Genome-wide strategies for discovering genetic influences on cognition and cognitive disorders: Methodological considerations

References

• Abdolmaleky , H. M. , Faraone , S. V. , Glatt , S. J. and Tsuang , M. T. 2004 . Meta-analysis of association between the T102C polymorphism of the 5HT2a receptor gene and schizophrenia . Schizophrenia Research , 67 ( 1 ) : 53 – 62 .
   PubMed Web of Science ®Google Scholar
• Abi-Dargham , A. , Mawlawi , O. , Lombardo , I. , Gil , R. , Martinez , D. Huang , Y. 2002 . Prefrontal dopamine D1 receptors and working memory in schizophrenia . Journal of Neuroscience , 22 ( 9 ) : 3708 – 3719 .
   PubMed Web of Science ®Google Scholar
• Almasy , L. , Gur , R. C. , Haack , K. , Cole , S. A. , Calkins , M. E. Peralta , J. M. 2008 . A genome screen for quantitative trait loci influencing schizophrenia and neurocognitive phenotypes . American Journal of Psychiatry , 165 ( 9 ) : 1185 – 1192 .
   PubMed Web of Science ®Google Scholar
• Altshuler , D. , Brooks , L. D. , Chakravarti , A. , Collins , F. S. , Daly , M. J. and Donnelly , P. 2005 . A haplotype map of the human genome . Nature , 437 ( 7063 ) : 1299 – 1320 .
   PubMed Web of Science ®Google Scholar
• Anand , A. , Li , Y. , Wang , Y. , Wu , J. , Gao , S. Bukhari , L. 2005 . Antidepressant effect on connectivity of the mood-regulating circuit: An FMRI study . Neuropsychopharmacology , 30 ( 7 ) : 1334 – 1344 .
   PubMed Web of Science ®Google Scholar
• Anderson , M. T. and Ter Braak , C. 2002 . Permutation test for multi-factorial analysis of variance . Journal of Statistical Computation and Simulation , 73 ( 2 ) : 85 – 113 .
   Web of Science ®Google Scholar
• Arking , D. E. , Pfeufer , A. , Post , W. , Kao , W. H. , Newton-Cheh , C. Ikeda , M. 2006 . A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization . Nature Genetics , 38 ( 6 ) : 644 – 651 .
   PubMed Web of Science ®Google Scholar
• Bacanu , S. A. , Devlin , B. and Roeder , K. 2000 . The power of genomic control . American Journal of Human Genetics , 66 ( 6 ) : 1933 – 1944 .
   PubMed Web of Science ®Google Scholar
• Balding , D. J. 2006 . A tutorial on statistical methods for population association studies . Nature Reviews Genetics , 7 ( 10 ) : 781 – 791 .
   PubMed Web of Science ®Google Scholar
• Barabasi , A. L. 2007 . Network medicine: From obesity to the “diseasome” . New England Journal of Medicine , 357 ( 4 ) : 404 – 407 .
   PubMed Web of Science ®Google Scholar
• Basile , V. S. , Masellis , M. , Potkin , S. G. and Kennedy , J. L. 2002 . Pharmacogenomics in schizophrenia: The quest for individualized therapy . Human Molecular Genetics , 11 ( 20 ) : 2517 – 2530 .
   PubMed Web of Science ®Google Scholar
• Benjamini , & Hochberg . 1995 . Controlling the false discovery rate: A practical and powerful approach to multiple testing . Journal of the Royal Statistical Society: Series B , 57 , 289 – 300 .
   Web of Science ®Google Scholar
• Blokland , G. A. , McMahon , K. L. , Hoffman , J. , Zhu , G. , Meredith , M. Martin , N. G. 2008 . Quantifying the heritability of task-related brain activation and performance during the N-back working memory task: A twin fMRI study . Biological Psychology , 79 ( 1 ) : 70 – 79 .
   PubMed Web of Science ®Google Scholar
• Botstein , D. and Risch , N. 2003 . Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease . Nature Genetics , 33 ( Suppl ) : 228 – 237 .
