text:
schizophrenia was decreased in late adolescence. CONCLUSION: The observed changes imply that molecular mechanisms critical for adolescent brain development are disturbed in schizophrenia patients.},
affiliation = {Institute of Biotechnology, University of Cambridge, Cambridge, UK. ljwh2@cam.ac.uk},
pages = {28},
volume = {2},
year = {2009},
month = {Jan},
language = {eng},
date-added = {2010-03-31 20:05:44 +0200},
date-modified = {2010-03-31 20:05:44 +0200},
doi = {10.1186/1755-8794-2-28},
pii = {1755-8794-2-28},
pmid = {19457239},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Harris-2009-BMC%20medical%20genomics_Gene%20expression%20in%20t.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10036},
rating = {0}
}

@article{Cohen:2007p1520,
author = {Y Cohen and N Gafni and P Hanani},
title = {Translating and Adapting a Test, yet another Source of Variance; the Standard Error of Translation},
affiliation = {National Institute for Testing {\&} Evaluation (NITE), Jerusalem, Israel},
year = {2007},
date-added = {2010-01-07 15:49:36 +0100},
date-modified = {2010-01-07 15:50:20 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cohen-2007-_Translating%20and%20Adap.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1520},
rating = {0}
}

@article{Bouchard:2004p11475,
author = {T J Bouchard},
journal = {Current Directions in Psychological Science},
title = {Genetic Influence on Human
Psychological Traits. A survey},
abstract = {There is now a large body of evidence that supports the conclusion that individual differences in most, if not all, reliably measured psychological traits, normal and abnormal, are substantively influenced by genetic factors. This fact has important implications for research and theory building in psychology, as evidence of genetic influence unleashes a cascade of questions regarding the sources of variance in such traits. A brief list of those questions is provided, and representative findings regarding genetic and environmental influences are presented for the domains of personality, intelligence, psycho- logical interests, psychiatric illnesses, and social attitudes. These findings are consistent with those reported for the traits of other species and for many human physical traits, suggesting that they may represent a general biological phenomenon.},
number = {4},
pages = {148--151},
volume = {13},
year = {2004},
date-added = {2010-05-01 17:25:00 +0200},
date-modified = {2010-07-29 19:24:52 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bouchard-2004-Current%20Directions%20in%20Psychological%20Science_Genetic%20Influence%20on-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11475},
rating = {0}
}

@article{Cawley:2006p2304,
author = {G C Cawley and N L C Talbot and M Girolami},
journal = {NIPS},
title = {Sparse Multinomial Logistic Regression via Bayesian L1 Regularisation},
abstract = {Multinomial logistic regression provides the standard penalised maximum- likelihood solution to multi-class pattern recognition problems. More recently, the development of sparse multinomial logistic regression models has found ap- plication in text processing and microarray classification, where explicit identifi- cation of the most informative features is of value. In this paper, we propose a sparse multinomial logistic regression method, in which the sparsity arises from the use of a Laplace prior, but where the usual regularisation parameter is inte- grated out analytically. Evaluation over a range of benchmark datasets reveals this approach results in similar generalisation performance to that obtained using cross-validation, but at greatly reduced computational expense.},
year = {2006},
date-added = {2010-01-10 12:17:37 +0100},
date-modified = {2010-01-10 12:18:26 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cawley-2006-NIPS_Sparse%20Multinomial%20L.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2304},
rating = {0}
}

@article{Schaid:1998p1409,
author = {D J Schaid and C Rowland},
journal = {Am J Hum Genet},
title = {Use of parents, sibs, and unrelated controls for detection of associations between genetic markers and disease},
abstract = {Detecting the association between genetic markers and complex diseases can be a critical first step toward identification of the genetic basis of disease. Misleading associations can be avoided by choosing as controls the parents of diseased cases, but the availability of parents often limits this design to early-onset disease. Alternatively, sib controls offer a valid design. A general multivariate score statistic is presented, to detect the association between a multiallelic genetic marker locus and affection status; this general approach is applicable to designs that use parents as controls, sibs as controls, or even unrelated controls whose genotypes do not fit Hardy-Weinberg proportions or that pool any combination of these different designs. The benefit of this multivariate score statistic is that it will tend to be the most powerful method when multiple marker alleles are associated with affection status. To plan these types of studies, we present methods to compute sample size and power, allowing for varying sibship sizes, ascertainment criteria, and genetic models of risk. The results indicate that sib controls have less power than parental controls and that the power of sib controls can be increased by increasing either the number of affected sibs per sibship or the number of unaffected control sibs. The sample-size results indicate that the use of sib controls to test for associations, by use of either a single-marker locus or a genomewide screen, will be feasible for markers that have a dominant effect and for common alleles having a recessive effect. The results presented will be useful for investigators planning studies using sibs as controls.},
affiliation = {Departments of Health Sciences Research and Medical Genetics, Mayo Clinic/Mayo Foundation, Rochester, MN 55905, USA. schaid@mayo.edu},
number = {5},
pages = {1492--506},
volume = {63},
year = {1998},
month = {Nov},
language = {eng},
keywords = {Gene Frequency, Models: Genetic, Nuclear Family, Male, Parents, Models: Statistical, Genotype, Humans, Genetic Markers, Female, Genetic Diseases: Inborn},
date-added = {2010-01-07 12:18:35 +0100},
date-modified = {2010-07-29 19:13:31 +0200},
doi = {10.1086/302094},
pii = {S0002-9297(07)61581-X},
pmid = {9792877},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1409},
rating = {0}
}

@article{Chang:2007p6382,
author = {Chih-Hung Chang and Benjamin D Wright and David Cella and Ron D Hays},
journal = {Journal of Clinical Epidemiology},
title = {The SF-36 physical and mental health factors were confirmed in cancer and HIV/AIDS patients},
abstract = {BACKGROUND AND OBJECTIVE: This study assesses the extent to which the RAND-36/SF-36 items measure physical and mental health (PH and MH), as implied by existing summary scoring systems. METHODS: A total of 1,714 heterogeneous cancer and HIV/AIDS patients were recruited from five institutions. Of these, 56% were women; 81% Caucasians; and about 10% were from each of the major cancer types and HIV/AIDS. RESULTS: Analyses of the SF-36 confirmed the two dimensions of health namely physical and mental. However, item fit statistics and residual factor analysis revealed that some items intended to represent the PH dimension fit better with the MH dimension. CONCLUSION: This paper demonstrated the value of Rasch residual factor analysis for understanding and enhancing interpretation of health.},
affiliation = {Buehler Center on Aging, Institute for Healthcare Studies, Division of General Internal Medicine, and Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. chchang@northwestern.edu},
number = {1},
pages = {68--72},
volume = {60},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Adult, Attitude to Health, Humans, Factor Analysis: Statistical, Aged, Quality of Life, HIV Infections, Psychometrics, Mental Health, Female, Health Status Indicators, Male, Activities of Daily Living, Neoplasms, Middle Aged},
date-added = {2010-02-23 08:23:09 +0100},
date-modified = {2010-02-23 08:23:13 +0100},
doi = {10.1016/j.jclinepi.2006.07.001},
pii = {S0895-4356(06)00262-9},
pmid = {17161756},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Chang-2007-Journal%20of%20Clinical%20Epidemiology_The%20SF-36%20physical%20a.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6382},
rating = {4}
}

@article{Krzanowski:2006,
author = {W J Krzanowski},
journal = {Biometrics},
title = {Sensitivity in metric scaling and analysis of distance},
pages = {239--244},
volume = {62},
year = {2006},
date-added = {2010-01-10 11:33:24 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Krzanowski-2006-Biometrics_Sensitivity%20in%20metri.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2057},
rating = {0}
}

@article{Lecoutre:2005p11762,
author = {B Lecoutre},
journal = {Modulad},
title = {Et si vous {\'e}tiez un bay{\'e}sien qui s'ignore?},
number = {32},
pages = {92--105},
year = {2005},
date-added = {2010-05-23 10:09:59 +0200},
date-modified = {2010-07-29 19:40:18 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lecoutre-2005-Modulad_Et%20si%20vous%20%C3%A9tiez%20un.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11762},
rating = {0}
}

@article{vanderLaan:2006p4682,
author = {Mark J van der Laan and Alan E Hubbard},
journal = {Statistical Applications in Genetics and Molecular Biology},
title = {Quantile-function based null distribution in resampling based multiple testing},
abstract = {Simultaneously testing a collection of null hypotheses about a data generating distribution based on a sample of independent and identically distributed observations is a fundamental and important statistical problem involving many applications. Methods based on marginal null distributions (i.e., marginal p-values) are attractive since the marginal p-values can be based on a user supplied choice of marginal null distributions and they are computationally trivial, but they, by necessity, are known to either be conservative or to rely on assumptions about the dependence structure between the test-statistics. Re-sampling based multiple testing (Westfall and Young, 1993) involves sampling from a joint null distribution of the test-statistics, and controlling (possibly in a, for example, step-down fashion) the user supplied type-I error rate under this joint null distribution for the test-statistics. A generally asymptotically valid null distribution avoiding the need for the subset pivotality condition for the vector of test-statistics was proposed in Pollard, van der Laan (2003) for null hypotheses about general real valued parameters. This null distribution was generalized in Dudoit, vanderLaan, Pollard (2004) to general null hypotheses and test-statistics. In ongoing recent work van der Laan, Hubbard (2005), we propose a new generally asymptotically valid null distribution for the test-statistics and a corresponding bootstrap estimate, whose marginal distributions are user supplied, and can thus be set equal to the (most powerful) marginal null distributions one would use in univariate testing to obtain a p-value. Previous proposed null distributions either relied on a restrictive subset pivotality condition (Westfall and Young) or did not guarantee this latter property (Dudoit, vanderLaan, Pollard, 2004). It is argued and illustrated that the resulting new re-sampling based multiple testing methods provide more accurate control of the wished Type-I error in finite samples and are more powerful. We establish formal results and investigate the practical performance of this methodology in a simulation and data analysis.},
affiliation = {Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA. laan@stat.berkeley.edu},
pages = {Article14},
volume = {5},
year = {2006},
month = {Jan},
language = {eng},
keywords = {Epidemiologic Research Design, Computer Simulation, Sampling Studies, Statistical Distributions, Probability, Chi-Square Distribution, Selection Bias, Data Interpretation: Statistical, Models: Statistical, Genomics, Proteomics},
date-added = {2010-01-30 16:12:43 +0100},
date-modified = {2010-01-30 16:12:53 +0100},
doi = {10.2202/1544-6115.1199},
pmid = {17049025},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4682},
rating = {4}
}

@article{Murray:2010p4607,
author = {C J L Murray and A Tandon and J A Salomon and C D Mathers and R Sadana},
title = {New approaches to enhance cross-population comparability of survey results},
date-added = {2010-01-29 22:56:22 +0100},
date-modified = {2010-01-29 22:57:06 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Murray--_New%20approaches%20to%20en.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4607},
rating = {0}
}

