Detection of SNP-SNP interactions in trios of parents with schizophrenic children

Genetic Epidemiology

Volumn 34, Issue 5, 2010, Pages 396-406

  Li, Qing ^a   Fallin, M Daniele ^a   Louis, Thomas A ^a   Lasseter, Virginia K ^b   McGrath, John A ^b   Avramopoulos, Dimitri ^b   Wolyniec, Paula S ^b   Valle, David ^b   Liang, Kung Yee ^a   Pulver, Ann E ^b   Ruczinski, Ingo ^a  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Case parent trios; Interaction; Logic regression; Single nucleotide polymorphisms

Indexed keywords

ARTICLE; CHILD; CONTROLLED STUDY; GENETIC RISK; GENOTYPE PHENOTYPE CORRELATION; HUMAN; INTERACTIONS WITH DNA; MAJOR CLINICAL STUDY; MULTIGENE FAMILY; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOTYPE; HAPLOTYPES; HUMANS; JEWS; LOGISTIC MODELS; MALE; MODELS, GENETIC; PARENTS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SCHIZOPHRENIA;

EID: 77954203935     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20488     Document Type: Article

References (35)

1. Baba H, Suzuki T, Arai H, Emson PC. 2004. Expression of nNOS and soluble guanylate cyclase in schizophrenic brain. Neuroreport 15:677-680. (Pubitemid 38457159)
2. Baron M. 1986. Genetics of schizophrenia: I. Familial patterns and mode of inheritance. Biol Psychiatry 21:1051-1066
3. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265. (Pubitemid 40202029)
4. Benyamin B, Visscher PM, McRae AF. 2009. Family-based genome-wide association studies. Pharmacogenomics 10:181-190.
5. Blaveri E, Kalsi G, Lawrence J, Quested D, Moorey H, Lamb G, Kohen D, Shiwach R, Chowdhury U, Curtis D, McQuillin A, Gramoustianou ES, Gurling HM. 2001. Genetic association studies of schizophrenia using the 8p21-22 genes: prepronociceptin (PNOC), neuronal nicotinic cholinergic receptor alpha polypeptide 2 (CHRNA2) and arylamine n-acetyltransferase 1 (NAT1). Eur J Hum Genet 9:469-472. (Pubitemid 32577185)
6. Bredt DS, Snyder SH. 1992. Nitric oxide, a novel neuronal messenger Neuron 8:3-11.
7. Carter CL, Chung CS. 1980. Segregation analysis of schizophrenia under a mixed genetic model. Hum Hered 30:350-356. (Pubitemid 11167826)
8. Chiu YF, McGrath JA, Thornquist MH, Wolyniec PS, Nestadt G, Swartz KL, Lasseter VK, Liang KY, Pulver AE. 2002. Genetic heterogeneity in schizophrenia ii: conditional analyses of affected schizophrenia sibling pairs provide evidence for an interaction between markers on chromosome 8p and 14q. Mol Psychiatry 7:658-664.
9. Dai JY, Ruczinski I, LeBlanc M, Kooperberg C. 2006. Imputation methods to improve inference in SNP association studies. Genet Epidemiol 30:690-702. (Pubitemid 44851516)
10. Fallin MD, Lasseter VK, Avramopoulos D, Nicodemus KK,Wolyniec PS, McGrath JA, Steel G, Nestadt G, Liang KY, Huganir RL, Valle D, Pulver AE. 2005. Bipolar I disorder and schizophrenia: a 440-single-nucleotide polymorphism screen of 64 candidate genes among Ashkenazi Jewish case-parent trios. Am J Hum Genet 77:918-936. (Pubitemid 41698514)
11. Gogos JA, Gerber DJ. 2006. Schizophrenia susceptibility genes: emergence of positional candidates and future directions. Trends Pharmacol Sci 27:226-233.
12. Harrison PJ, Owen MJ. 2003. Genes for schizophrenia? Recent findings and their pathophysiological implications. Lancet 361:417-419.
13. Hoft NR, Corley RP, McQueen MB, Schlaepfer IR, Huizinga D, Ehringer MA. 2009. Genetic association of the CHRNA6 and CHRNB3 genes with tobacco dependence in a nationally representative sample. Neuropsychopharmacology 34:698-706.
14. Hogg RC, Raggenbass M, Bertrand D. 2003. Nicotinic acetylcholine receptors: from structure to brain function. Rev Physiol Biochem Pharmacol 147:1-46.
15. Jurewicz I, Owen RJ, O'Donovan MC, Owen MJ. 2001. Searching for susceptibility genes in schizophrenia. Eur Neuropsychopharmacol 11:395-398.