   PubMed Web of Science ®Google Scholar
• Brzustowicz , L. M. 2008 . NOS1AP in schizophrenia . Current Psychiatry Reports , 10 ( 2 ) : 158 – 163 .
   PubMedGoogle Scholar
• Calhoun , V. D. , Liu , J. and Adali , T. 2009 . A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data . Neuroimage , 45 ( Suppl. 1 ) : S163 – S172 .
   Web of Science ®Google Scholar
• Cardon , L. R. and Bell , J. I. 2001 . Association study designs for complex diseases . Nature Reviews Genetics , 2 ( 2 ) : 91 – 99 .
   PubMed Web of Science ®Google Scholar
• Cardon , L. R. and Palmer , L. J. 2003 . Population stratification and spurious allelic association . Lancet , 361 ( 9357 ) : 598 – 604 .
   PubMed Web of Science ®Google Scholar
• Chanock , S. J. , Manolio , T. , Boehnke , M. , Boerwinkle , E. , Hunter , D. J. Thomas , G. 2007 . Replicating genotype-phenotype associations . Nature , 447 ( 7145 ) : 655 – 660 .
   PubMed Web of Science ®Google Scholar
• Chapman , J. and Clayton , D. 2007 . Detecting association using epistatic information . Genetic Epidemiology , 31 ( 8 ) : 894 – 909 .
   PubMed Web of Science ®Google Scholar
• Clayton , D. and McKeigue , P. M. 2001 . Epidemiological methods for studying genes and environmental factors in complex diseases . Lancet , 358 ( 9290 ) : 1356 – 1360 .
   PubMed Web of Science ®Google Scholar
• Corneveaux , J. J. , Liang , W. S. , Reiman , E. M. , Webster , J. A. , Myers , A. J. , Zismann , V. L. , et al. ( in press ). Evidence for an association between KIBRA and late-onset Alzheimer's disease . Neurobiology of Aging . Epub ahead of print September 11, 2008 .
   Google Scholar
• de Bakker , P. I. , Yelensky , R. , Pe'er , I. , Gabriel , S. B. , Daly , M. J. and Altshuler , D. 2005 . Efficiency and power in genetic association studies . Nature Genetics , 37 ( 11 ) : 1217 – 1223 .
   PubMed Web of Science ®Google Scholar
• Dean , B. , Keriakous , D. , Scarr , E. and Thomas , E. A. 2007 . Gene expression profiling in Brodmann's area 46 from subjects with schizophrenia . Australian and New Zealand Journal of Psychiatry , 41 ( 4 ) : 308 – 320 .
   PubMed Web of Science ®Google Scholar
• Dennis , G. Jr , Sherman , B. T. , Hosack , D. A. , Yang , J. , Gao , W. Lane , H. C. 2003 . DAVID: Database for Annotation, Visualization, and Integrated Discovery . Genome Biology , 4 ( 5 ) : P3
   PubMed Web of Science ®Google Scholar
• Devlin , B. and Roeder , K. 1999 . Genomic control for association studies . Biometrics , 55 ( 4 ) : 997 – 1004 .
   PubMed Web of Science ®Google Scholar
• Devlin , B. , Bacanu , S. A. , & Roeder , K. 2004 . Genomic control to the extreme . Nature Genetics , 36 (11) , 1129 – 1130 ; author reply 1131 .
   PubMed Web of Science ®Google Scholar
• Di Piero , V. , Ferracuti , S. , Sabatini , U. and Pantano , P. 1994 . A cerebral blood flow study on tonic pain activation in man . Pain , 56 ( 2 ) : 167 – 173 .
   PubMed Web of Science ®Google Scholar
• Dudbridge , F. and Gusnanto , A. 2008 . Estimation of significance thresholds for genomewide association scans . Genetics Epidemiology , 32 ( 3 ) : 227 – 234 .
   PubMed Web of Science ®Google Scholar
• Dudoit , S and van de Laan , M. J. 2008 . Multiple testing procedures with application to genomics , New York : Springer Verlag .