@article{Robinson:2008p5887,
author = {Peter N Robinson and Sebastian K{\"o}hler and Sebastian Bauer and Dominik Seelow and Denise Horn and Stefan Mundlos},
journal = {Am J Hum Genet},
title = {The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease},
abstract = {There are many thousands of hereditary diseases in humans, each of which has a specific combination of phenotypic features, but computational analysis of phenotypic data has been hampered by lack of adequate computational data structures. Therefore, we have developed a Human Phenotype Ontology (HPO) with over 8000 terms representing individual phenotypic anomalies and have annotated all clinical entries in Online Mendelian Inheritance in Man with the terms of the HPO. We show that the HPO is able to capture phenotypic similarities between diseases in a useful and highly significant fashion.},
affiliation = {Institute for Medical Genetics, Charit{\'e}-Universit{\"a}tsmedizin Berlin, 13353 Berlin, Germany. peter.robinson@charite.de},
number = {5},
pages = {610--5},
volume = {83},
year = {2008},
month = {Nov},
language = {eng},
keywords = {Software, Humans, Databases: Genetic, Computational Biology, Genetic Diseases: Inborn, Phenotype},
date-added = {2010-02-17 15:25:05 +0100},
date-modified = {2010-02-17 15:25:05 +0100},
doi = {10.1016/j.ajhg.2008.09.017},
pii = {S0002-9297(08)00535-1},
pmid = {18950739},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Robinson-2008-Am%20J%20Hum%20Genet_The%20Human%20Phenotype.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5887},
rating = {0}
}

@article{Baiocchi:2004p4644,
author = {G Baiocchi},
journal = {Journal of Statistical Software},
title = {Using Perl for Statistics: Data Processing and Statistical Computing},
abstract = {In this paper we show how Perl, an expressive and extensible high-level programming language, with network and object-oriented programming support, can be used in process- ing data for statistics and statistical computing. The paper is organized in two parts. In Part I, we introduce the Perl programming language, with particular emphasis on the fea- tures that distinguish it from conventional languages. Then, using practical examples, we demonstrate how Perl's distinguishing features make it particularly well suited to perform labor intensive and sophisticated tasks ranging from the preparation of data to the writing of statistical reports. In Part II we show how Perl can be extended to perform statistical computations using modules and by ``embedding'' specialized statistical applications. We provide example on how Perl can be used to do simple statistical analyses, perform com- plex statistical computations involving matrix algebra and numerical optimization, and make statistical computations more easily reproducible. We also investigate the numerical and statistical reliability of various Perl statistical modules. Important computing issues such as ease of use, speed of calculation, and efficient memory usage, are also considered.},
number = {1},
volume = {11},
year = {2004},
date-added = {2010-01-30 15:55:03 +0100},
date-modified = {2010-01-30 15:55:46 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Baiocchi-2004-Journal%20of%20Statistical%20Software_Using%20Perl%20for%20Stati.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4644},
rating = {0}
}

@article{Herold:2009p377,
author = {Christine Herold and Tim Becker},
journal = {Bioinformatics},
title = {Genetic association analysis with FAMHAP: a major program update},
abstract = {FAMHAP is an established software for haplotype association analysis of nuclear families. We have released a major update that comprises various new features for case-control data. Furthermore, weprovide an additional program runFamhap that allows users to start the same method repeatedly for varying sets of genetic markers. In addition, a platform-independent graphical user interface (GUI) was developed to simplify the usage of both FAMHAP and runFamhap. The runFamhap program greatly facilitates the application of FAMHAP to genome-wide association studies (GWAS) and supports flexible genome-wide haplotype analysis. As an example, we describe application to HapMap data. AVAILABILITY: The software is available at http://famhap.meb.uni-bonn.de},
affiliation = {Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany. herold@imbie.meb.uni-bonn.de},
number = {1},
pages = {134--6},
volume = {25},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Software, Humans, Computational Biology, Haplotypes, Genome-Wide Association Study},
date-added = {2010-01-03 11:49:04 +0100},
date-modified = {2010-01-03 11:49:04 +0100},
doi = {10.1093/bioinformatics/btn581},
pii = {btn581},
pmid = {19015131},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Herold-2009-Bioinformatics_Genetic%20association.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p377},
rating = {0}
}

@article{Myaskovsky:2006p13148,
author = {L Myaskovsky and M A Dew and M L McNulty and G E Switzer and A F DiMartini and R L Kormos and K R McCurry},
journal = {Am J Transplant},
title = {Trajectories of change in quality of life in 12-month survivors of lung or heart transplant},
abstract = {Survival and functional outcomes for lung transplant recipients continue to lag behind those for heart recipients. Whether these poorer physical outcomes translate into poorer quality of life (QOL) for lung recipients relative to heart recipients is unknown. Lung versus heart transplant recipients' perceptions of QOL were longitudinally compared at three time-points across the first year posttransplant. Additionally, potentially important predictors of patient QOL were examined. Adult transplant recipients (N = 199) participated in semi-structured interviews that included measures of QOL, optimism, mastery, social support, religiosity and coping. Temporal patterns of QOL change were compared between lung and heart recipients who survived until 1 year posttransplant using mixed-model, hierarchical analysis of variance (ANOVA). Demographic and psychosocial predictors were examined with multiple regression analysis to identify the unique effects of each variable on QOL 1 year posttransplant. While heart recipients' QOL across several domains was higher shortly after transplant, lung patients' QOL improved and was equivalent to that of heart recipients by 1 year posttransplant. Greater optimism and support from friends predicted better QOL in physical, psychological and social domains. Conversely, avoidant coping strategies predicted poorer physical functioning. Thus, while clinical interventions designed to improve QOL posttransplant should be tailored to transplant recipients' initial psychosocial assets and liabilities, they need not be distinguished by transplant type.},
affiliation = {V.A. Center for Health Equity Research and Promotion, University of Pittsburgh, Pennsylvania, USA. myaskovskyl@upmc.edu},
number = {8},
pages = {1939--47},
volume = {6},
year = {2006},
month = {Aug},
language = {eng},
keywords = {Follow-Up Studies, Male, Heart Transplantation, Time Factors, Health, Treatment Outcome, Graft Survival, Female, Middle Aged, Quality of Life, Humans, Questionnaires, Lung Transplantation},
date-added = {2010-06-26 11:07:27 +0200},
date-modified = {2010-06-26 11:07:28 +0200},
doi = {10.1111/j.1600-6143.2006.01395.x},
pii = {AJT1395},
pmid = {16889548},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13148},
rating = {0}
}

@article{Revuelta:2004,
author = {Javier Revuelta},
journal = {Psychometrika},
title = {Analysis of distractor difficulty in Multiple-Choice items},
abstract = {Two psychometric models are presented for evaluating the difficulty of the distractors in multiple-choice items. They are based on the criterion of rising distractor selection ratios, which facilitates interpretation of the subject and item parameters. Statistical inferential tools are developed in a Bayesian framework: modal a posteriori estimation by application of an EM algorithm and model evaluation by monitoring posterior predictive replications of the data matrix. An educational example with real data is included to exemplify the application of the models and compare them with the nominal categories model.},
number = {2},
pages = {217--234},
volume = {69},
year = {2004},
date-added = {2010-01-10 11:33:25 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2067},
rating = {0}
}

@article{Zoanetti:2006p2385,
author = {N Zoanetti and P Griffin and R J Adams},
title = {Applications of Item Response Theory to identify and account for suspect rater data},
year = {2006},
date-added = {2010-01-10 19:33:47 +0100},
date-modified = {2010-07-29 20:16:39 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zoanetti-2006-_Applications%20of%20Item.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2385},
rating = {0}
}

@article{Lennox:1996p6829,
author = {R D Lennox and G A Zarkin and J W Bray},
journal = {J Subst Abuse},
title = {Latent variable models of alcohol-related constructs},
abstract = {This study examines the improvement in validity coefficients and structural relationships derived from formally modeling latent variables of adverse alcohol-related constructs. Results of a confirmatory factor analysis of responses from 8,755 participants in the 1988 National Household Survey of Drug Abuse support a three-factor model of alcohol abuse, dependence, and adverse consequences. A comparison of construct intercorrelations shows latent variables to be superior to measurement approaches using unweighted sums, quantity x frequency calculation, and single-item measurement.},
affiliation = {Applied Psychometrics Laboratory, Research Triangle Institute, Research Triangle Park, NC 27709-2194, USA.},
number = {2},
pages = {241--50},
volume = {8},
year = {1996},
month = {Jan},
language = {eng},
keywords = {Psychometrics, Female, Male, Adult, Humans, Adolescent, Alcoholism, Middle Aged, Internal-External Control, Reproducibility of Results, Health Knowledge: Attitudes: Practice, Alcohol Drinking, Personality Assessment},
date-added = {2010-03-06 09:31:33 +0100},
date-modified = {2010-03-06 09:31:39 +0100},
pii = {S0899-3289(96)90282-5},
pmid = {8880663},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lennox-1996-J%20Subst%20Abuse_Latent%20variable%20mode.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6829},
rating = {3}
}

@article{Molko:2003p4970,
author = {Nicolas Molko and Arnaud Cachia and Denis Rivi{\`e}re and Jean Fran{\c c}ois Mangin and Marie Bruandet and Denis Le Bihan and Laurent Cohen and Stanislas Dehaene},
journal = {Neuron},
title = {Functional and structural alterations of the intraparietal sulcus in a developmental dyscalculia of genetic origin},
abstract = {Cognitive theories of numerical representation suggest that understanding of numerical quantities is driven by a magnitude representation associated with the intraparietal sulcus and possibly under genetic control. The aim of this study was to investigate, using fMRI and structural imaging, the interaction between the abnormal development of numerical representation in an X-linked condition, Turner syndrome (TS), and the development of the intraparietal sulcus. fMRI during exact and approximate calculation in TS showed an abnormal modulation of intraparietal activations as a function of number size. Morphological analysis revealed an abnormal length, depth, and sulcal geometry of the right intraparietal sulcus, suggesting an important disorganization of this region in TS. Thus, a genetic form of developmental dyscalculia can be related to both functional and structural anomalies of the right intraparietal sulcus, suggesting a crucial role of this region in the development of arithmetic abilities.},
affiliation = {INSERM U 562, Cognitive Neuroimaging, Service Hospitalier Fr{\'e}d{\'e}ric Joliot, CEA/DSV, IFR 49 Orsay, France. molko@wanadoo.fr},
number = {4},
pages = {847--58},
volume = {40},
year = {2003},
month = {Nov},
language = {eng},
keywords = {Parietal Lobe, Brain Mapping, Mathematics, Magnetic Resonance Imaging, Functional Laterality, Nervous System Malformations, Genetic Variation, Chromosomes: Human: X, Male, Adult, Female, Turner Syndrome, Learning Disorders, Humans, Nerve Net, Neuropsychological Tests, Neural Pathways},
date-added = {2010-02-05 00:05:31 +0100},
date-modified = {2010-02-05 00:05:31 +0100},
pii = {S0896627303006706},
pmid = {14622587},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Molko-2003-Neuron_Functional%20and%20struc.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4970},
rating = {0}
}

