Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Kinnamon, Daniel D ^a   Hershberger, Ray E ^a   Martin, Eden R ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MONTE CARLO METHOD; PROBABILITY; RISK ASSESSMENT; RISK FACTOR; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; SYSTEMATIC ERROR; TREND STUDY; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC PREDISPOSITION; GENETICS; HUMAN; METHODOLOGY; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; STATISTICAL MODEL;

BASE SEQUENCE; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; RISK FACTORS;

EID: 84857169577     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030238     Document Type: Article

References (39)

1. Bodmer W, Bonilla C, (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695-701.
2. Pritchard JK, (2001) Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69: 124-137.
3. McClellan J, King M-C, (2010) Genetic heterogeneity in human disease. Cell 141: 210-217.
4. Schork NJ, Murray SS, Frazer KA, Topol EJ, (2009) Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 19: 212-219.
5. Li B, Leal SM, (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83: 311-321.
6. Madsen BE, Browning SR, (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5: e1000384.
7. Morris AP, Zeggini E, (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34: 188-193.
8. Hoffmann TJ, Marini NJ, Witte JS, (2010) Comprehensive Approach to Analyzing Rare Genetic Variants. PLoS ONE 5: e13584.
9. Sul JH, Han B, He D, Eskin E, (2011) An Optimal Weighted Aggregated Association Test for Identification of Rare Variants Involved in Common Diseases. Genetics 188: 181-188.
10. Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832-838.
11. Ionita-Laza I, Buxbaum JD, Laird NM, Lange C, (2011) A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease. PLoS Genet 7: e1001289.
12. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, et al. (2011) Testing for an Unusual Distribution of Rare Variants. PLoS Genet 7: e1001322.
13. Wu MC, Lee S, Cai T, Li Y, Boehnke M, et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89: 82-93.
14. Hudson RR, (1985) The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
15. Kimchi-Sarfaty C, Oh JM, Kim I-W, Sauna ZE, Calcagno AM, et al. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528.
16. Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, et al. (2011) A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nat Genet 43: 242-245.
17. Westfall PH, Young SS, (1993) Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment New York John Wiley & Sons.
18. Little RJA, Rubin DB, (2002) Statistical Analysis with Missing Data. 2nd ed Hoboken John Wiley & Sons.
19. Chapman J, Whittaker J, (2008) Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol 32: 560-566.
20. Hoh J, Wille A, Ott J, (2001) Trimming, Weighting, and Grouping SNPs in Human Case-Control Association Studies. Genome Res 11: 2115-2119.
21. Hoh J, Ott J, (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4: 701-709.
22. Rampersaud E, Kinnamon DD, Hamilton K, Khuri S, Hershberger RE, et al. (2010) Common susceptibility variants examined for association with dilated cardiomyopathy. Ann Hum Genet 74: 110-116.
23. Weir B, Cockerham CC, (1979) Estimation of linkage disequilibrium in randomly mating populations. Heredity 42: 105-111.
24. Sasieni PD, (1997) From genotypes to genes: Doubling the sample size. Biometrics 53: 1253-1261.
25. Slager SL, Schaid DJ, (2001) Case-control studies of genetic markers: Power and sample size approximations for Armitage's test for trend. Hum Hered 52: 149-153.
26. Freidlin B, Zheng G, Li Z, Gastwirth JL, (2002) Trend tests for case-control studies of genetic markers: power, sample size and robustness. Hum Hered 53: 146-152.
27. Casella G, Berger RL, (2002) Statistical Inference. 2nd ed Pacific Grove, CA Duxbury Press.
28. Timm NH, (2002) Applied Multivariate Analysis New York Springer.
29. Antonarkis S, (2010) Human Genome and Sequence Variation. In: Speicher M, Antonarkis S, Motulsky A, editors. Vogel and Motulsky's Human Genetics 4th Edition New York Springer pp. 31-53.
30. Hudson RR, (1983) Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 23: 183-201.
31. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
32. Nachman MW, Crowell SL, (2000) Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
33. Thomas D, (2004) Statistical Methods in Genetic Epidemiology New York Oxford University Press.
34. Matsumoto M, Nishimura T, (1998) Mersenne-Twister: A 623-dimensionally equidistributed uniform pseudo-random number generator. ACM Trans Model Comput Simul 8: 3-30.
35. Davison AC, Hinkley DV, (1997) Bootstrap Methods and their Application New York Cambridge University Press.
36. Goodnight JH, (1979) A tutorial on the SWEEP operator. Am Stat 33: 149-158.
37. Ernst MD, (2004) Permutation Methods: A Basis for Exact Inference. Stat Sci 19: 676-685.
38. McIntyre LM, Martin ER, Simonsen KL, Kaplan NL, (2000) Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association. Genet Epidemiol 19: 18-29.
39. Leemis LM, Trivedi KS, (1996) A comparison of approximate interval estimators for the Bernoulli parameter. Am Stat 50: 63-68.