   Google Scholar
• Durrant , C. , Zondervan , K. T. , Cardon , L. R. , Hunt , S. , Deloukas , P. and Morris , A. P. 2004 . Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes . American Journal of Human Genetics , 75 ( 1 ) : 35 – 43 .
   PubMed Web of Science ®Google Scholar
• Efron , B. and Tibshirani , R. 2002 . Empirical bayes methods and false discovery rates for microarrays . Genetic Epidemiology , 23 ( 1 ) : 70 – 86 .
   PubMed Web of Science ®Google Scholar
• Egan , M. F. , Goldberg , T. E. , Kolachana , B. S. , Callicott , J. H. , Mazzanti , C. M. Straub , R. E. 2001 . Effect of COMT Val108/158 Met genotype on frontal lobe function and risk for schizophrenia . Proceedings of the National Academy of Sciences of the United States of America , 98 ( 12 ) : 6917 – 6922 .
   PubMed Web of Science ®Google Scholar
• Ennis , S. , Jomary , C. , Mullins , R. , Cree , A. , Chen , X. Macleod , A. 2008 . Association between the SERPING1 gene and age-related macular degeneration: A two-stage case-control study . Lancet , 372 ( 9652 ) : 1828 – 1834 .
   PubMed Web of Science ®Google Scholar
• Evans , D. M. , Marchini , J. , Morris , A. P. and Cardon , L. R. 2006 . Two-stage two-locus models in genome-wide association . PLoS Genetics , 2 ( 9 ) : e157
   Web of Science ®Google Scholar
• Fallin , D. and Schork , N. J. 2000 . Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data . American Journal of Human Genetics , 67 ( 4 ) : 947 – 959 .
   PubMed Web of Science ®Google Scholar
• Fallin , D. , Cohen , A. , Essioux , L. , Chumakov , I. , Blumenfeld , M. Cohen , D. 2001 . Genetic analysis of case/control data using estimated haplotype frequencies: Application to APOE locus variation and Alzheimer's disease . Genome Research , 11 ( 1 ) : 143 – 151 .
   PubMed Web of Science ®Google Scholar
• Fisher , R. A. 1935 . Design of experiments , Edinburgh : Oliver & Boyd .
   Google Scholar
• Freedman , M. L. , Reich , D. , Penney , K. L. , McDonald , G. J. , Mignault , A. A. Patterson , N. 2004 . Assessing the impact of population stratification on genetic association studies . Nature Genetics , 36 ( 4 ) : 388 – 393 .
   PubMed Web of Science ®Google Scholar
• Gianola , D. and de los Campos , G. 2008 . Inferring genetic values for quantitative traits non-parametrically . Genetical Research , 90 ( 6 ) : 525 – 540 .
   Web of Science ®Google Scholar
• Glazier , A. M. , Nadeau , J. H. and Aitman , T. J. 2002 . Finding genes that underlie complex traits . Science , 298 ( 5602 ) : 2345 – 2349 .
   PubMed Web of Science ®Google Scholar
• Gottesman , II. and Gould , T. D. 2003 . The endophenotype concept in psychiatry: Etymology and strategic intentions . American Journal of Psychiatry , 160 ( 4 ) : 636 – 645 .
   PubMed Web of Science ®Google Scholar
• Gray , J. A. and Roth , B. L. 2007 . Molecular targets for treating cognitive dysfunction in schizophrenia . Schizophrenia Bulletin , 33 ( 5 ) : 1100 – 1119 .
   PubMed Web of Science ®Google Scholar
• Hecker , M. , Lambeck , S. , Toepfer , S. , van Someren , E. and Guthke , R. 2009 . Gene regulatory network inference: Data integration in dynamic models – A review . Biosystems , 96 ( 1 ) : 86 – 103 .