@article{Howard:2009p8355,
author = {Matthew O Howard and Brian E Perron},
journal = {BMC Psychiatry},
title = {A survey of inhalant use disorders among delinquent youth: prevalence, clinical features, and latent structure of DSM-IV diagnostic criteria},
abstract = {BACKGROUND: Inhalant use is among the most pernicious and poorly understood forms of adolescent substance use. Many youth in the juvenile justice system have used inhalants, but little is known about inhalant use disorders (IUDs) in antisocial youth populations. The purpose of this study was to examine the prevalence, clinical features, and latent structure of DSM-IV IUDs in a state population of antisocial youth. METHODS: Cross-sectional survey conducted in 2003. Of 740 youth residing in Missouri State Division of Youth Services' (MDYS) residential treatment facilities at the time the study was conducted, 723 (97.7%) completed interviews. Eighty-seven percent were male, with a mean age of 15.5 (SD = 1.2). Nearly 4 in 10 youth (38.5%; n = 279) reported lifetime inhalant use. Youth ranged from very mildly to severely antisocial. RESULTS: Of 279 inhalant users, 52 (18.6%) met DSM-IV inhalant abuse criteria and 79 (28.3%) met inhalant dependence criteria. Five of 10 IUD criteria were met by > 10% of the total sample. Latent class analyses demonstrated a substantial concordance between DSM-IV-defined IUDs and an empirically-derived classification based on responses to DSM-IV IUD diagnostic criteria. CONCLUSION: IUDs and constituent criteria were prevalent among youth in the juvenile justice system. Two groups of problem inhalant users were identified, symptomatic users-DSM-IV inhalant abuse and highly symptomatic users-DSM-IV inhalant dependence, which differed primarily in severity of inhalant-related problems. Inhalant screening, prevention and treatment efforts in juvenile justice settings are rarely delivered, but critically needed.},
affiliation = {University of North Carolina at Chapel Hill, Tate-Turner-Kuralt Building, Campus Box 3550, 325 Pittsboro Street, Chapel Hill, NC 27599-3550, USA. mohoward@email.unc.edu},
pages = {8},
volume = {9},
year = {2009},
month = {Jan},
language = {eng},
keywords = {Male, Young Adult, Administration: Inhalation, Female, Humans, Adolescent, Prevalence, Child, Juvenile Delinquency, Substance-Related Disorders, Psychiatric Status Rating Scales, Cross-Sectional Studies, Residential Facilities, Diagnostic and Statistical Manual of Mental Disorders},
date-added = {2010-03-21 12:59:08 +0100},
date-modified = {2010-03-21 12:59:08 +0100},
doi = {10.1186/1471-244X-9-8},
pii = {1471-244X-9-8},
pmid = {19267939},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Howard-2009-BMC%20Psychiatry_A%20survey%20of%20inhalant.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8355},
rating = {0}
}

@article{Baser:2009p11801,
author = {Onur Baser},
journal = {Value Health},
title = {Too Much Ado about Instrumental Variable Approach: Is the Cure Worse than the Disease?},
abstract = {ABSTRACT Objective: To review the efficacy of instrumental variable (IV) models in addressing a variety of assumption violations to ensure standard ordinary least squares (OLS) estimates are consistent. IV models gained popularity in outcomes research because of their ability to consistently estimate the average causal effects even in the presence of unmeasured confounding. However, in order for this consistent estimation to be achieved, several conditions must hold. In this article, we provide an overview of the IV approach, examine possible tests to check the prerequisite conditions, and illustrate how weak instruments may produce inconsistent and inefficient results. Methods: We use two IVs and apply Shea's partial R-square method, the Anderson canonical correlation, and Cragg-Donald tests to check for weak instruments. Hall-Peixe tests are applied to see if any of these instruments are redundant in the analysis. Results: A total of 14,952 asthma patients from the MarketScan Commercial Claims and Encounters Database were examined in this study. Patient health care was provided under a variety of fee-for-service, fully capitated, and partially capitated health plans, including preferred provider organizations, point of service plans, indemnity plans, and health maintenance organizations. We used controller-reliever copay ratio and physician practice/prescribing patterns as an instrument. We demonstrated that the former was a weak and redundant instrument producing inconsistent and inefficient estimates of the effect of treatment. The results were worse than the results from standard regression analysis. Conclusion: Despite the obvious benefit of IV models, the method should not be used blindly. Several strong conditions are required for these models to work, and each of them should be tested. Otherwise, bias and precision of the results will be statistically worse than the results achieved by simply using standard OLS.},
affiliation = {STATinMED Research, LLC, and Department of Surgery, University of Michigan, Ann Arbor, MI, USA.},
pages = {},
year = {2009},
month = {May},
language = {ENG},
date-added = {2010-05-23 10:40:49 +0200},
date-modified = {2010-05-23 10:40:49 +0200},
doi = {10.1111/j.1524-4733.2009.00567.x},
pii = {VHE567},
pmid = {19497084},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Baser-2009-Value%20Health_Too%20Much%20Ado%20about%20I.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11801},
rating = {0}
}

@article{Newell:2010p4740,
author = {A Newell and H A Simon},
title = {Computer science as empirical inquiry: Symbols and search},
date-added = {2010-01-30 16:26:38 +0100},
date-modified = {2010-01-30 16:27:22 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Newell--_Computer%20science%20as.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4740},
rating = {0}
}

@article{Carey:2005p10330,
author = {Gregory Carey},
journal = {Behav Genet},
title = {The intraclass covariance matrix},
abstract = {Introduced by C.R. Rao in 1945, the intraclass covariance matrix has seen little use in behavioral genetic research, despite the fact that it was developed to deal with family data. Here, I reintroduce this matrix, and outline its estimation and basic properties for data sets on pairs of relatives. The intraclass covariance matrix is appropriate whenever the research design or mathematical model treats the ordering of the members of a pair as random. Because the matrix has only one estimate of a population variance and covariance, both the observed matrix and the residual matrix from a fitted model are easy to inspect visually; there is no need to mentally average homologous statistics. Fitting a model to the intraclass matrix also gives the same log likelihood, likelihood-ratio (LR) chi2, and parameter estimates as fitting that model to the raw data. A major advantage of the intraclass matrix is that only two factors influence the LR chi2--the sampling error in estimating population parameters and the discrepancy between the model and the observed statistics. The more frequently used interclass covariance matrix adds a third factor to the chi2--sampling error of homologous statistics. Because of this, the degrees of freedom for fitting models to an intraclass matrix differ from fitting that model to an interclass matrix. Future research is needed to establish differences in power-if any--between the interclass and the intraclass matrix.},
affiliation = {Department of Psychology and Institute for Behavioral Genetics, University of Colorado, Boulder, CO 80309-0345, USA. gregory.carey@colorado.edu},
number = {5},
pages = {667--70},
volume = {35},
year = {2005},
month = {Sep},
language = {eng},
keywords = {Twins, Humans, Animals, Models: Genetic, Genetic Variation, Algorithms, Linear Models, Models: Statistical, Chi-Square Distribution, Twin Studies as Topic, Likelihood Functions, Genetics: Behavioral},
date-added = {2010-04-02 18:14:09 +0200},
date-modified = {2010-07-29 20:09:06 +0200},
doi = {10.1007/s10519-005-5877-1},
pmid = {16184492},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Carey-2005-Behav%20Genet_The%20intraclass%20covar.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p10330},
rating = {0}
}

@article{Fox:2005p12801,
author = {J-P Fox and C A W Glas},
journal = {Statistica Neerlandica},
title = {Bayesian modification indices for IRT models},
abstract = {Bayesian modification indices are presented that provide information for the process of model evaluation and model modification. These indices can be used to investigate the improvement in a model if fixed parameters are re-specified as free parameters. The indices can be seen as a Bayesian analogue to the modification indices commonly used in a frequentist framework. The aim is to provide diagnostic information for multi-parameter models where the number of possible model violations and the related number of alternative models is too large to render estimation of each alternative practical. As an example, the method is applied to an item response theory (IRT) model, that is, to the two-parameter model. The method is used to investigate differential item functioning and violations of the assump- tion of local independence.},
number = {1},
pages = {95--106},
volume = {59},
year = {2005},
date-added = {2010-06-18 22:41:07 +0200},
date-modified = {2010-06-18 22:46:58 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Fox-2005-Statistica%20Neerlandica_Bayesian%20modificatio-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12801},
rating = {0}
}

@article{Romano:2006p4358,
author = {Joseph P Romano and Azeem M Shaikh},
journal = {arXiv},
title = {Stepup procedures for control of generalizations of the familywise error  rate},
abstract = { Consider the multiple testing problem of testing null hypotheses {\$}H_1,...,H_s{\$}. A classical approach to dealing with the multiplicity problem is to restrict attention to procedures that control the familywise error rate ({\$}\mathit{FWER}{\$}), the probability of even one false rejection. But if {\$}s{\$} is large, control of the {\$}\mathit{FWER}{\$} is so stringent that the ability of a procedure that controls the {\$}\mathit{FWER}{\$} to detect false null hypotheses is limited. It is therefore desirable to consider other measures of error control. This article considers two generalizations of the {\$}\mathit{FWER}{\$}. The first is the {\$}k-\mathit{FWER}{\$}, in which one is willing to tolerate {\$}k{\$} or more false rejections for some fixed {\$}k\geq 1{\$}. The second is based on the false discovery proportion ({\$}\mathit{FDP}{\$}), defined to be the number of false rejections divided by the total number of rejections (and defined to be 0 if there are no rejections). Benjamini and Hochberg [J. Roy. Statist. Soc. Ser. B 57 (1995) 289-300] proposed control of the false discovery rate ({\$}\mathit{FDR}{\$}), by which they meant that, for fixed {\$}\alpha{\$}, {\$}E(\mathit{FDP})\leq\alpha{\$}. Here, we consider control of the {\$}\mathit{FDP}{\$} in the sense that, for fixed {\$}\gamma{\$} and {\$}\alpha{\$}, {\$}P\{\mathit{FDP}>\gamma\}\leq \alpha{\$}. Beginning with any nondecreasing sequence of constants and {\$}p{\$}-values for the individual tests, we derive stepup procedures that control each of these two measures of error control without imposing any assumptions on the dependence structure of the {\$}p{\$}-values. We use our results to point out a few interesting connections with some closely related stepdown procedures. We then compare and contrast two {\$}\mathit{FDP}{\$}-controlling procedures obtained using our results with the stepup procedure for control of the {\$}\mathit{FDR}{\$} of Benjamini and Yekutieli [Ann. Statist. 29 (2001) 1165-1188]. },
annote = {Published in: Annals of Statistics 2006, Vol. 34, No. 4, 1850-1873

Published at http://dx.doi.org/10.1214/009053606000000461 in the
  Annals of Statistics (http://www.imstat.org/aos/) by the Institute of
  Mathematical Statistics (http://www.imstat.org)},
eprint = {math/0611266v1},
volume = {math.ST},
year = {2006},
month = {Jan},
keywords = {62J15 (Primary), stat.TH, math.ST},
date-added = {2010-01-27 18:30:00 +0100},
date-modified = {2010-01-27 18:30:00 +0100},
doi = {10.1214/009053606000000461},
pmid = {math/0611266v1},
URL = {http://arxiv.org/abs/math/0611266v1},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4358},
rating = {0}
}

@article{Johansson:2003p8013,
author = {Carolina Johansson and Matth{\"a}eus Willeit and Christina Smedh and Jenny Ekholm and Tiina Paunio and Tuula Kiesepp{\"a} and Dirk Lichtermann and Nicole Praschak-Rieder and Alexander Neumeister and Lars-G{\"o}ran Nilsson and Siegfried Kasper and Leena Peltonen and Rolf Adolfsson and Martin Schalling and Timo Partonen},
journal = {Neuropsychopharmacology},
title = {Circadian clock-related polymorphisms in seasonal affective disorder and their relevance to diurnal preference},
abstract = {Disturbed circadian rhythms have been observed in seasonal affective disorder (SAD). The aim of this study was to further investigate this connection, and to test for potential association between polymorphisms in circadian clock-related genes and SAD, seasonality (seasonal variations in mood and behavior), or diurnal preference (morningness-eveningness tendencies). A total of 159 European SAD patients and 159 matched controls were included in the genetic analysis, and subsets were screened for seasonality (n=177) and diurnal preference (n=92). We found that diurnal preference was associated with both SAD and seasonality, supporting the hypothesis of a link between circadian rhythms and seasonal depression. The complete case-control material was genotyped for polymorphisms in the CLOCK, Period2, Period3, and NPAS2 genes. A significant difference between patients and controls was found for NPAS2 471 Leu/Ser (chi(2)=9.90, Bonferroni corrected P=0.035), indicating a recessive effect of the leucine allele on disease susceptibility (chi(2)=6.61, Bonferroni corrected P=0.050). Period3 647 Val/Gly was associated with self-reported morningness-eveningness scores (n=92, one-way ANOVA: F=4.99, Bonferroni corrected P=0.044), with higher scores found in individuals with at least one glycine allele (t=3.1, Bonferroni corrected P=0.013). A second, population-based sample of individuals selected for high (n=127) or low (n=98) degrees of seasonality, was also genotyped for NPAS2 471 Leu/Ser. There was no significant difference between these seasonality extreme groups, and none of the polymorphisms studied were associated with seasonality in the SAD case-control material (n=177). In conclusion, our results suggest involvement of circadian clock-related polymorphisms both in susceptibility to SAD and diurnal preference.},
affiliation = {Neurogenetics Unit, Department of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden. carolina.johansson@cmm.ki.se},
number = {4},
pages = {734--9},
volume = {28},
year = {2003},
month = {Apr},
language = {eng},
keywords = {Basic Helix-Loop-Helix Transcription Factors, Proteins, Trans-Activators, Nerve Tissue Proteins, Case-Control Studies, Statistics: Nonparametric, CLOCK Proteins, Period Circadian Proteins, Polymorphism: Genetic, Circadian Rhythm, Genotype, Analysis of Variance, Male, Humans, Transcription Factors, Seasonal Affective Disorder, Chi-Square Distribution, Female, Nuclear Proteins},
date-added = {2010-03-20 19:35:27 +0100},
date-modified = {2010-03-20 19:35:27 +0100},
doi = {10.1038/sj.npp.1300121},
pii = {1300121},
pmid = {12655319},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Johansson-2003-Neuropsychopharmacology_Circadian%20clock-rela.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8013},
rating = {0}
}