16. Karson CN, GriffinWS, Mrak RE, Husain M, Dawson TM, Snyder SH, Moore NC, Sturner WQ. 1996. Nitric oxide synthase (NOS) in schizophrenia: increases in cerebellar vermis. Mol Chem Neuropathol 27:275-284. (Pubitemid 26142651)
17. Kishi T, Ikeda M, Kitajima T, Yamanouchi Y, Kinoshita Y, Kawashima K, Okochi T, Inada T, Ozaki N, Iwata N. 2008. Genetic association analysis of tagging SNPs in alpha4 and beta2 subunits of neuronal nicotinic acetylcholine receptor genes (CHRNA4 and CHRNB2) with schizophrenia in the Japanese populations. JNeural Transm 115: 1457-1461.
18. Kooperberg C, Ruczinski I. 2005. Identifying interacting SNPs using Monte Carlo logic regression. Genet Epidemiol 28:157-170.
19. Kooperberg C, Ruczinski I, LeBlanc ML, Hsu L. 2001. Sequence analysis using logic regression. Genet Epidemiol 21:S626-S631. (Pubitemid 32958934)
20. Laird NM, Lange C. 2006. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 7:385-394.
21. Li MD, Lou XY, Chen G, Ma JZ, Elston RC. 2008. Gene-gene interactions among CHRNA4, CHRNB2, BDNF, and NTRK2 in nicotine dependence. Biol Psychiatry 64:951-957.
22. Li Q, Louis TA, Fallin MD, Ruczinski I. 2009. Trio logic regression - detection of SNP-SNP interactions in case-parent trios. Working Paper 194, Johns Hopkins Department of Biostatistics.
23. Luca VD, Voineskos S, Wong G, Kennedy JL. 2006. Genetic interaction between alpha4 and beta2 subunits of high affinity nicotinic receptor: analysis in schizophrenia. Exp Brain Res 174:292-296. (Pubitemid 44421106)
24. Mobascher A, Winterer G. 2008. The molecular and cellular neurobiology of nicotine abuse in schizophrenia. Pharmacopsychiatry 41:S51-S59.
25. Novere NL, Corringer PJ, Changeux JP. 2002. The diversity of subunit composition in nAChRs: evolutionary origins, physiologic and pharmacologic consequences. J Neurobiol 53:447-456.
26. Ochoa EL, Lasalde-Dominicci J. 2007. Cognitive deficits in schizophrenia: focus on neuronal nicotinic acetylcholine receptors and smoking. Cell Mol Neurobiol 27:609-639. (Pubitemid 47038107)
27. Papadopolou S, Hartmann P, Lips KS, Kummer W, Haberberger RV. 2004. Nicotinic receptor mediated stimulation of NO-generation in neurons of rat thoracic dorsal root ganglia. Neurosci Lett 361:32-35. (Pubitemid 38609209)
28. Reif A, Herterich S, Strobel A, Ehlis AC, Saur D, Jacob CP, Wienker T, Topner T, Fritzen S, Walter U, Schmitt A, Fallgatter AJ, Lesch KP. 2006. A neuronal nitric oxide synthase (NOS-I) haplotype associated with schizophrenia modifies prefrontal cortex function. Mol Psychiatry 11:286-300. (Pubitemid 43316060)
29. Risch N, Baron M. 1984. Segregation analysis of schizophrenia and related disorders. Am J Hum Genet 36:1039-1059. (Pubitemid 15205735)
30. Ruczinski I, Kooperberg C, Leblanc M. 2003. Logic regression. J Comput Graphical Stat 12:475-511.
31. Shinkai T, Ohmori O, Hori H, Nakamura J. 2002. Allelic association of the neuronal nitric oxide synthase (NOS1) gene with schizophrenia. Mol Psychiatry 7:560-563.
32. Spielman RS, Ewens WJ. 1996. The tdt and other family-based tests for linkage disequilibrium and association. Am J Hum Genet 59:983-989.
33. Weinberg CR, Wilcox AJ, Lie RT. 1998. A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting. Am J Hum Genet 62:969-978.
34. Xuei X, Flury-Wetherill L, Almasy L, Bierut L, Tischfield J, Schuckit JrM, JIN, Foroud T, Edenberg HJ. 2008. Association analysis of genes encoding the nociceptin receptor (OPRL1) and its endogenous ligand (PNOC) with alcohol or illicit drug dependence. Addict Biol 13:80-87. (Pubitemid 351202134)
35. Zeiger JS, Haberstick BC, Schlaepfer I, Collins AC, Corley RP, Crowley TJ, Hewitt JK, Hopfer CJ, Lessem J, McQueen MB, Rhee SH, Ehringer MA. 2008. The neuronal nicotinic receptor subunit genes (CHRNA6 and CHRNB3) are associated with subjective responses to tobacco. Hum Mol Genet 17:724-734. (Pubitemid 351292261)