   PubMed Web of Science ®Google Scholar
• Helgadottir , A. , Thorleifsson , G. , Manolescu , A. , Gretarsdottir , S. , Blondal , T. Jonasdottir , A. 2007 . A common variant on chromosome 9p21 affects the risk of myocardial infarction . Science , 316 ( 5830 ) : 1491 – 1493 .
   PubMed Web of Science ®Google Scholar
• Hidalgo , C. A. , Blumm , N. , Barabasi , A. L. and Christakis , N. A. 2009 . A dynamic network approach for the study of human phenotypes . PLoS Computational Biology , 5 ( 4 ) : e1000353
   PubMed Web of Science ®Google Scholar
• Hikida , T. , Jaaro-Peled , H. , Seshadri , S. , Oishi , K. , Hookway , C. Kong , S. 2007 . Dominant-negative DISC1 transgenic mice display schizophrenia-associated phenotypes detected by measures translatable to humans . Proceedings of the National Academy of Sciences of the United States of America , 104 ( 36 ) : 14501 – 14506 .
   PubMed Web of Science ®Google Scholar
• Hill , W. G. , Goddard , M. E. and Visscher , P. M. 2008 . Data and theory point to mainly additive genetic variance for complex traits . PLoS Genetics , 4 ( 2 ) : e1000008
   Web of Science ®Google Scholar
• Hirschhorn , J. N. and Daly , M. J. 2005 . Genome-wide association studies for common diseases and complex traits . Nature Reviews Genetics , 6 ( 2 ) : 95 – 108 .
   PubMed Web of Science ®Google Scholar
• Hoffmann , T. J. , Lange , C. , Vansteelandt , S. , & Laird , N. M. 2009 . Gene-environment interaction tests for dichotomous traits in trios and sibships . Genetic Epidemiology .
   PubMed Web of Science ®Google Scholar
• Jiang , R. , Tang , W. , Wu , X. and Fu , W. 2009 . A random forest approach to the detection of epistatic interactions in case-control studies . BMC Bioinformatics , 10 ( Suppl. 1 ) : S65
   PubMed Web of Science ®Google Scholar
• Jung , B. C. , Jhun , M. and Song , S. H. 2006 . A new random permutation test in ANOVA models . Statistical Paper Springer-Verlag , 48 , 2006 : 47 – 62 .
   Google Scholar
• Kamatani , N. , Sekine , A. , Kitamoto , T. , Iida , A. , Saito , S. Kogame , A. 2004 . Large-scale single-nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP Maps, of 199 drug-related genes in 752 subjects: The analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs . American Journal of Human Genetics , 75 ( 2 ) : 190 – 203 .
   PubMed Web of Science ®Google Scholar
• Karlsgodt , K. H. , Glahn , D. C. , van Erp , T. G. , Therman , S. , Huttunen , M. Manninen , M. 2007 . The relationship between performance and fMRI signal during working memory in patients with schizophrenia, unaffected co-twins, and control subjects . Schizophrenia Research , 89 ( 1–3 ) : 191 – 197 .
   PubMed Web of Science ®Google Scholar
• Keedwell , P. , Drapier , D. , Surguladze , S. , Giampietro , V. , Brammer , M. , & Phillips , M. ( in press ). Neural markers of symptomatic improvement during antidepressant therapy in severe depression: Subgenual cingulate and visual cortical responses to sad, but not happy, facial stimuli are correlated with changes in symptom score . Journal of Psychopharmacology . Epub ahead of print, September 18, 2008 .
   Web of Science ®Google Scholar
• Kennedy , J. L. , Farrer , L. A. , Andreasen , N. C. , Mayeux , R. and St George-Hyslop , P. 2003 . The genetics of adult-onset neuropsychiatric disease: Complexities and conundra? . Science , 302 ( 5646 ) : 822 – 826 .
   PubMed Web of Science ®Google Scholar
• Kruglyak , L. 2008 . The road to genome-wide association studies . Nature Reviews Genetics , 9 ( 4 ) : 314 – 318 .
   PubMed Web of Science ®Google Scholar
• Lander , E. and Kruglyak , L. 1995 . Genetic dissection of complex traits: Guidelines for interpreting and reporting linkage results . Nature Genetics , 11 ( 3 ) : 241 – 247 .