@article{Haley:1994p5964,
author = {S M Haley and C A McHorney and J E Ware},
journal = {Journal of Clinical Epidemiology},
title = {Evaluation of the MOS SF-36 physical functioning scale (PF-10): I. Unidimensionality and reproducibility of the Rasch item scale},
abstract = {Indexes developed to measure physical functioning as an essential component of general health status are often based on sets of hierarchically-structured items intended to represent a broad underlying concept. Rasch Item Response Theory (IRT) provides a methodology to examine the hierarchical structure, unidimensionality, and reproducibility of item positions (calibrations) along a scale. Data gathered on the 10-item Physical Functioning Scale (PF-10) from a large sample of Medical Outcomes Study patients (N = 3445) were used to examine the hierarchical order, unidimensionality, and reproducibility of item calibrations. Rasch-IRT analyses generated an empirical item hierarchy, confirmed the unidimensionality of the PF-10 for most patients, and established the reproducibility of item calibrations across patient populations and repeated tests. These findings support the content validity of the PF-10 as a measure of physical functioning and suggest that valid Rasch-IRT summary scores could be generated as an alternative to the current Likert summative scores. Unidimensionality and reproducibility of the item scale are essential prerequisites for the development of Rasch-based person measures of physical functioning that can be used across populations and over repeated tests.},
affiliation = {Health Institute, New England Medical Center Hospitals, Boston, MA 02111, USA.},
number = {6},
pages = {671--84},
volume = {47},
year = {1994},
month = {Jun},
language = {eng},
keywords = {Aged, Reproducibility of Results, Health Status Indicators, Activities of Daily Living, Chronic Disease, Middle Aged, Humans},
date-added = {2010-02-18 23:29:00 +0100},
date-modified = {2010-02-18 23:29:00 +0100},
pii = {0895-4356(94)90215-1},
pmid = {7722580},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5964},
rating = {0}
}

@article{Wang:2007p4000,
author = {Rui Wang and Stephen W Lagakos and James H Ware and David J Hunter and Jeffrey M Drazen},
journal = {N Engl J Med},
title = {Statistics in medicine--reporting of subgroup analyses in clinical trials},
number = {21},
pages = {2189--94},
volume = {357},
year = {2007},
month = {Nov},
language = {eng},
keywords = {Quality Control, Data Interpretation: Statistical, Statistics as Topic, Clinical Trials as Topic},
date-added = {2010-01-17 23:24:15 +0100},
date-modified = {2010-07-29 19:53:14 +0200},
doi = {10.1056/NEJMsr077003},
pii = {357/21/2189},
pmid = {18032770},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Wang-2007-N%20Engl%20J%20Med_Statistics%20in%20medici.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4000},
rating = {0}
}

@article{Matsuo:2009p9683,
author = {Koji Matsuo and Mark Nicoletti and Kiyotaka Nemoto and John P Hatch and Marco A M Peluso and Fabiano G Nery and Jair C Soares},
journal = {Hum Brain Mapp},
title = {A voxel-based morphometry study of frontal gray matter correlates of impulsivity},
abstract = {Impulsivity is a personality trait exhibited by healthy individuals, but excessive impulsivity is associated with some mental disorders. Lesion and functional neuroimaging studies indicate that the ventromedial prefrontal region (VMPFC), including the orbitofrontal cortex (OFC), anterior cingulate cortex (ACC) and medial prefrontal cortex, and the amygdala may modulate impulsivity and aggression. However, no morphometric study has examined the association between VMPFC and impulsivity. We hypothesized that healthy subjects with high impulsivity would have smaller volumes in these brain regions compared with those with low impulsivity. Sixty-two healthy subjects were studied (age 35.4 +/- 12.1 years) using a 1.5-T MRI system. The Barratt impulsiveness scale (BIS) was used to assess impulsivity. Images were processed using an optimized voxel-based morphometry (VBM) protocol. We calculated the correlations between BIS scale scores and the gray matter (GM) and white matter (WM) volumes of VMPFC and amygdala. GM volumes of the left and right OFC were inversely correlated with the BIS total score (P = 0.04 and 0.02, respectively). Left ACC GM volumes had a tendency to be inversely correlated with the BIS total score (P = 0.05). Right OFC GM volumes were inversely correlated with BIS nonplanning impulsivity, and left OFC GM volumes were inversely correlated with motor impulsivity. There were no significant WM volume correlations with impulsivity. The results of this morphometry study indicate that small OFC volume relate to high impulsivity and extend the prior finding that the VMPFC is involved in the circuit modulating impulsivity.},
affiliation = {Department of Psychiatry, University of Texas Health Science Center at San Antonio, Texas, USA.},
note = {genim},
number = {4},
pages = {1188--95},
volume = {30},
year = {2009},
month = {Apr},
language = {eng},
keywords = {Functional Laterality, Aged, Psychiatric Status Rating Scales, Frontal Lobe, Middle Aged, Adult, Male, Brain Mapping, Female, Magnetic Resonance Imaging, Humans, Impulsive Behavior, Young Adult, Statistics as Topic, Image Processing: Computer-Assisted},
date-added = {2010-03-25 15:10:28 +0100},
date-modified = {2010-03-25 18:18:53 +0100},
doi = {10.1002/hbm.20588},
pmid = {18465751},
URL = {http://www3.interscience.wiley.com/journal/119054049/abstract},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Matsuo-2009-Hum%20Brain%20Mapp_A%20voxel-based%20morpho.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9683},
rating = {0}
}

@article{Graham:2003p7446,
author = {Brent Graham and Glenn Regehr and James G Wright},
journal = {Journal of Clinical Epidemiology},
title = {Delphi as a method to establish consensus for diagnostic criteria},
abstract = {BACKGROUND/OBJECTIVES: To achieve a consensus, among a panel of experts, on the best clinical criteria for the clinical diagnosis of carpal tunnel syndrome (CTS). METHODS: Experts rated the diagnostic importance of items from the clinical history and physical examination for CTS. The ratings were expressed on a 10-cm visual analog scale. The average and standard deviation of the scores for each item were returned to the panelists. The panel members evaluated the items a second time with knowledge of the group responses from the first round. The scores were standardized to minimize scaling variations and, after the second round, the items were ranked in order of importance assigned by the group. Cronbach's alpha was used as a measure of homogeneity for the rankings. Increasing homogeneity was considered to be an indication of consensus among the panelists. RESULTS: Cronbach's alpha increased from 0.86 after the first round to 0.91 after the second iteration. Panelists who were relative outliers on the first round demonstrated a much higher correlation with the entire group after the second round. CONCLUSIONS: Delphi is an effective method of establishing consensus for certain clinical questions. Cronbach's alpha was a useful statistic for measuring the extent of consensus among the panel members. Delphi was chosen from the possible methods of group process because of its inherent feasibility. The absence of a need by the panelists to meet in person removed any constraint on the geographic location of the panel members. In addition, the anonymous nature of Delphi was thought to be a key factor in avoiding a result that might be skewed by one or more persuasive panelists. Both of these characteristics were felt to be particularly important to the topic on which consensus was sought, the clinical diagnostic criteria for CTS. This movement in the opinions of some of the panelists appeared to result from the feedback of information describing the group opinion.},
affiliation = {Toronto Western Hospital, 399 Bathurst Street, FP-174 M5T 2S8, Toronto, ON, Canada. brent.graham@utoronto.ca},
number = {12},
pages = {1150--6},
volume = {56},
year = {2003},
month = {Dec},
language = {eng},
keywords = {Diagnosis, Consensus, Practice Guidelines as Topic, Delphi Technique, Humans, Carpal Tunnel Syndrome},
date-added = {2010-03-10 20:40:42 +0100},
date-modified = {2010-03-10 20:40:42 +0100},
pii = {S0895435603002117},
pmid = {14680664},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Graham-2003-Journal%20of%20Clinical%20Epidemiology_Delphi%20as%20a%20method%20t.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7446},
rating = {0}
}

@article{Cazier:2010p4224,
author = {Jean-Baptiste Cazier and Ian Tomlinson},
journal = {J Pathol},
title = {General lessons from large-scale studies to identify human cancer predisposition genes},
abstract = {There are now about 100 genes known to cause Mendelian inherited cancer syndromes, but these only explain a minor part of the familial clustering of the common cancers. The increased familial relative risk of cancer in the general population must largely involve genes of low- or moderate-penetrance. Until recently, attempts to identify cancer predisposition genes with low penetrance had proved similarly unrewarding. However, in the past 2 years, developments in this area have been rapid. In particular, the 'common disease-common variant' model of predisposition has come to the fore. In this model, alleles of high frequency (typically > 10%) and low penetrance (typically < two-fold increased lifetime risk) contribute substantially to susceptibility to the common human diseases, including cancers. Many common risk alleles for cancer have been found by genome-wide association studies (GWASs) in the form of tagging SNPs, although identification of the disease-causing variants generally remains a difficult problem. The 'common disease-common variant' model has recently been criticized by proponents of a 'common disease-rare variant' model. In fact, the conflict between the models is false and a more continuous approach, bounded only by technical limitations and sample sizes, appears to be more appropriate. In this review, we summarize the general findings from cancer GWASs and their problems, and discuss the issues of finding rarer variants and other forms of cancer-predisposing variation, such as copy number polymorphisms.},
affiliation = {Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.},
number = {2},
pages = {255--62},
volume = {220},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-01-21 10:58:58 +0100},
date-modified = {2010-01-21 10:58:58 +0100},
doi = {10.1002/path.2650},
pmid = {19927315},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4224},
rating = {0}
}

