Detecting associated single-nucleotide polymorphisms on the X chromosome in case control genome-wide association studies

Statistical Methods in Medical Research

Volumn 26, Issue 2, 2017, Pages 567-582

  Chen, Zhongxue ^a   Ng, Hon Keung Tony ^b   Li, Jing ^a   Liu, Qingzhong ^c   Huang, Hanwen ^d  

^a INDIANA UNIVERSITY   (United States)

^b SOUTHERN METHODIST UNIVERSITY   (United States)

^c SAM HOUSTON STATE UNIVERSITY   (United States)

^d UNIVERSITY OF GEORGIA   (United States)

Author keywords

Chromosome X; combining p values; generalized genetic model; GWAS; single nucleotide polymorphism; trend test

Indexed keywords

ALLELE; ARTICLE; CASE CONTROL STUDY; CONTROLLED STUDY; FEMALE; GENERALIZED GENETIC MODEL; GENETIC MODEL; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMAN; INTERMETHOD COMPARISON; MALE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; ALZHEIMER DISEASE; BIOLOGICAL MODEL; BIOSTATISTICS; COMPUTER SIMULATION; DNA METHYLATION; ENZYMOLOGY; GENETIC MARKER; GENETICS; PROCEDURES; PROMOTER REGION; STATISTICS AND NUMERICAL DATA;

GENETIC MARKER; ORNITHINE CARBAMOYLTRANSFERASE;

ALLELES; ALZHEIMER DISEASE; BIOSTATISTICS; CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, X; COMPUTER SIMULATION; DNA METHYLATION; FEMALE; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MODELS, GENETIC; ORNITHINE CARBAMOYLTRANSFERASE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC;

EID: 85018769637     PISSN: 09622802     EISSN: 14770334     Source Type: Journal    
DOI: 10.1177/0962280214551815     Document Type: Article

References (30)

1. Ober C, Loisel DA, Gilad Y,. Sex-specific genetic architecture of human disease. Nat Rev Genet 2008; 9 (12): 911-911.
2. Manolio TA,. Genomewide association studies and assessment of the risk of disease. N Engl J Med 2010; 363 (2): 166-176.
3. Loley C, Ziegler A, König IR,. Association tests for X-chromosomal markers-a comparison of different test statistics. Hum Hered 2011; 71 (1): 23-36.
4. Clayton D,. Testing for association on the X chromosome. Biostatistics 2008; 9 (4): 593-593.
5. Clayton DG,. Sex chromosomes and genetic association studies. Gen Med 2009; 1 (11): 1-7.
6. Zheng G, Joo J, Zhang C, et al. Testing association for markers on the X chromosome. Genet Epidemiol 2007; 31 (8): 834-843.
7. Ziegler A, König IR, Pahlke F,. A statistical approach to genetic epidemiology: Concepts and applications, with an e-learning platform, Weinheim: Wiley-VCh, 2010.
8. Carrel L, Willard HF,. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005; 434 (7031): 400-404.
9. Hickey PF, Bahlo M,. X chromosome association testing in genome wide association studies. Genet Epidemiol 2011; 35 (7): 664-670.
10. Chen Z, Ng HKT,. A robust method for testing association in genome-wide association studies. Hum Hered 2012; 73 (1): 26-34.
11. Owen AB,. Karl Pearson's meta-analysis revisited. Ann Statist 2009; 37 (6B): 3867-3892.
12. Fisher RA,. Statistical methods for research workers, Edinburgh: Oliver and Boyd, 1932.
13. Esary JD, Proschan F, Walkup DW,. Association of random variables, with applications. Ann Math Stat 1967; 38: 1466-1474.
14. Chen Z, Liu Q, Nadarajah S,. A new statistical approach to detecting differentially methylated loci for case control illumina array methylation data. Bioinformatics 2012; 28 (8): 1109-1113.
15. Chen Z, Huang H, Liu J, et al. Detecting differentially methylated loci for illumina array methylation data based on human ovarian cancer data. BMC Med Gen 2013; 6 (Suppl 1): S9-S9.
16. Chen Z,. A new association test based on chi-square partition for case-control GWA studies. Genet Epidemiol 2011; 35 (7): 658-663.
17. Chen Z,. Association tests through combining p-values for case control genome-wide association studies. Stat Probab Lett 2013; 83 (8): 1854-1862.
18. Huang H, Chen Z, Huang X,. Age-adjusted nonparametric detection of differential DNA methylation with case-control designs. BMC Bioinform 2013; 14 (1): 86-86.
19. Chen Z, Huang H, Ng HKT,. An improved robust association test for gwas with multiple diseases. Stat Probab Lett 2014; 91: 153-161.
20. Chen Z,. A new association test based on disease allele selection for case-control genome-wide association studies. BMC Genom 2014; 15: 358-358.
21. Chen Z, Liu Q,. A new approach to account for the correlations among single nucleotide polymorphisms in genome-wide association studies. Hum Hered 2011; 72 (1): 1-9.
22. Hansmannel F, Lendon C, Pasquier F, et al. Is the ornithine transcarbamylase gene a genetic determinant of Alzheimer's disease? Neurosci Lett 2009; 449 (1): 76-80.
23. Bensemain F, Hot D, Ferreira S, et al. Evidence for induction of the ornithine transcarbamylase expression in Alzheimer's disease. Mol Psych 2009; 14 (1): 106-106.
24. Sasieni PD,. From genotypes to genes: doubling the sample size. Biometrics 1997; 53 (4): 1253-1261.
25. Chen Z, Huang H and Ng HKT. Testing for association in case-control genome-wide association studies with shared controls. Stat Met Med Res. Published online 1 February, 2013. doi:101177/0962280212474061.
26. Chen Z, Huang H, Ng HKT,. Design and analysis of multiple diseases genome-wide association studies without controls. Gene 2012; 510 (1): 87-92.
27. Chen Z, Nadarajah S,. Comments on 'Choosing an optimal method to combine p-values' by Sungho Won, Nathan Morris, Qing Lu and Robert C. Elston, Statistics in Medicine 2009; 28: 1537-1553. Stat Med 2011; 30 (24): 2959-2961.
28. Chen Z,. Is the weighted z-test the best method for combining probabilities from independent tests? J Evol Biol 2011; 24 (4): 926-930.
29. Lancaster H,. The combination of probabilities: an application of orthonormal functions. Aust J Stat 1961; 3: 20-33.
30. Chen Z, Nadarajah S,. On the optimally weighted z-test for combining probabilities from independent studies. Comput Stat Data Anal 2014; 70: 387-394.