   PubMed Web of Science ®Google Scholar
• Lee , S. H. , van der Werf , J. H. , Hayes , B. J. , Goddard , M. E. and Visscher , P. M. 2008 . Predicting unobserved phenotypes for complex traits from whole-genome SNP data . PLoS Genetics , 4 ( 10 ) : e1000231
   PubMed Web of Science ®Google Scholar
• Lee , S. S. , Sun , L. , Kustra , R. and Bull , S. B. 2008 . EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis . Bioinformatics , 24 ( 14 ) : 1603 – 1610 .
   PubMed Web of Science ®Google Scholar
• Lewis , D. A. and Gonzalez-Burgos , G. 2008 . Neuroplasticity of neocortical circuits in schizophrenia . Neuropsychopharmacology , 33 ( 1 ) : 141 – 165 .
   PubMed Web of Science ®Google Scholar
• Lewontin , R. C. 1958 . A general method for investigating the equilibrium of gene frequency in a population . Genetics , 43 ( 3 ) : 419 – 434 .
   PubMedGoogle Scholar
• Li , J. 2007 . Marker selection for whole-genome association studies with two-stage designs using dense single-nucleotide polymorphisms . BMC Proceedings , 1 ( Suppl. 1 ) : S136
   Google Scholar
• Lin , S. , Chakravarti , A. and Cutler , D. J. 2004 . Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies . Nature Genetics , 36 ( 11 ) : 1181 – 1188 .
   PubMed Web of Science ®Google Scholar
• Lohmueller , K. E. , Pearce , C. L. , Pike , M. , Lander , E. S. and Hirschhorn , J. N. 2003 . Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease . Nature Genetics , 33 ( 2 ) : 177 – 182 .
   PubMed Web of Science ®Google Scholar
• Manly 1997 . Randomization, bootstrap, and monte carlo methods in biology (2nd ed.). London : Chapman and Hall ,.
   Google Scholar
• Manoach , D. S. , Press , D. Z. , Thangaraj , V. , Searl , M. M. , Goff , D. C. Halpern , E. 1999 . Schizophrenic subjects activate dorsolateral prefrontal cortex during a working memory task, as measured by fMRI . Biological Psychiatry , 45 ( 9 ) : 1128 – 1137 .
   PubMed Web of Science ®Google Scholar
• McCarthy , M. I. , Abecasis , G. R. , Cardon , L. R. , Goldstein , D. B. , Little , J. Ioannidis , J. P. 2008 . Genome-wide association studies for complex traits: Consensus, uncertainty and challenges . Nature Reviews Genetics , 9 ( 5 ) : 356 – 369 .
   PubMed Web of Science ®Google Scholar
• McClearn , G. E. , Johansson , B. , Berg , S. , Pedersen , N. L. , Ahern , F. Petrill , S. A. 1997 . Substantial genetic influence on cognitive abilities in twins 80 or more years old . Science , 276 ( 5318 ) : 1560 – 1563 .
   PubMed Web of Science ®Google Scholar
• Menon , V. , Anagnoson , R. T. , Mathalon , D. H. , Glover , G. H. and Pfefferbaum , A. 2001 . Functional neuroanatomy of auditory working memory in schizophrenia: Relation to positive and negative symptoms . Neuroimage , 13 ( 3 ) : 433 – 446 .
   PubMed Web of Science ®Google Scholar
• Meyer-Lindenberg , A. and Weinberger , D. R. 2006 . Intermediate phenotypes and genetic mechanisms of psychiatric disorders . Nature Reviews Neuroscience , 7 ( 10 ) : 818 – 827 .
   PubMed Web of Science ®Google Scholar
• Meyer-Lindenberg , A. , Nichols , T. , Callicott , J. H. , Ding , J. , Kolachana , B. , Buckholtz , J. , et al. . 2006 . Impact of complex genetic variation in COMT on human brain function . Molecular Psychiatry , 11 (9) , 867 – 877 , 797 .