@article{Xu:2009p12825,
author = {Zhenzhen Xu and John D Kalbfleisch},
journal = {Biometrics},
title = {Propensity Score Matching in Randomized Clinical Trials},
abstract = {Summary. Cluster randomization trials with relatively few clusters have been widely used in recent years for evaluation of health-care strategies. On average, randomized treatment assignment achieves balance in both known and unknown confounding factors between treatment groups, however, in practice investigators can only introduce a small amount of stratification and cannot balance on all the important variables simultaneously. The limitation arises especially when there are many confounding variables in small studies. Such is the case in the INSTINCT trial designed to investigate the effectiveness of an education program in enhancing the tPA use in stroke patients. In this article, we introduce a new randomization design, the balance match weighted (BMW) design, which applies the optimal matching with constraints technique to a prospective randomized design and aims to minimize the mean squared error (MSE) of the treatment effect estimator. A simulation study shows that, under various confounding scenarios, the BMW design can yield substantial reductions in the MSE for the treatment effect estimator compared to a completely randomized or matched-pair design. The BMW design is also compared with a model-based approach adjusting for the estimated propensity score and Robins-Mark-Newey E-estimation procedure in terms of efficiency and robustness of the treatment effect estimator. These investigations suggest that the BMW design is more robust and usually, although not always, more efficient than either of the approaches. The design is also seen to be robust against heterogeneous error. We illustrate these methods in proposing a design for the INSTINCT trial.},
affiliation = {Department of Biostatistics, University of Michigan, Ann Arbor, Michighan 48109, U.S.A.},
pages = {},
year = {2009},
month = {Nov},
language = {ENG},
date-added = {2010-06-21 19:59:31 +0200},
date-modified = {2010-06-21 19:59:32 +0200},
doi = {10.1111/j.1541-0420.2009.01364.x},
pii = {BIOM1364},
pmid = {19995353},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12825},
rating = {0}
}

@article{Grant:2007p6778,
author = {Bridget F Grant and Thomas C Harford and Bengt O Muth{\'e}n and Hsiao-ye Yi and Deborah S Hasin and Frederick S Stinson},
journal = {Drug Alcohol Depend},
title = {DSM-IV alcohol dependence and abuse: further evidence of validity in the general population},
abstract = {BACKGROUND: In order to understand the validity of the Diagnostic and Statistical Manual of Mental Disorders, 4th ed. (DSM-IV) alcohol abuse and dependence diagnoses, studies are needed in both clinical and general population samples. The purpose of this study was to examine the construct and criterion-oriented validity of DSM-IV alcohol dependence and abuse in the general population with respect to factor structure and their relationship to family history of alcoholism, treatment utilization, and psychiatric comorbidity. METHODS: This analysis is based on data from the 2001-2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC), in which nationally representative data were collected in personal interviews conducted with one randomly selected adult in each sample household or group quarters. A subset (n=26,946) of the NESARC sample (total n=43,093) who reported drinking one or more drinks during the year preceding the interview formed the basis of analyses. Latent variable modeling was used to assess the concurrent validity of DSM-IV alcohol abuse and dependence symptom items. RESULTS: The latent variable modeling yielded one major factor related to alcohol dependence, a second factor related to alcohol abuse and a third smaller factor defined by tolerance. The validity of alcohol dependence in general population samples was further supported by statistically significant associations with family history of alcoholism, treatment utilization, and psychiatric and medical comorbidities. CONCLUSIONS: The factor structure and relationship to external criterion variables observed in the study provide support for the further validity of DSM-IV alcohol dependence in the general population, whereas support for the validity of DSM-IV abuse was equivocal.},
affiliation = {Laboratory of Epidemiology and Biometry, Division of Intramural Clinical and Biological Research, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892-9304, USA. bgrant@willco.niaaa.nih.gov},
number = {2-3},
pages = {154--66},
volume = {86},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Female, Male, Adult, Humans, Adolescent, United States, Middle Aged, Aged, Models: Statistical, Epidemiologic Studies, Reproducibility of Results, Alcohol-Related Disorders, Health Surveys, Diagnostic and Statistical Manual of Mental Disorders},
date-added = {2010-03-05 22:19:39 +0100},
date-modified = {2010-03-05 22:19:40 +0100},
doi = {10.1016/j.drugalcdep.2006.05.019},
pii = {S0376-8716(06)00203-1},
pmid = {16814489},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6778},
rating = {0}
}

@inproceedings{Gower:1998,
author = {AR Gower and B Belanger and MJ Williams},
journal = {Proceedings},
title = {Using focus groups with respondents and interviewers to evaluate the questionnaire and interviewing procedures after the survey has taken place},
pages = {404--409},
year = {1998},
date-added = {2010-01-03 19:34:17 +0100},
date-modified = {2010-01-03 19:34:18 +0100},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1011},
rating = {0}
}

@article{deVet:2003p6834,
author = {H C W de Vet and C B Terwee and L M Bouter},
journal = {Journal of Clinical Epidemiology},
title = {Clinimetrics and psychometrics: two sides of the same coin},
pages = {1146--1147},
volume = {56},
year = {2003},
date-added = {2010-03-06 10:29:51 +0100},
date-modified = {2010-03-06 10:30:31 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/de%20Vet-2003-Journal%20of%20Clinical%20Epidemiology_Clinimetrics%20and%20psy.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6834},
rating = {0}
}

@article{Beral:1979,
author = {V Beral and C Chilvers and P Fraser},
journal = {J Epidemiol Community Health},
title = {On the estimation of relative risk from vital statistical data},
abstract = {A method is described for the determination of a measure of relative risk from vital statistical data. If the frequency of disease in a population is linearly related to the level of exposure to a given factor, then a measure of the relative risk can be estimated from the slope and intercept of the regression line. For example, when the exposure is measured in terms of the proportion of the population exposed to the factor, then the relative risk is equal to [Formula: see text] This offers an indirect but simple and inexpensive method for estimating relative risk. It should be used with caution, particularly where confounding factors may be responsible for the apparent association between disease and factor. Applications of the method to estimate the relative risk of (a) circulatory diseases in women using oral contraceptives and (b) ovarian cancer in women with different average family sizes, both yielded relative risk estimates comparable with those obtained from case-control and prospective studies.},
pages = {159--162},
volume = {33},
year = {1979},
date-added = {2010-01-03 19:36:09 +0100},
date-modified = {2010-07-29 19:33:58 +0200},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1077},
rating = {0}
}

@article{Sepulveda:2008p1690,
author = {R Sep{\'u}lveda and J L Vicente-Villard{\'o}n and M P Galindo},
journal = {Stat Med},
title = {The Biplot as a diagnostic tool of local dependence in latent class models. A medical application},
abstract = {Latent class models (LCMs) can be used to assess diagnostic test performance when no reference test (a gold standard) is available, considering two latent classes representing disease or non-disease status. One of the basic assumptions in such models is that of local or conditional independence: all indicator variables (tests) are statistically independent within each latent class. However, in practice this assumption is often violated; hence, the two-LCM fits the data poorly. In this paper, we propose the use of Biplot methods to identify the conditional dependence between pairs of manifest variables within each latent class. Additionally, we propose incorporating such dependence in the corresponding latent class using the log-linear formulation of the model.},
affiliation = {Department of Statistics, University of Salamanca, Salamanca, Spain. rsepulve2001@yahoo.es},
number = {11},
pages = {1855--69},
volume = {27},
year = {2008},
month = {May},
language = {eng},
keywords = {Data Interpretation: Statistical, Diagnostic Tests: Routine, Forecasting, Models: Statistical},
date-added = {2010-01-09 18:34:05 +0100},
date-modified = {2010-01-09 18:34:05 +0100},
doi = {10.1002/sim.3194},
pmid = {18265437},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Sep%C3%BAlveda-2008-Stat%20Med_The%20Biplot%20as%20a%20diag.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1690},
rating = {0}
}

@article{Indurkhya:2010p13824,
author = {A Indurkhya and A von Eye},
title = {The Power of Tests in Configural Frequency Analysis},
abstract = {Specification of a null hypothesis is central to the interpretation of types and an- titypes in Configural Frequency Analysis (CFA). When the observed frequency of a variable category exceeds (or is less than) its corresponding expected frequency, the variable category is considered a type (or antitype). This article attempts to help the researcher to determine whether types or antitypes can be expected to emerge based on power and sample size considerations. Results are presented for the special cases of 2x2 and 2x2x2 tables respectively for First Order CFA.},
date-added = {2010-07-29 12:55:48 +0200},
date-modified = {2010-07-29 12:57:00 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Indurkhya--_The%20Power%20of%20Tests%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p13824},
rating = {0}
}

@article{Schmitt:2007p11169,
author = {D P Schmitt and J Allik and R R Mccrae and V Benet-Martinez},
journal = {Journal of Cross-Cultural Psychology},
title = {THE GEOGRAPHIC DISTRIBUTION OF BIG FIVE PERSONALITY TRAITS. Patterns and Profiles of Human Self-Description Across 56 Nations},
abstract = {The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness. As part of the International Sexuality Description Project, the BFI was translated from English into 28 languages and administered to 17,837 individuals from 56 nations. The resulting cross-cultural data set was used to address three main questions: Does the factor structure of the English BFI fully replicate across cultures? How valid are the BFI trait profiles of individual nations? And how are personality traits distributed throughout the world? The five-dimensional structure was robust across major regions of the world. Trait levels were related in predictable ways to self-esteem, sociosexuality, and national personality profiles. People from the geographic regions of South America and East Asia were significantly different in open- ness from those inhabiting other world regions. The discussion focuses on limitations of the current data set and important directions for future research.},
year = {2007},
date-added = {2010-04-25 21:14:36 +0200},
date-modified = {2010-07-29 20:44:44 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Schmitt-2007-Journal%20of%20Cross-Cultural%20Psychology_THE%20GEOGRAPHIC%20DISTR.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p11169},
rating = {4}
}

@article{Tan:2009p8860,
author = {Hao Yang Tan},
journal = {Ann Acad Med Singap},
title = {Cognitive dysfunction in schizophrenia: a perspective from the clinic to genetic brain mechanisms},
abstract = {Schizophrenia is a brain disease with differing symptomatic presentations, outcomes, and complex genetic mechanisms. A selection of recent work integrating clinical observations, human brain imaging and genetics will be reviewed. While the mechanics of brain dysfunction in schizophrenia remains to be well understood, the emerging evidence suggests that a number of interacting genetic mechanisms in dopaminergic and glutamatergic systems affect fundamental disease-related cognitive brain processes and may do so early in disease neurodevelopment. The availability of new imaging and genetic technologies, and institutional support for research in the translational neurosciences, extends the hope that increased understanding of these brain processes could yield meaningful clinical applications.},
affiliation = {Genes, Cognition and Psychosis Program, National Institute of Mental Health, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1364, USA. tanh@mail.nih.gov},
number = {5},
pages = {420--5},
volume = {38},
year = {2009},
month = {May},
language = {eng},
keywords = {Schizophrenia, Cognition Disorders, Dopamine, Glutamic Acid, Magnetic Resonance Imaging, Humans, Neurosciences},
date-added = {2010-03-22 12:39:07 +0100},
date-modified = {2010-03-22 12:39:07 +0100},
pmid = {19521642},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tan-2009-Ann%20Acad%20Med%20Singap_Cognitive%20dysfunctio.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8860},
rating = {0}
}

@article{Bedo:2009p4929,
author = {J Bedo and G Macintyre and I Haviv and A Kowalczyk},
journal = {Nature Precedings},
title = {SIMPLE SVM BASED WHOLE-GENOME SEGMENTATION},
abstract = {We present a support vector machine (SVM) based framework for DNA segmen- tation into binary classes. Two applications are explored: transcription start site prediction and transcription factor binding prediction. Experiments demonstrate our approach has sig- nificantly better performance than other methods on both tasks.},
number = {3811.1},
year = {2009},
date-added = {2010-02-02 11:49:30 +0100},
date-modified = {2010-02-02 11:50:32 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bedo-2009-Nature%20Precedings_SIMPLE%20SVM%20BASED%20WHO.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4929},
rating = {0}
}

