A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease

Genetic Epidemiology

Volumn 33, Issue 8, 2009, Pages 657-667

  Allen, Andrew S ^a   Satten, Glen A ^b  

^a DUKE CLINICAL RESEARCH INSTITUTE   (United States)

^b NATIONAL CENTER FOR CHRONIC DISEASE PREVENTION AND HEALTH PROMOTION   (United States)

Author keywords

Association; Genome wide; GWAS; Haplotype sharing; Parkinson's disease

Indexed keywords

CALPASTATIN;

ARTICLE; CHROMOSOME 9; CONFOUNDING VARIABLE; EFFECT SIZE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENOME ANALYSIS; HAPLOTYPE; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PARKINSON DISEASE; POPULATION BASED CASE CONTROL STUDY; POPULATION DISTRIBUTION; QUALITY CONTROL; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; UNCERTAINTY; VALIDATION PROCESS;

AGED; AGED, 80 AND OVER; CALCIUM-BINDING PROTEINS; CHROMOSOMES, HUMAN, PAIR 9; COMPUTATIONAL BIOLOGY; FEMALE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 68549110018     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20417     Document Type: Article

References (32)

1. Adamec E, Mohan P, Vonsattel JP, Nixon RA. 2002. Calpain activation in neurodegenerative diseases: confocal immunofluorescence study with antibodies specifically recognizing the active form of calpain 2. Acta Neuropathol 104:92-104. (Pubitemid 36075364)
2. Allen AS, Satten GA. 2007a. Statistical models for haplotype sharing in case-parent trio data. Hum Hered 64:35-44.
3. Allen AS, Satten GA. 2007b. Association mapping via a class of haplotype-sharing statistics. BMC Proc 1:S123.
4. Allen AS, Satten GA. 2008. Robust estimation and testing of haplotype effects in case-control studies. Genet Epidemiol 32:29-40.
5. Bourgain C, Genin E, Quesneville H, Clerget-Darpoux F. 2000. Search for multifactorial disease susceptibility genes in founder populations. Ann Hum Genet 64:255-265. (Pubitemid 30692033)
6. Brinza D, Zelikovsky A. 2008. 2SNP: scalable phasing method for trios and unrelated individuals. IEEE/ACM Trans Comput Biol Bioinfor 5:313-318. (Pubitemid 351695271)
7. Camins A, Verdaguer E, Folch J, Pallàs M. 2006. Involvement of calpain activation in neurodegenerative processes. CNS Drug Rev 12:135-148. (Pubitemid 44300381)
8. Crocker SJ, Smith PD, Jackson-Lewis V, Lamba WR, Hayley SP, Grimm E, Callaghan SM, Slack RS, Melloni E, Przedborski S, Robertson GS, Anisman H, Merali Z, Park DS. 2003. Inhibition of calpains prevents neuronal and behavioral deficits in an MPTP mouse model of Parkinson's disease. J Neurosci 23:4081-4091. (Pubitemid 36958427)
9. Epstein MP, Allen AS, Satten GA. 2007. A simple and improved correction for population stratification in case-control studies. Am J Hum Genet 80:921-930.
10. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB. 2007. A whole-genome association study of major determinants for host control of HIV-1. Science 5:944-947. (Pubitemid 47301321)
11. Fung HC, Scholz S, Matarin M, Simón-Sánchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodríguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. 2006. Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 5: 911-916. (Pubitemid 44556544)
12. Gelb DJ, Oliver E, Gilman S. 1999. Diagnostic criteria for Parkinson disease. Arch Neurol 56:33-39.
13. Goll DE, Thompson VF, Li H,WeiW, Cong J. 2003. The calpain system. Physiol Rev 83:731-801.
14. Gusev A, Mandoiu II, Pasaniuc B. 2008. Highly scalable genotype phasing by entropy minimization. IEEE/ACM Trans Comput Biol Bioinform 5:252-261. (Pubitemid 351695265)
15. Huang Y, Wang KK. 2001. The calpain family and human diseases. Trends Mol Med 7:355-362.
16. Hughes AJ, Daniel SE, Kilford L, Lees AJ. 1992. Accuracy of clinical diagnosis of idiopathic Parkinson's disease: a clinico-pathological study of 100 cases. J Neurol Neurosurg Psychiatry 55:181-184.
17. Imhoff JP. 1961. Computing the distribution of quadratic forms in normal variables. Biometrika 48:419-426.
18. Marchini J, Howie B, Myers S, McVean G, Donnelly P. 2007. A new multipoint method for genome-wide association studies via imputation of genotypes. Nat Genet 39:906-913. (Pubitemid 47014502)
19. Mouatt-Prigent A, Karlsson J, Agid Y, Hirsch E. 1996. Increase m-calpain expression in the mesencephalon of patients with Parkinson's disease but not in neurodegenerative disorders involving the mesencephalon: a role in nerve cell death? Neuroscience 73:979-987.
20. Nolte IM, de Vries AR, Spijker GT, Jansen RC, Brinza D, Zelikovsky A, te Meerman GJ. 2007. Whole genome association analysis by haplotype sharing length based methods. BMC Proc 1:S129.
21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81:559-575. (Pubitemid 47330214)
22. Raynaud F, Marcilhac A. 2006. Implication of calpain in neuronal apoptosis: a possible regulation of Alzheimer's disease. FEBS J 273:3437-3443. (Pubitemid 44086944)
23. Saito K, Elce J, Hamos J, Nixon R. 1993. Widespread activation of calcium-activated neutral proteinase (calpain) in the brain in Alzheimer disease: a potential molecular basis for neuronal degeneration. Proc Nat Acad Sci USA 90:2628-2632. (Pubitemid 23113469)
24. Scheffe H. 1959. The Analysis of Variance. New York: Wiley.
25. Serfling RJ. 1980. Approximation Theorems of Mathematical Statistics. New York: Wiley.
26. Shields DC, Schaecher KE, Saido TC, Banik NL. 1999. A putative mechanism of demyelination in multiple sclerosis by a proteolytic enzyme, calpain. Proc Natl Acad Sci USA 96:11486-11491.
27. Shukla M, Rajgopal Y, Babu PP. 2006. Activation of calpains, calpastatin and spectrin cleavage in the brain during the pathology of fatal murine cerebral malaria. Neurochem Int 48:108-113.
28. The Wellcome Trust Case Control Consortium. 2007. Genomewide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661-678.
29. Tsuji T, Shimohama S, Kimura J, Shimizu K. 1998. m-Calpain (calcium-activated neutral proteinase) in Alzheimer's disease brains. Neurosci Lett 248:109-112. (Pubitemid 28275944)
30. Tzeng JY, Devlin B, Wasserman L, Roeder K. 2003. On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. Am J Hum Genet 72:891-902. (Pubitemid 36403308)
31. van der Meulen MA, te Meerman GJ. 1997. Haplotype sharing analysis in affected individuals from nuclear families with at least one affected offspring. Genet Epidemiol 14:915-919.
32. Zatz M, Starling A. 2005. Calpains and disease. N Engl J Med 352:2413-2423.