155–161
12. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106(23):9362–9367
13. Holle R, Happich M, Lowel H, Wichmann HE, Group MKS (2005) KORA–a research platform for population based health research. Gesundheitswesen 67(Suppl 1):S19–S25
14. Holmans P, Green EK, Pahwa JS, Ferreira MA, Purcell SM, Sklar P, Owen MJ, O’Donovan MC, Craddock N (2009) Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am J Hum Genet 85(1):13–24
15. Jane-wit D, Altuntas CZ, Johnson JM, Yong S, Wickley PJ, Clark P, Wang Q, Popovic ZB, Penn MS, Damron DS et al (2007) Beta 1-adrenergic receptor autoantibodies mediate dilated cardiomyopathy by agonistically inducing cardiomyocyte apoptosis. Circulation 116(4):399–410
16. Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D’Eustachio P, Jassal B, Lewis S, Wu G et al (2003) The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harb Symp Quant Biol 68:237–243
17. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30
18. Karp PD, Riley M, Paley SM, Pellegrini-Toole A (2002) The MetaCyc database. Nucleic Acids Res 30(1):59–61
19. Keller A, Backes C, Lenhof HP (2007) Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinform 8:290
20. Khatri P, Sirota M, Butte AJ (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8(2):e1002375
21. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308(5720):385–389
22. Korkmaz S, Zitron E, Bangert A, Seyler C, Li S, Hegedus P, Scherer D, Li J, Fink T, Schweizer PA et al (2013) Provocation of an autoimmune response to cardiac voltage-gated sodium channel NaV1.5 induces cardiac conduction defects in rats. J Am Coll Cardiol 62(4):340–349
23. Li X, Luo R, Jiang R, Chen R, Hua W (2012) Human leukocyte antigen-DQ beta 1 chain (DQB1) gene polymorphisms are associated with dilated cardiomyopathy: a systematic review and meta-analysis. Heart Lung J Crit Care 41(4):360–367
24. Liu G, Jiang Y, Wang P, Feng R, Jiang N, Chen X, Song H, Chen Z (2012) Cell adhesion molecules contribute to Alzheimer’s disease: multiple pathway analyses of two genome-wide association studies. J Neurochem 120(1):190–198
25. Lu D, Lian H, Zhang X, Shao H, Huang L, Qin C, Zhang L (2010) LMNA E82K mutation activates FAS and mitochondrial pathways of apoptosis in heart tissue specific transgenic mice. PLoS One 5(12):e15167
26. Meder B, Ruhle F, Weis T, Homuth G, Keller A, Franke J, Peil B, Lorenzo Bermejo J, Frese K, Huge A et al (2014) A genome-wide association study identifies 6p21 as novel risk locus for dilated cardiomyopathy. Eur Heart J 35(16):1069–1077
27. Pankuweit S, Ruppert V, Jonsdottir T, Muller HH, Meyer T, German Competence Network of Heart F (2013) The HLA class II allele DQB1 0309 is associated with dilated cardiomyopathy. Gene 531(2):180–183
28. Purevjav E, Nelson DP, Varela JJ, Jimenez S, Kearney DL, Sanchez XV, DeFreitas G, Carabello B, Taylor MD, Vatta M et al (2007) Myocardial Fas ligand expression increases susceptibility to AZT-induced cardiomyopathy. Cardiovasc Toxicol 7(4):255–263
29. Saccone SF, Bolze R, Thomas P, Quan J, Mehta G, Deelman E, Tischfield JA, Rice JP (2010) SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. Nucleic Acids Res 38(Web Server issue):W201–W209
30. Shi T, Moravec CS, Perez DM (2013) Novel proteins associated with human dilated cardiomyopathy: selective reduction in alpha(1A)-adrenergic receptors and increased desensitization proteins. J Recept Signal Transduct Res 33(2):96–106
31. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545–15550
32. Wang K, Li M, Bucan M (2007) Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81(6):1278–1283
33. Xiao H, Wang M, Du Y, Yuan J, Cheng X, Chen Z, Zou A, Wei F, Zhao G, Liao YH (2011) Arrhythmogenic autoantibodies against calcium channel lead to sudden death in idiopathic dilated cardiomyopathy. Eur J Heart Fail 13(3):264–270