@article{Foundation:2008p2440,
author = {R Foundation},
title = {R: Regulatory Compliance and Validation Issues A Guidance Document for the Use of R in Regulated Clinical
Trial Environments},
year = {2008},
date-added = {2010-01-11 23:50:02 +0100},
date-modified = {2010-01-11 23:50:33 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Foundation-2008-_R%20Regulatory%20Compli.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2440},
rating = {0}
}

@article{Slavkovic:2010p12849,
author = {A B Slavkovic and J Lee},
journal = {Statistical Methodology},
title = {Synthetic two-way contingency tables that preserve conditional frequencies},
abstract = {In the area of statistical limitation, releasing synthetic data sets has become a popular method for limiting the risks of disclosure of sensitive information and at the same time maintaining analytic utility of data. However, less work has been done on how to create synthetic contingency tables that preserve some summary statistics of the original table. Studies in this area have primarily focused on generating replacement tables that preserve the margins of the original table since the latter support statistical inferences for a large set of parametric tests and models. Yet, not all synthetic tables that preserve a set of margins yield consistent results. In this paper, we propose alternative synthetic table releases. We describe how to generate complete two-way contingency tables that have the same set of observed conditional frequencies by using tools from computational algebra. We study both the disclosure risk and the data utility associated with such synthetic tabular data releases, and compare them to the traditionally released synthetic tables.},
pages = {225--239},
volume = {7},
year = {2010},
date-added = {2010-06-21 20:13:46 +0200},
date-modified = {2010-07-29 20:06:22 +0200},
doi = {10.1016/j.stamet.2009.11.002},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Slavkovic-2010-Statistical%20Methodology_Synthetic%20two-way%20co.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12849},
rating = {0}
}

@article{Yang:2006p1532,
author = {C-C Yang},
journal = {Computational Statistics},
title = {Evaluating latent class analysis models in qualitative phenotype identification},
abstract = {The paper is aimed to investigate the performance of information criteria in selecting latent class analysis models which are often used in research of phenotype identification. Six information criteria and a sample size adjustment (Psychometrika 52 (1987) 333) are compared under various sample sizes and model dimensionalities. The simulation design is particularly meaningful for phenotypic research in practice. Results show that improvements by the sample size adjustment are considerable. In addition, the sample size and model dimensionality effects are found to be influential in the simulation study.},
affiliation = {Graduate School of Educational Measurement {\&} Statistics, National Taichung Teachers College,
140 MinSheng Road, Taichung 403, Taiwan},
pages = {1090--1104},
volume = {50},
year = {2006},
keywords = {Latent class analysis, Model selections, Information criteria, E-M algorithm, Phenotype identifications},
date-added = {2010-01-07 16:08:42 +0100},
date-modified = {2010-07-29 19:24:30 +0200},
doi = {10.1016/j.csda.2004.11.004},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Yang-2006-Computational%20Statistics_Evaluating%20latent%20cl.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1532},
rating = {0}
}

@article{Cook:2005p7861,
author = {Karon F Cook and Kimberly J O'Malley and Toni S Roddey},
journal = {Health Serv Res},
title = {Dynamic assessment of health outcomes: time to let the CAT out of the bag?},
abstract = {BACKGROUND: The use of item response theory (IRT) to measure self-reported outcomes has burgeoned in recent years. Perhaps the most important application of IRT is computer-adaptive testing (CAT), a measurement approach in which the selection of items is tailored for each respondent. OBJECTIVE. To provide an introduction to the use of CAT in the measurement of health outcomes, describe several IRT models that can be used as the basis of CAT, and discuss practical issues associated with the use of adaptive scaling in research settings. PRINCIPAL POINTS: The development of a CAT requires several steps that are not required in the development of a traditional measure including identification of "starting" and "stopping" rules. CAT's most attractive advantage is its efficiency. Greater measurement precision can be achieved with fewer items. Disadvantages of CAT include the high cost and level of technical expertise required to develop a CAT. CONCLUSIONS: Researchers, clinicians, and patients benefit from the availability of psychometrically rigorous measures that are not burdensome. CAT outcome measures hold substantial promise in this regard, but their development is not without challenges.},
affiliation = {Veterans Affairs Measurement of Excellence Training Resource Information Center, Houston Center of Quality Care and Utilization Studies, Houston, TX 77007, USA.},
number = {5 Pt 2},
pages = {1694--711},
volume = {40},
year = {2005},
month = {Oct},
language = {eng},
keywords = {Psychometrics, Outcome Assessment (Health Care), Technology Assessment: Biomedical, Quality of Life, Health Services Research, Software, Models: Theoretical, Reproducibility of Results, Humans},
date-added = {2010-03-20 19:00:47 +0100},
date-modified = {2010-03-20 19:00:47 +0100},
doi = {10.1111/j.1475-6773.2005.00446.x},
pii = {HESR446},
pmid = {16179003},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Cook-2005-Health%20Serv%20Res_Dynamic%20assessment%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7861},
rating = {0}
}

@article{Feveile:2007p8393,
author = {Helene Feveile and Ole Olsen and Annie Hogh},
journal = {BMC Med Res Methodol},
title = {A randomized trial of mailed questionnaires versus telephone interviews: response patterns in a survey},
abstract = {BACKGROUND: Data for health surveys are often collected using either mailed questionnaires, telephone interviews or a combination. Mode of data collection can affect the propensity to refuse to respond and result in different patterns of responses. The objective of this paper is to examine and quantify effects of mode of data collection in health surveys. METHODS: A stratified sample of 4,000 adults residing in Denmark was randomised to mailed questionnaires or computer-assisted telephone interviews. 45 health-related items were analyzed; four concerning behaviour and 41 concerning self assessment. Odds ratios for more positive answers and more frequent use of extreme response categories (both positive and negative) among telephone respondents compared to questionnaire respondents were estimated. Tests were Bonferroni corrected. RESULTS: For the four health behaviour items there were no significant differences in the response patterns. For 32 of the 41 health self assessment items the response pattern was statistically significantly different and extreme response categories were used more frequently among telephone respondents (Median estimated odds ratio: 1.67). For a majority of these mode sensitive items (26/32), a more positive reporting was observed among telephone respondents (Median estimated odds ratio: 1.73). The overall response rate was similar among persons randomly assigned to questionnaires (58.1%) and to telephone interviews (56.2%). A differential nonresponse bias for age and gender was observed. The rate of missing responses was higher for questionnaires (0.73-6.00%) than for telephone interviews (0-0.51%). The "don't know" option was used more often by mail respondents (10-24%) than by telephone respondents (2-4%). CONCLUSION: The mode of data collection affects the reporting of self assessed health items substantially. In epidemiological studies, the method effect may be as large as the effects under investigation. Caution is needed when comparing prevalences across surveys or when studying time trends.},
affiliation = {National Research Centre for the Working Environment, Copenhagen, Denmark. hfe@nrcwe.dk},
pages = {27},
volume = {7},
year = {2007},
month = {Jan},
language = {eng},
keywords = {Male, Consumer Participation, Interviews as Topic, Research Design, Self Assessment (Psychology), Postal Service, Female, Odds Ratio, Questionnaires, Health Surveys, Humans, Health Behavior, Denmark, Telephone, Attitude to Health, Adult},
date-added = {2010-03-21 13:09:32 +0100},
date-modified = {2010-03-21 13:09:32 +0100},
doi = {10.1186/1471-2288-7-27},
pii = {1471-2288-7-27},
pmid = {17592653},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Feveile-2007-BMC%20Med%20Res%20Methodol_A%20randomized%20trial%20o.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p8393},
rating = {0}
}

@article{Edwards:2008p3189,
author = {M C Edwards},
journal = {IMPS},
title = {Item factor analysis: Where we've been and where we might be going},
year = {2008},
date-added = {2010-01-14 20:48:27 +0100},
date-modified = {2010-01-14 20:48:54 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Edwards-2008-IMPS_Item%20factor%20analysis.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3189},
rating = {0}
}

@article{Lockwood:2007,
author = {J R Lockwood and D F McCaffrey and L S Hamilton and B Stecher and V-N Le and J F Martinez},
journal = {Journal of Educational Measurement},
title = {The Sensitivity of Value-Added Teacher Effect Estimates to Different Mathematics Achievement Measures},
number = {1},
pages = {47--67},
volume = {44},
year = {2007},
date-added = {2010-01-10 11:33:10 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Lockwood-2007-Journal%20of%20Educational%20Measurement_The%20Sensitivity%20of%20V.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1985},
rating = {0}
}

@article{MeyerLindenberg:2008p3513,
author = {Andreas Meyer-Lindenberg and Kristin K Nicodemus and Michael F Egan and Joseph H Callicott and Venkata Mattay and Daniel R Weinberger},
journal = {Neuroimage},
title = {False positives in imaging genetics},
abstract = {Imaging genetics provides an enormous amount of functional-structural data on gene effects in living brain, but the sheer quantity of potential phenotypes raises concerns about false discovery. Here, we provide the first empirical results on false positive rates in imaging genetics. We analyzed 720 frequent coding SNPs without significant association with schizophrenia and a subset of 492 of these without association with cognitive function. Effects on brain structure (using voxel-based morphometry, VBM) and brain function, using two archival imaging tasks, the n-back working memory task and an emotional face matching task, were studied in whole brain and regions of interest and corrected for multiple comparisons using standard neuroimaging procedures. Since these variants are unlikely to impact relevant brain function, positives obtained provide an upper empirical estimate of the false positive association rate. In a separate analysis, we randomly permuted genotype labels across subjects, removing any true genotype-phenotype association in the data, to derive a lower empirical estimate. At a set correction level of 0.05, in each region of interest and data set used, the rate of positive findings was well below 5% (0.2-4.1%). There was no relationship between the region of interest and the false positive rate. Permutation results were in the same range as empirically derived rates. The observed low rates of positives provide empirical evidence that the type I error rate is well controlled by current commonly used correction procedures in imaging genetics, at least in the context of the imaging paradigms we have used. In fact, our observations indicate that these statistical thresholds are conservative.},
affiliation = {Unit for Systems Neuroscience in Psychiatry, National Institute for Mental Health, NIH, DHHS, 9000 Rockville Pike, Bethesda, MD 20892-1365, USA. a.meyer-lindenberg@zi-mannheim.de},
number = {2},
pages = {655--61},
volume = {40},
year = {2008},
month = {Apr},
language = {eng},
keywords = {Adult, Schizophrenia, False Positive Reactions, Female, Male, Magnetic Resonance Imaging, Humans},
date-added = {2010-01-15 15:46:48 +0100},
date-modified = {2010-03-07 11:08:14 +0100},
doi = {10.1016/j.neuroimage.2007.11.058},
pii = {S1053-8119(07)01080-4},
pmid = {18201908},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Meyer-Lindenberg-2008-Neuroimage_False%20positives%20in%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3513},
read = {Yes},
rating = {4}
}

@article{Ericson:1969p6318,
author = {W A Ericson},
journal = {Journal of the Royal Society, Serie B},
title = {Subjective Bayesian Models in Sampling Finite Populations},
number = {2},
pages = {195--233},
volume = {31},
year = {1969},
date-added = {2010-02-20 21:13:16 +0100},
date-modified = {2010-07-29 19:38:24 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Ericson-1969-Journal%20of%20the%20Royal%20Society%20Serie%20B_Subjective%20Bayesian.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6318},
rating = {0}
}

