Genome-wide association studies in nephrology: Using known associations for data checks

American Journal of Kidney Diseases

Volumn 65, Issue 2, 2015, Pages 217-222

  Wuttke, Matthias ^a   Schaefer, Franz ^b   Wong, Craig S ^c   Köttgen, Anna ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^c UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

(SNP); chronic kidney disease (CKD); data checking systematic error; Genetic marker; Genome wide association; positive control; renal trait cystatin C; Single nucleotide polymorphism; Study (GWAS)

Indexed keywords

CREATININE; CYSTATIN C; URIC ACID;

CHRONIC KIDNEY DISEASE; CREATININE BLOOD LEVEL; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC TRAIT; GLOMERULUS FILTRATION RATE; HEREDITY; HOMEOSTASIS; HUMAN; KIDNEY CLEARANCE; KIDNEY FUNCTION; KIDNEY TUBULE ABSORPTION; NEPHROLOGY; PHENOTYPE; PROTEIN BLOOD LEVEL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; URIC ACID BLOOD LEVEL; GENETIC DATABASE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; PROCEDURES; RENAL INSUFFICIENCY, CHRONIC; STANDARDS;

DATABASES, GENETIC; GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEPHROLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; RENAL INSUFFICIENCY, CHRONIC;

EID: 84921558445     PISSN: 02726386     EISSN: 15236838     Source Type: Journal    
DOI: 10.1053/j.ajkd.2014.09.019     Document Type: Article

References (24)

1. Most P.J. van der, A. Vaez, and B.P. Prins QCGWAS: a flexible R package for automated quality control of genome-wide association results [published online ahead of print January 13, 2014] Bioinformatics 30 8 2014 1185 1186
2. C. Fuchsberger, D. Taliun, P.P. Pramstaller, and C. Pattaro GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data Bioinformatics 28 3 2012 444 445
3. A. Parsa, W.H. Kao, and D. Xie APOL1 risk variants, race, and progression of chronic kidney disease N Engl J Med 369 23 2013 2183 2196
4. G. Genovese, D.J. Friedman, and M.D. Ross Association of trypanolytic ApoL1 variants with kidney disease in African Americans Science 329 5993 2010 841 845
5. A.D. Johnson, M. Kavousi, and A.V. Smith Genome-wide association meta-analysis for total serum bilirubin levels Hum Mol Genet 18 14 2009 2700 2710
6. H.I. Feldman, L.J. Appel, and G.M. Chertow The Chronic Renal Insufficiency Cohort (CRIC) Study: design and methods J Am Soc Nephrol 14 7 suppl 2 2003 S148 S153
7. M.N. Weedon, H. Lango, and C.M. Lindgren Genome-wide association analysis identifies 20 loci that influence adult height Nat Genet 40 5 2008 575 583
8. A. Kottgen, N.L. Glazer, and A. Dehghan Multiple loci associated with indices of renal function and chronic kidney disease Nat Genet 41 6 2009 712 717
9. S.L. Furth, S.R. Cole, and M. Moxey-Mims Design and methods of the Chronic Kidney Disease in Children (CKiD) prospective cohort study Clin J Am Soc Nephrol 1 5 2006 1006 1015
10. E. Wuhl, A. Trivelli, and S. Picca Strict blood-pressure control and progression of renal failure in children N Engl J Med 361 17 2009 1639 1650
11. U. Querfeld, A. Anarat, and A.K. Bayazit The Cardiovascular Comorbidity in Children with Chronic Kidney Disease (4C) Study: objectives, design, and methodology Clin J Am Soc Nephrol 5 9 2010 1642 1648
12. A. Doring, C. Gieger, and D. Mehta SLC2A9 influences uric acid concentrations with pronounced sex-specific effects Nat Genet 40 4 2008 430 436
13. L.A. Inker, C.H. Schmid, and H. Tighiouart Estimating glomerular filtration rate from serum creatinine and cystatin C N Engl J Med 367 1 2012 20 29
14. A.S. Levey, J. Coresh, and T. Greene Expressing the Modification of Diet in Renal Disease Study equation for estimating glomerular filtration rate with standardized serum creatinine values Clin Chem 53 4 2007 766 772
15. G.J. Schwartz, M.F. Schneider, and P.S. Maier Improved equations estimating GFR in children with chronic kidney disease using an immunonephelometric determination of cystatin C Kidney Int 82 4 2012 445 453
16. C.A. Anderson, F.H. Pettersson, G.M. Clarke, L.R. Cardon, A.P. Morris, and K.T. Zondervan Data quality control in genetic case-control association studies Nat Protoc 5 9 2010 1564 1573
17. G.R. Abecasis, A. Auton, and L.D. Brooks An integrated map of genetic variation from 1,092 human genomes Nature 491 7422 2012 56 65
18. O. Delaneau, J. Marchini, and J.F. Zagury A linear complexity phasing method for thousands of genomes Nat Methods 9 2 2012 179 181
19. B.N. Howie, P. Donnelly, and J. Marchini A flexible and accurate genotype imputation method for the next generation of genome-wide association studies PLoS Genet 5 6 2009 e1000529
20. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 7145 2007 661 678
21. R. Magi, and A.P. Morris GWAMA: software for genome-wide association meta-analysis BMC Bioinformatics 11 2010 288
22. R.J. Pruim, R.P. Welch, and S. Sanna LocusZoom: regional visualization of genome-wide association scan results Bioinformatics 26 18 2010 2336 2337
23. A. Kottgen, C. Pattaro, and C.A. Boger New loci associated with kidney function and chronic kidney disease Nat Genet 42 5 2010 376 384
24. C. Wallace, S.J. Newhouse, and P. Braund Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia Am J Hum Genet 82 1 2008 139 149