   PubMed Web of Science ®Google Scholar
• Moore , J. H. 2003 . The ubiquitous nature of epistasis in determining susceptibility to common human diseases . Human Heredity , 56 ( 1–3 ) : 73 – 82 .
   PubMed Web of Science ®Google Scholar
• Moore , J. H. 2008 . Analysis of gene-gene interactions . Current Protocols in Human Genetics , Chapter 1, Unit 1. 14 .
   PubMedGoogle Scholar
• Papassotiropoulos , A. , Stephan , D. A. , Huentelman , M. J. , Hoerndli , F. J. , Craig , D. W. Pearson , J. V. 2006 . Common Kibra alleles are associated with human memory performance . Science , 314 ( 5798 ) : 475 – 478 .
   PubMed Web of Science ®Google Scholar
• Perneger , T. V. 1998 . What's wrong with Bonferroni adjustments . British Medical Journal , 316 ( 7139 ) : 1236 – 1238 .
   PubMed Web of Science ®Google Scholar
• Phillips , P. C. 2008 . Epistasis: The essential role of gene interactions in the structure and evolution of genetic systems . Nature Reviews Genetics , 9 ( 11 ) : 855 – 867 .
   PubMed Web of Science ®Google Scholar
• Potkin , Kennedy , & Basile . 2002a . Brain imaging and pharmacogenetics in Alzheimer's disease and schizophrenia . In B. Lerer Pharmacogenetics of psychotropic drugs . Cambridge : Cambridge University Press .
   Google Scholar
• Potkin , Kennedy , & Basile 2002b . Combining brain imaging and pharmacogenetics in understanding clinical response in Alzheimer's disease and schizophrenia . In B. Lerer Pharmacogenetics of psychotropic drugs (pp. 391 – 400 ). Cambridge : Cambridge University Press .
   Google Scholar
• Potkin , Anand , R. , Alphs , L. , & Fleming , K. 2003 . Neurocognitive performance does not correlate with suicidality in schizophrenic and schizoaffective patients at risk for suicide . Schizophrenia Research , 59 (1) , 59 – 66 .
   PubMed Web of Science ®Google Scholar
• Potkin , S. G. , Turner , J. A. , Brown , G. G. , McCarthy , G. , Greve , D. N. Glover , G. H. 2009a . Working memory and DLPFC inefficiency in schizophrenia: The FBIRN study . Schizophrenia Bulletin , 35 ( 1 ) : 19 – 31 .
   PubMed Web of Science ®Google Scholar
• Potkin , S. G. , Turner , J. A. , Fallon , J. A. , Lakatos , A. , Keator , D. B. Guffanti , G. 2009b . Gene discovery through imaging genetics: Identification of two novel genes associated with schizophrenia . Molecular Psychiatry , 14 ( 4 ) : 416 – 428 .
   PubMed Web of Science ®Google Scholar
• Potkin , S. G. , Turner , J. A. , Guffanti , G. , Lakatos , A. , Fallon , J. H. Nguyen , D. D. 2009c . A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype . Schizophrenia Bulletin , 35 ( 1 ) : 96 – 108 .
   PubMed Web of Science ®Google Scholar
• Price , A. , Patterson , N. , Plenge , R. , Weinblatt , M. , Shadick , N. and Da , R. 2006 . Principal components analysis corrects for stratification in genome-wide association studies . Nature Genetics , 38 ( 8 ) : 904 – 909 .
   PubMed Web of Science ®Google Scholar
• Purcell , S. , Cherny , S. S. and Sham , P. C. 2003 . Genetic power calculator: Design of linkage and association genetic mapping studies of complex traits . Bioinformatics , 19 ( 1 ) : 149 – 150 .
   PubMed Web of Science ®Google Scholar
• Purcell , S. , Neale , B. , Todd-Brown , K. , Thomas , L. , Ferreira , M. A. Bender , D. 2007 . PLINK: A tool set for whole-genome association and population-based linkage analyses . American Journal of Human Genetics , 81 ( 3 ) : 559 – 575 .
   PubMed Web of Science ®Google Scholar
• Robbins , T. W. and Roberts , A. C. 2007 . Differential regulation of fronto-executive function by the monoamines and acetylcholine . Cerebral Cortex , 17 ( Suppl. 1 ) : i151 – i160 .
   Web of Science ®Google Scholar
• Rothman , K. J. 1990 . Statistics in nonrandomized studies . Epidemiology , 1 ( 6 ) : 417 – 418 .
   PubMedGoogle Scholar
• Rothman , K. J. 1998 . Modern epidemiology , 2nd ed , Philadelphia : Lippincott Williams & Wilkins .
   Google Scholar
• Roffman , J. L. , Weiss , A. P. , Goff , D. C. , Rauch , S. L. and Weinberger , D. R. 2006 . Neuroimaging-genetic paradigms: A new approach to investigate the pathophysiology and treatment of cognitive deficits in schizophrenia . Harvard Review of Psychiatry , 14 ( 2 ) : 78 – 91 .
   PubMed Web of Science ®Google Scholar
• Salvi , E. , Guffanti , G. , Orro , A. , Lupoli , S. , Torri , F. , Potkin , S. , et al. ( in press ) Ancestry correction in genome-wide association studies: Comparison of different methods to control for population stratification . Briefings in Bioinformatics .
   Google Scholar
• Samani , N. J. , Erdmann , J. , Hall , A. S. , Hengstenberg , C. , Mangino , M. Mayer , B. 2007 . Genomewide association analysis of coronary artery disease . New England Journal of Medicine , 357 ( 5 ) : 443 – 453 .
   PubMed Web of Science ®Google Scholar
• Seasholtz , T. M. , Wessel , J. , Rao , F. , Rana , B. K. , Khandrika , S. Kennedy , B. P. 2006 . Rho kinase polymorphism influences blood pressure and systemic vascular resistance in human twins: Role of Heredity . Hypertension , 47 ( 5 ) : 937 – 947 .
   PubMed Web of Science ®Google Scholar
• Serre , D. , Montpetit , A. , Pare , G. , Engert , J. C. , Yusuf , S. Keavney , B. 2008 . Correction of population stratification in large multi-ethnic association studies . PLoS ONE , 3 ( 1 ) : e1382
   PubMed Web of Science ®Google Scholar
• Shenton , M. E. , Dickey , C. C. , Frumin , M. and McCarley , R. W. 2001 . A review of MRI findings in schizophrenia . Schizophrenia Research , 49 ( 1–2 ) : 1 – 52 .
   PubMed Web of Science ®Google Scholar
• Shifman , S. , Bronstein , M. , Sternfeld , M. , Pisante-Shalom , A. , Lev-Lehman , E. Weizman , A. 2002 . A highly significant association between a COMT haplotype and schizophrenia . American Journal of Human Genetics , 71 ( 6 ) : 1296 – 1302 .
   PubMed Web of Science ®Google Scholar
• Skol , A. D. , Scott , L. J. , Abecasis , G. R. and Boehnke , M. 2007 . Optimal designs for two-stage genome-wide association studies . Genetic Epidemiology , 31 ( 7 ) : 776 – 788 .
   PubMed Web of Science ®Google Scholar
• Slawski , M. , Daumer , M. and Boulesteix , A. L. 2008 . CMA: A comprehensive Bioconductor package for supervised classification with high dimensional data . BMC Bioinformatics , 9 : 439
   PubMed Web of Science ®Google Scholar
• Stranger , B. E. , Forrest , M. S. , Clark , A. G. , Minichiello , M. J. , Deutsch , S. Lyle , R. 2005 . Genome-wide associations of gene expression variation in humans . PLoS Genetics , 1 ( 6 ) : e78
   Web of Science ®Google Scholar
• Tamminga , C. A. 2006 . The neurobiology of cognition in schizophrenia . Journal of Clinical Psychiatry , 67 (Suppl. 9) , 9 – 13 ; discussion 36–42 .
   PubMed Web of Science ®Google Scholar
• Teo , Y. Y. 2008 . Common statistical issues in genome-wide association studies: A review on power, data quality control, genotype calling and population structure . Current Opinion in Lipidology , 19 ( 2 ) : 133 – 143 .
   PubMed Web of Science ®Google Scholar
• Thomas , D. C. 2006 . Are we ready for genome-wide association studies? . Cancer Epidemiology Biomarkers Prevention , 15 ( 4 ) : 595 – 598 .
   PubMed Web of Science ®Google Scholar
• Thomas , P. D. , Campbell , M. J. , Kejariwal , A. , Mi , H. , Karlak , B. Daverman , R. 2003 . PANTHER: A library of protein families and subfamilies indexed by function . Genome Research , 13 ( 9 ) : 2129 – 2141 .
   PubMed Web of Science ®Google Scholar
• Thomas , D. C. , Haile , R. W. and Duggan , D. 2005 . Recent developments in genomewide association scans: A workshop summary and review . American Journal of Human Genetics , 77 ( 3 ) : 337 – 345 .
   PubMed Web of Science ®Google Scholar
• Vawter , M. P. , Shannon Weickert , C. , Ferran , E. , Matsumoto , M. , Overman , K. Hyde , T. M. 2004 . Gene expression of metabolic enzymes and a protease inhibitor in the prefrontal cortex are decreased in schizophrenia . Neurochemical Research , 29 ( 6 ) : 1245 – 1255 .
   PubMed Web of Science ®Google Scholar
• Walters , J. T. and Owen , M. J. 2007 . Endophenotypes in psychiatric genetics . Molecular Psychiatry , 12 ( 10 ) : 886 – 890 .
   PubMed Web of Science ®Google Scholar
• Wang , L. Y. , Comaniciu , D. and Fasulo , D. 2006 . Exploiting interactions among polymorphisms contributing to complex disease traits with boosted generative modeling . Journal of Computational Biology , 13 ( 10 ) : 1673 – 1684 .
   PubMed Web of Science ®Google Scholar
• Weinberger , D. R. , Berman , K. F. and Zec , R. F. 1986 . Physiologic dysfunction of dorsolateral prefrontal cortex in schizophrenia: I. Regional cerebral blood flow evidence . Archives of General Psychiatry , 43 ( 2 ) : 114 – 124 .
   PubMed Web of Science ®Google Scholar
• Westfall , P. H. and Young , S. S. 1993 . Resampling-based multiple testing: Examples and methods for p-value adjustment , New York : John Wiley & Sons .
   Google Scholar
• WTCCC 2007 . Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls . Nature , 447 (7145) , 661 – 678 .
   PubMed Web of Science ®Google Scholar
• Yamada , R. and Okada , Y. 2009 . An optimal dose-effect mode trend test for SNP genotype tables . Genetic Epidemiology , 33 ( 2 ) : 114 – 127 .
   PubMed Web of Science ®Google Scholar
• Ziegler , A. , Konig , I. R. and Thompson , J. R. 2008 . Biostatistical aspects of genome-wide association studies . Biometrical Journal , 50 ( 1 ) : 8 – 28 .
   PubMed Web of Science ®Google Scholar
• Zielenski , J. 2000 . Genotype and phenotype in cystic fibrosis . Respiration , 67 ( 2 ) : 117 – 133 .
   PubMed Web of Science ®Google Scholar
• Zondervan , K. T. and Cardon , L. R. 2004 . The complex interplay among factors that influence allelic association . Nature Reviews Genetics , 5 ( 2 ) : 89 – 100 .
   PubMed Web of Science ®Google Scholar
• Zondervan , K. T. and Cardon , L. R. 2007 . Designing candidate gene and genome-wide case-control association studies . Nature Protocols , 2 ( 10 ) : 2492 – 2501 .
   PubMed Web of Science ®Google Scholar