@article{Tarca:2007p1604,
author = {Adi L Tarca and Vincent J Carey and Xue-wen Chen and Roberto Romero and Sorin Dr{\u a}ghici},
journal = {PLoS Comput Biol},
title = {Machine learning and its applications to biology},
number = {6},
pages = {e116},
volume = {3},
year = {2007},
month = {Jun},
language = {eng},
keywords = {Pattern Recognition: Automated, Cluster Analysis, Models: Biological, Algorithms, Artificial Intelligence, Computer Simulation, Biology},
date-added = {2010-01-07 17:00:09 +0100},
date-modified = {2010-01-07 17:00:09 +0100},
doi = {10.1371/journal.pcbi.0030116},
pii = {1553-734X-3-6-e116},
pmid = {17604446},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Tarca-2007-PLoS%20Comput%20Biol_Machine%20learning%20and.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1604},
rating = {0}
}

@article{Saunders:2005p4522,
author = {Jana C Saunders and Craig A Cookman},
journal = {Gastroenterol Nurs},
title = {A clarified conceptual meaning of hepatitis C-related depression},
abstract = {A clarified conceptual meaning of depression in individuals with hepatitis C virus infection is proposed based on a critical review of literature. Moving beyond an exclusively biomedical perspective, depression in hepatitis C is explained by a cluster of factors that incorporate physiological, psychological, and social dimensions. Symptom experience, stigma, and uncertainty are factors that span the complex nature of depression in individuals with hepatitis C. This broadened perspective incorporates individual and societal values and beliefs regarding hepatitis C and encompasses the multidimensional complexity of depression in hepatitis C. Hepatitis C-related depression presents an enormous challenge for nurses because of its interference with treatment adherence and significant negative impact on the individual's quality of life. Nursing theorists, researchers, and clinicians may benefit from a clear conceptual understanding of the unique nature of depression in this growing segment of the U.S. population. This clarified conceptual meaning needs to be validated through qualitative, quantitative, and longitudinal studies with this population. It is hoped that future theorists, researchers, and practitioners will contribute to our conceptual understanding, resulting in improved quality of life for this special population.},
affiliation = {Texas Tech University Health Sciences Center, Lubbock, USA. jana.saunders@ttuhsc.edu},
number = {2},
pages = {123-9; quiz 130--1},
volume = {28},
year = {2005},
month = {Jan},
language = {eng},
keywords = {Stereotyping, Models: Nursing, Nursing Research, Depressive Disorder, Activities of Daily Living, Hepatitis C, Quality of Life, United States, Self Concept, Adaptation: Psychological, Nursing Theory, Nurse's Role, Attitude to Health, Life Change Events, Humans, Uncertainty, Risk Factors, Models: Psychological, Affect, Internal-External Control},
date-added = {2010-01-29 22:11:18 +0100},
date-modified = {2010-01-29 22:11:18 +0100},
pii = {00001610-200503000-00006},
pmid = {15832112},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p4522},
rating = {0}
}

@article{Kintner:2008p6600,
author = {Eileen K Kintner and Alla Sikorskii},
journal = {Health Qual Life Outcomes},
title = {Reliability and construct validity of the Participation in Life Activities Scale for children and adolescents with asthma: an instrument evaluation study},
abstract = {BACKGROUND: The purpose of this study was to evaluate the reliability and construct validity of the Participation in Life Activities Scale, an instrument designed to measure older school-age child and early adolescent level of involvement in chosen pursuits. METHODS: A cross-sectional design was used. The convenience sample consisted of 313 school-age children and early adolescents with asthma, ages 9-15 years. The self-report summative scale of interest is a 3-indicator survey. Higher scores are reflective of higher levels of participation. Internal consistency reliability and construct validity for the entire sample and sub groups of the sample were evaluated. RESULTS: The instrument was deemed sound for the entire sample as well as sub groups based on sex, race, age, socioeconomic status, and severity of illness. Cronbach's alpha coefficient for internal consistency reliability for the entire sample was .74. Exploratory factor analysis indicated a single component solution (loadings .79-.85) accounting for 66% of the explained variance. Construct validity was established by testing the posed relationship between participation in life activities scores and severity of illness. Confirmatory factor analysis revealed a good fit between the data and specified model, chi2(10, n = 302) = 8.074, p = .62. CONCLUSION: This instrument could be used (a) in clinical settings to diagnose restricted participation in desired activities, guide decision-making about treatment plans to increase participation, and motivate behavioral change in the management of asthma; and (b) in research settings to explore factors influencing and consequences of restricted and unrestricted participation, and as an outcome measure to evaluate the effectiveness of programs designed to foster child and early adolescent management of asthma.},
affiliation = {Michigan State University College of Nursing, East Lansing, MI, USA. kintner@msu.edu},
pages = {43},
volume = {6},
year = {2008},
month = {Jan},
language = {eng},
keywords = {Factor Analysis: Statistical, Female, Activities of Daily Living, Health Status Indicators, Adolescent, Asthma, Male, Reproducibility of Results, Psychometrics, Humans, Child, Cross-Sectional Studies},
date-added = {2010-03-03 19:40:55 +0100},
date-modified = {2010-03-03 19:40:56 +0100},
doi = {10.1186/1477-7525-6-43},
pii = {1477-7525-6-43},
pmid = {18533017},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Kintner-2008-Health%20and%20Quality%20of%20Life%20Outcomes_Reliability%20and%20cons.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6600},
rating = {0}
}

@article{Roche:2010p12124,
author = {A Roche},
title = {EM algorithm and variants: an informal tutorial},
date-added = {2010-05-30 10:08:04 +0200},
date-modified = {2010-05-30 10:08:42 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Roche--_EM%20algorithm%20and%20var.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12124},
rating = {0}
}

@article{Turner:2010p6527,
author = {Dan Turner and Holger J Sch{\"u}nemann and Lauren E Griffith and Dorcas E Beaton and Anne M Griffiths and Jeffrey N Critch and Gordon H Guyatt},
journal = {Journal of Clinical Epidemiology},
title = {The minimal detectable change cannot reliably replace the minimal important difference},
abstract = {OBJECTIVE: We compared the minimal important difference (MID) with the minimal detectable change (MDC) generated by distribution-based methods. STUDY DESIGN: Studies of two quality-of-life instruments (Chronic Respiratory Questionnaire [CRQ] and Rhinoconjunctivitis Quality of Life Questionnaire [RQLQ]) and two physician-rated disease-activity indices (Pediatric Ulcerative Colitis Activity Index [PUCAI] and Pediatric Crohn's Disease Activity Index [PCDAI]) provided longitudinal data. The MID values were calculated from global ratings of change (small change for CRQ and RQLQ; moderate for PUCAI and PCDAI) using receiver-operating characteristic (ROC) curve and mean change. Results were compared with five distribution-based strategies. RESULTS: Of the methods used to calculate the MDC, the 95% limits of agreement and the reliable change index yielded the largest estimates. In the patient-rated psychometric instruments, 0.5 SD was always greater than 1 standard error of measurements (SEM), and both fell between the mean change and the ROC estimates, on two of four occasions. The reliable change index came closest to MID of moderate change. CONCLUSION: For patient-rated psychometric instruments, 0.5 SD and 1 SEM provide values closest to the anchor-based estimates of MID derived from small change, and the reliable change index for physician-rated clinimetric indices based on moderate change. Lack of consistency across measures suggests that distribution-based approaches should act only as temporary substitutes, pending availability of empirically established anchor-based MID values.},
affiliation = {Pediatric Gastroenterology Unit, Shaare Zedek Medical Center, Jerusalem 91031, Israel. turnerjd2001@walla.com},
number = {1},
pages = {28--36},
volume = {63},
year = {2010},
month = {Jan},
language = {eng},
date-added = {2010-02-24 20:35:49 +0100},
date-modified = {2010-02-24 20:35:49 +0100},
doi = {10.1016/j.jclinepi.2009.01.024},
pii = {S0895-4356(09)00190-5},
pmid = {19800198},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Turner-2010-Journal%20of%20Clinical%20Epidemiology_The%20minimal%20detectab.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p6527},
rating = {0}
}

@article{Zhang:2004,
author = {N L Zhang},
journal = {Journal of Machine Learning},
title = {Hierarchical Latent Class Models for Cluster Analysis},
pages = {697--723},
volume = {5},
year = {2004},
date-added = {2010-01-03 19:37:35 +0100},
date-modified = {2010-07-29 19:34:44 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Zhang-2004-Journal%20of%20Machine%20Learning_Hierarchical%20Latent.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1113},
rating = {0}
}

@article{Poon:2010p12862,
author = {L K M Poon and N L Zhang and T Chen and Y Wang},
journal = {ICML},
title = {Variable Selection in Model-Based Clustering: To Do or To Facilitate},
abstract = {Variable selection for cluster analysis is a dif- ficult problem. The difficulty originates not only from the lack of class information but also the fact that high-dimensional data are often multifaceted and can be meaningfully clustered in multiple ways. In such a case the effort to find one subset of attributes that presumably gives the ``best'' clustering may be misguided. It makes more sense to facilitate variable selection by domain ex- perts, that is, to systematically identify var- ious facets of a data set (each being based on a subset of attributes), cluster the data along each one, and present the results to the domain experts for appraisal and selection. In this paper, we propose a generalization of the Gaussian mixture model, show its abil- ity to cluster data along multiple facets, and demonstrate it is often more reasonable to fa- cilitate variable selection than to perform it.},
year = {2010},
date-added = {2010-06-24 12:39:45 +0200},
date-modified = {2010-06-24 12:40:38 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Poon-2010-ICML_Variable%20Selection%20i.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12862},
rating = {0}
}

@article{Eckert:2007p3594,
author = {L Eckert},
title = {LA META-REGRESSION COMME METHODOLOGIE DE COMPARAISONS INDIRECTES :
Une r{\'e}ponse aux exigences contemporaines de l'{\'e}valuation du m{\'e}dicament},
year = {2007},
date-added = {2010-01-15 21:22:55 +0100},
date-modified = {2010-01-15 21:23:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Eckert-2007-_LA%20META-REGRESSION%20C.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3594},
rating = {0}
}

@article{Goldstein:2009p1406,
author = {David B Goldstein},
journal = {N Engl J Med},
title = {Common genetic variation and human traits},
affiliation = {Center for Human Genome Variation, Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA.},
number = {17},
pages = {1696--8},
volume = {360},
year = {2009},
month = {Apr},
language = {eng},
keywords = {Genomics, Genome-Wide Association Study, Diabetes Mellitus: Type 2, Drug Design, Body Height, Disease, Genetic Predisposition to Disease, Polymorphism: Single Nucleotide, Risk, Humans, Genetic Variation},
date-added = {2010-01-07 12:17:13 +0100},
date-modified = {2010-07-29 19:53:14 +0200},
doi = {10.1056/NEJMp0806284},
pii = {NEJMp0806284},
pmid = {19369660},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Goldstein-2009-N%20Engl%20J%20Med_Common%20genetic%20varia.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p1406},
rating = {0}
}

@article{Nolin:1999p3600,
author = {P Nolin},
journal = {Revue Qu{\'e}b{\'e}coise de Psychologie},
title = {ANALYSES PSYCHOM{\'E}TRIQUES DE L'ADAPTATION FRAN{\c C}AISE DU CALIFORNIA VERBAL LEARNING TEST (CVLT)},
abstract = {Le California Verbal Learning Test (CVLT) est un instrument neuropsychologique issu des mod{\`e}les de la psychologie cognitive qui produit un portrait dynamique de l'apprentissage verbal. Le but de la pr{\'e}sente recherche est d'{\'e}tudier la valeur psychom{\'e}trique de l'adaptation fran{\c c}aise du CVLT. Les donn{\'e}es recueillies aupr{\`e}s de 309 sujets normaux {\^a}g{\'e}s de 17 {\`a} 90 ans, de 25 patients ayant subi un traumatisme cranio-enc{\'e}phalique (TCE) et de 22 sujets bilingues ont permis d'apporter un soutien {\`a} cette forme du CVLT. La fid{\'e}lit{\'e} de la version fran{\c c}aise est d{\'e}montr{\'e}e {\`a} l'aide de trois analyses de consistance interne. Les indices de fid{\'e}lit{\'e} sont 0,93, 0,82 et 0,83. La validit{\'e} de la version fran{\c c}aise est support{\'e}e par une analyse factorielle d{\'e}montrant qu'il s'agit d'un outil qui couvre six construits th{\'e}oriques de l'apprentissage, tel que souhait{\'e} lors de sa construction. La validit{\'e} concomitante est appuy{\'e}e par de fortes corr{\'e}lations entre les r{\'e}sultats du CVLT fran{\c c}ais et ceux du WMS-R. Par ailleurs, les r{\'e}sultats d{\'e}montrent {\'e}galement la capacit{\'e} de cet instrument de d{\'e}tecter de fa{\c c}on significative les d{\'e}ficits de la m{\'e}moire chez une population de sujets TCE. Enfin, des corr{\'e}lations significatives et une absence de diff{\'e}rences sont obtenues entre les rendements donn{\'e}s dans la majorit{\'e} des variables des versions anglaise et fran{\c c}aise du CVLT. Toutefois, le nombre total de mots, le score de progression et le score de regroupements s{\'e}mantiques soulignent des diff{\'e}rences entre les deux formes. Il semble donc pr{\'e}matur{\'e} de conclure en leur {\'e}quivalence. L'utilisation de l'adaptation du CVLT est n{\'e}anmoins propos{\'e}e aux chercheurs et aux cliniciens qui travaillent en langue fran{\c c}aise en raison du support psychom{\'e}trique apport{\'e} par la pr{\'e}sente {\'e}tude et des biais possibles li{\'e}s {\`a} la langue avec une simple traduction mot {\`a} mot de la version anglaise.},
number = {1},
volume = {20},
year = {1999},
date-added = {2010-01-15 21:40:18 +0100},
date-modified = {2010-01-15 21:40:52 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Nolin-1999-Revue%20Que%CC%81be%CC%81coise%20de%20Psychologie_ANALYSES%20PSYCHOME%CC%81TR.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p3600},
rating = {0}
}

@article{Elias:1998p5161,
author = {S Elias and J Hattie and G Douglas},
title = {An Assessment of Various Item Response Model and Structural Equation Model Fit Indices To Detect Unidimensionality},
abstract = {A fundamental problem in structural modeling and item response modeling is to determine whether a set items is unidimensional. Both models have a plethora of fit indicators, and the aim of this study is to compare the Stout T-statistic derived within item response modeling with many competing indices used in structural equation modeling to assess unidimensionality. Given that it is rare to find a ``perfectly'' unidimensional test, a further aim is to ascertain how many items from a second dimension are necessary before the various indices indicate that the item set is no longer ``essentially'' unidimensional.},
year = {1998},
date-added = {2010-02-07 12:23:14 +0100},
date-modified = {2010-02-07 12:23:51 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Elias-1998-_An%20Assessment%20of%20Var-1.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p5161},
rating = {0}
}

@misc{Blais:2003,
author = {Jean-Guy Blais and Nathalie Loye},
journal = {Miscellaneous},
title = {Une {\'e}tude de l'accord et de la fid{\'e}lit{\'e} inter juges comparant un mod{\`e}le de la th{\'e}orie de la g{\'e}n{\'e}ralisabilit{\'e} et un mod{\`e}le de la famille de Rasch},
year = {2003},
date-added = {2010-01-10 11:33:25 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Blais-2003-Miscellaneous_Une%20%C3%A9tude%20de%20l'accor.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2220},
rating = {0}
}

@article{Revelle:1979,
author = {W Revelle and T Rocklin},
journal = {Multivariate Behavioral Research},
title = {Very Simple Structure: An alternative procedure for estimating the optimal number of interpretable factors},
pages = {403--414},
volume = {14},
year = {1979},
date-added = {2010-01-10 11:33:22 +0100},
date-modified = {2010-01-10 11:33:25 +0100},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Revelle-1979-Multivariate%20Behavioral%20Research_Very%20Simple%20Structur.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p2158},
rating = {0}
}

@article{terBraak:2004p12007,
author = {C J F ter Braak and A P Schaffers},
journal = {Ecology},
title = {Co-Correspondence Analysis: a new ordination method to relate two community compositions},
abstract = {A new ordination method, called co-correspondence analysis, is developed to relate two types of communities (e.g., a plant community and an animal community) sampled at a common set of sites in a direct way. The method improves the simple, indirect approach of applying correspondence analysis (reciprocal averaging) to the separate species data sets and correlating the resulting ordination axes. Co-correspondence analysis maxi- mizes the weighted covariance between weighted averaged species scores of one community and weighted averaged species scores of the other community. It thus attempts to identify the patterns that are common to both communities. Both a symmetric descriptive and an asymmetric predictive form are developed. The symmetric form relates to co-inertia analysis and the asymmetric, predictive form to partial least-squares regression. In two examples the predictive power of co-correspondence analysis is compared with that of canonical correspondence analyses on syntaxonomic and environmental data. In the first example, carabid beetles in roadside verges are shown to be more closely related to plant species composition than to vegetation structure (biomass, height, roughness, among others), and, in the second example, bryophytes in spring meadows are shown to be more closely related to the species composition of the vascular plants than to the measured water chemistry.},
number = {3},
pages = {834--846},
volume = {85},
year = {2004},
date-added = {2010-05-23 17:35:33 +0200},
date-modified = {2010-05-23 17:36:40 +0200},
local-url = {file://localhost/Users/chl/Dropbox/Papers/ter%20Braak-2004-Ecology_Co-Correspondence%20An.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p12007},
rating = {0}
}

@article{Bartolucci:2010p7573,
author = {Francesco Bartolucci},
journal = {Stat Med},
title = {On the conditional logistic estimator in two-arm experimental studies with non-compliance and before-after binary outcomes},
abstract = {The behavior of the conditional logistic estimator is analyzed under a causal model for two-arm experimental studies with possible non-compliance in which the effect of the treatment is measured by a binary response variable. We show that, when non-compliance may only be observed in the treatment arm, the effect (measured on the logit scale) of the treatment on compliers and that of the control on non-compliers can be identified and consistently estimated under mild conditions. The same does not happen for the effect of the control on compliers. A simple correction of the conditional logistic estimator is then proposed, which allows us to considerably reduce the bias in estimating this quantity and the causal effect of the treatment over control on compliers. A two-step estimator results on the basis of which we can also set up a Wald test for the hypothesis of absence of a causal effect of the treatment. The asymptotic properties of the estimator are studied by exploiting the general theory on maximum likelihood estimation of misspecified models. Finite-sample properties of the estimator and of the related Wald test are studied by simulation. The extension of the approach to the case of missing responses is also outlined. The approach is illustrated by an application to a dataset deriving from a study on the efficacy of a training course on the breast self examination practice. Copyright (c) 2010 John Wiley {\&} Sons, Ltd.},
affiliation = {Department of Economics, Finance and Statistics, University of Perugia, 06123 Perugia, Italy.},
pages = {},
year = {2010},
month = {Mar},
language = {ENG},
date-added = {2010-03-14 11:02:14 +0100},
date-modified = {2010-03-14 11:02:15 +0100},
doi = {10.1002/sim.3860},
pmid = {20209479},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Bartolucci-2010-Stat%20Med_On%20the%20conditional%20l.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p7573},
rating = {0}
}

@article{Hopper:2005p9290,
author = {John L Hopper and D Timothy Bishop and Douglas F Easton},
journal = {Lancet},
title = {Population-based family studies in genetic epidemiology},
abstract = {Designs that involve families (the traditional strength of genetic epidemiology) and population-based sampling (the traditional strength of environmental epidemiology) allow investigation of both genes and environment, separately or together, and allow valid inference to the population. These case-control-family designs (including those involving twin pairs), can be regarded as retrospective cohort studies of relatives, and can be used for: determining familial risks and genetic models; estimating risk (penetrance) for measured genotypes; genetic association studies; stratifying risks by family history and known mutation status; and studying modifiers of risk in genetically susceptible individuals. Follow-up of families allows genetic and environmental risks to be studied prospectively. We discuss statistical methods, theoretical and practical strengths, limitations, and other issues. Given their versatility, population-based family studies could become a principal framework in epidemiology, and move genetics from its traditional focus on high-risk families to give it a wider clinical and population health relevance.},
affiliation = {University of Melbourne, Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, 723 Swanston Street, Carlton, Victoria 3053, Australia. j.hopper@unimelb.edu.au},
number = {9494},
pages = {1397--406},
volume = {366},
year = {2005},
month = {Jan},
language = {eng},
keywords = {Humans, Case-Control Studies, Research Design, Genetic Predisposition to Disease, Penetrance, Genetics: Population, Diseases in Twins, Family},
date-added = {2010-03-22 13:40:35 +0100},
date-modified = {2010-07-29 19:38:44 +0200},
doi = {10.1016/S0140-6736(05)67570-8},
pii = {S0140-6736(05)67570-8},
pmid = {16226618},
local-url = {file://localhost/Users/chl/Dropbox/Papers/Hopper-2005-Lancet_Population-based%20fam.pdf},
uri = {papers://58407365-8DEB-4C7D-995B-6322E39C7022/Paper/p9290},
read = {Yes},
rating = {0}
}

@article{Teo:2009p3387,
author = {Yik Y Teo and Andrew E Fry and Kanishka Bhattacharya and Kerrin S Small and Dominic P Kwiatkowski and Taane G Clark},
journal = {Genome Res},
title = {Genome-wide comparisons of variation in linkage disequilibrium},
abstract = {Current genome-wide surveys of common diseases and complex traits fundamentally aim to detect indirect associations where the single nucleotide polymorphisms (SNPs) carrying the association signals are not biologically active but are in linkage disequilibrium (LD) with some unknown functional polymorphisms. Reproducing any novel discoveries from these genome-wide scans in independent studies is now a prerequisite for the putative findings to be accepted. Significant differences in patterns of LD between populations can affect the portability of phenotypic associations when the replication effort or meta-analyses are attempted in populations that are distinct from the original population in which the genome-wide study is performed. Here, we introduce a novel method for genome-wide analyses of LD variations between populations that allow the identification of candidate regions with different patterns of LD. The evidence of LD variation provided by the introduced method correlated with the degree of differences in the frequencies of the most common haplotype across the populations. Identified regions also resulted in greater variation in the success of replication attempts compared with random regions in the genome. A separate permutation strategy introduced for assessing LD variation in the absence of genome-wide data also correctly identified the expected variation in LD patterns in two well-established regions undergoing strong population-specific evolutionary pressure. Importantly, this method addresses whether a failure to reproduce a disease association in a disparate population is due to underlying differences in LD structure with an unknown functional polymorphism, which is vital in the current climate of replicating and fine-mapping established findings from genome-wide association studies.},
affiliation = {Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom. teo@well.ox.ac.uk},
number = {10},
pages = {1849--60},
volume = {19},
year = {2009},
month = {Oct},
language = {eng},
keywords = {Case-Control Studies, Haplotypes, Gambia, Gene Frequency, Linkage Disequilibrium, Computer Simulation, Polymorphism: Single Nucleotide, Great Britain, Genetics: Population, Humans, Cohort Studies, Genome-Wide Association Study, Observer Variation},
date-added = {2010-01-15 14:39:59 +0100},
date-modified = {2010-01-15 14:39:59 +0100},
doi = {10.1101/gr.092189.109},
pii = {gr.092189.109},
pmid = {19541915},
uri = {papers://58407365-8DEB-4C7D-995B-6322E3

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib