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P C Sham

Publications and source records attributed to P C Sham.

At least 19 recordsLinked to original sources
PubMed2006

Computation of individual latent variable scores from data with multiple missingness patterns.

Latent variable models are used in biological and social sciences to investigate characteristics that are not directly measurable. The generation of individual scores of latent variables can simplify subsequent analyses. However, missing measurements in real data complicate the calculation of scores. Missing observations also result in different latent variable scores having different degrees of accuracy which should be taken into account in subsequent analyses. This manuscript presents a publicly available software tool that addresses both these problems, using as an example a dataset consisting of multiple ratings for ADHD symptomatology in children. The program computes latent variable scores with accompanying accuracy indices, under a 'user-specified' structural equation model, in data with missing data patterns. Since structural equation models encompass factor models, it can also be used for calculating factor scores. The program, documentation and a tutorial, containing worked examples and specimen input and output files, is available at http://statgen.iop.kcl.ac.uk/lsc .

Attention Deficit Disorder with Hyperactivity↗
PubMed2006

Combining functional and linkage disequilibrium information in the selection of tag SNPs.

UNLABELLED: We have developed an online program, WCLUSTAG, for tag SNP selection that allows the user to specify variable tagging thresholds for different SNPs. Tag SNPs are selected such that a SNP with user-specified tagging threshold C will have a minimum R2 of C with at least one tag SNP. This flexible feature is useful for researchers who wish to prioritize genomic regions or SNPs in an association study. AVAILABILITY: The online WCLUSTAG program is available at http://bioinfo.hku.hk/wclustag/

Algorithms↗
PubMed2006

A note on the power to detect transmission distortion in parent-child trios via the transmission disequilibrium test.

Transmission distortion refers to deviation from the normal 50:50 transmission of alleles from parents to offspring. Identification of genomic regions which undergo distortion is necessary for the correct interpretation of linkage and association studies, since tests of linkage using affected relative pairs and family based tests of association will yield spurious results in the presence of transmission distortion. With the increasing availability of genome-wide high density SNP data (e.g. from the International HapMap project), identification of these loci is now a real possibility. Here we present an analytical formula which demonstrates that the power to detect transmission distortion is a simple function of the number of heterozygous parents in the sample and the level of distortion at the locus. Our results indicate that whilst it will be possible to identify loci undergoing major levels of distortion using tens or hundreds of trios, large sample sizes in the order of tens of thousands of trios will be necessary to detect minor levels of distortion with appreciable power. The corollary is that genome-wide searches are unlikely to identify loci where the level of distortion is small, although they may serve to identify interesting regions worthy of follow up.

Adult↗
PubMed2006

Polymorphisms of the gene encoding adiponectin and glycaemic outcome of Chinese subjects with impaired glucose tolerance: a 5-year follow-up study.

AIMS/HYPOTHESIS: Polymorphisms of the gene encoding adiponectin (ADIPOQ) have previously been associated with type 2 diabetes in Europid and Japanese subjects, but not in Pima Indians. The aim of this study was to determine the contribution made by ADIPOQ gene variants to glycaemic status in southern Chinese individuals. SUBJECTS AND METHODS: Sixty unrelated subjects were screened for single-nucleotide polymorphisms (SNPs) in the ADIPOQ gene by direct sequencing. The association of tagging SNPs with the outcome of glycaemic status in 262 subjects with impaired glucose tolerance (IGT) was examined in a 5-year prospective study. RESULTS: We identified 15 polymorphisms in the ADIPOQ gene, ten of them constituting the tagging SNPs. At 5 years, 39.7% of the subjects with IGT had regressed to NGT, 41.2% had persistent IGT or impaired fasting glucose and 19.1% had developed diabetes. Only the T45G polymorphism was associated with persistent hyperglycaemia at 5 years (p=0.001). Haplotypes formed by the addition of other SNPs, as haplotype blocks or pairs, did not confer greater association than T45G alone. On logistic regression analysis, T45G independently predicted persistent hyperglycaemia at 5 years (OR=2.25, 95% CI 1.29-3.95, G carriers vs TT; p=0.005). It also predicted persistent hyperglycaemia in a nested case-control study involving 158 sex- and age-matched controls with persistent NGT (p=0.012, adjusted for BMI), and that of diabetes or glycaemia progression (p<0.05) in a meta-analysis that also included two published studies in Europid subjects. CONCLUSIONS/INTERPRETATION: Our findings support a significant role of this common ADIPOQ gene polymorphism in predicting glycaemic status in southern Chinese people.

Adiponectin↗
PubMed2006

Effect of environmental factors and gender on the heritability of bone mineral density and bone size.

Bone mineral density (BMD), a risk factor for osteoporosis, is believed to be under genetic control. The effect of environmental factors and gender on the heritability of BMD and bone size is ill-defined. In this study, heritability estimates (h2) were determined in 3,320 southern Chinese subjects from 1,019 families using the variance components model. The h2 for age, weight and height-adjusted BMD was 0.63-0.71 for females, and 0.74-0.79 for males; and for bone size, 0.44-0.64 for females and 0.32-0.86 for males. Adjustment for lifestyle factors including calcium and phytoestrogen intake, exercise, smoking and alcohol consumption altered the h2 differently in males and females. The proportion of variance in BMD and bone size explained by all covariates varied between skeletal sites, but was consistently greater in females than males. A significant gender difference was observed in the genetic variance of BMD and bone size at the hip but not the spine. In conclusion, a gender difference was observed in the degree of heritability of BMD and bone size at specific skeletal sites. Environmental influences contributed variably at different sites in the two sexes.

Adult↗
PubMed2006

Investigation of the ability of haplotype association and logistic regression to identify associated susceptibility loci.

While finely spaced markers are increasingly being used in case-control association studies in attempts to identify susceptibility loci, not enough is yet known as to the optimal spacing of such markers, their likely power to detect association, the relative merits of single marker versus multimarker analysis, or which methods of analysis may be optimal. Some investigations of these issues have used markers simulated under different theoretical models of population evolution. However the HapMap project and other sources provide real datasets which can be used to obtain a more realistic view of the performance of these approaches. SNPs around APOE and from two HapMap regions were used to obtain information regarding linkage disequilibrium (LD) relationships between polymorphisms, and these real patterns of LD were used to simulate datasets such as would be obtained in case-control studies were these SNPs to influence susceptibility to disease. The datasets obtained were analysed using tests for heterogeneity of estimated haplotype frequencies and using logistic regression analyses in which only main effects from each marker were considered. All markers surrounding the putative susceptibility locus were analysed, using sets of either 1, 2, 3 or 4 markers at a time. Some markers within 150 kb of the susceptibility locus were able to detect association. At distances less than 100 kb there was no correlation between the distance from the susceptibility locus and the strength of evidence for association. When the average inter-locus spacing is 25 kb many loci would not be detected, while when the spacing is as low as 2 kb one can be fairly confident that at least one marker will be in strong enough LD with the susceptibility locus to enable association to be detected, if the susceptibility locus has a strong enough effect relative to the sample size. With an inter-locus spacing of 4 kb some susceptibility loci did not have a marker locus in strong LD, potentially undermining the ability to detect association. There was little difference in the performance of haplotype-based analysis compared with logistic regression considering effects of each marker as separate. Multimarker analysis on occasion produced results which were much more highly significant than single marker analysis, but only very rarely. Our results support the view that if markers are randomly selected then a spacing as low as 2 kb is desirable. Multimarker analysis can sometimes be more powerful than single marker analysis so both should be performed. However, because it is rare for multimarker analysis to be much more highly significant than single marker analysis one should strongly suspect that when such results occur they may be due to mistakes in genotyping or through some other artefact. Haplotype analysis may be more prone to such problems than logistic regression, suggesting that the latter method might be preferred.

Apolipoproteins E↗
PubMed2006

Program report: GENECOUNTING support programs.

We describe a suite of programs which enhance the usability of GENECOUNTING, a program for estimating haplotype frequencies in unrelated subjects. The programs, called RUNGC, SCANASSOC, COMPGR, SCANGROUP and LDPAIRS, carry out likelihood ratio tests and permutation tests to detect differences in haplotype frequencies between cases and controls,or between predefined groups, and output likely haplotype assignments and tables of linkage disequilibrium statistics between all pairs of markers in a dataset.

Databases, Genetic↗
PubMed2005

Association analysis of monoamine genes with measures of depression and anxiety in a selected community sample of siblings.

Evidence indicates the genetic susceptibility to depression and anxiety is both overlapping and dimensional. In the current study, a quantitative phenotype had been created from several depression and anxiety-related measures in order to index this common genetic susceptibility (G). This has been studied in 119 sibships comprising 312 individuals, selected for extreme scores on G, from a community-based sample of 34,371 individuals. In a pathway based candidate gene study, we examined five microsatellite markers located within or nearby to five serotonin system genes (5HT2C, 5HT1D, 5HT1B, TPH1, and MAOB). Statistical analysis, carried out using QTDT, gave a significant association with a microsatellite downstream of TPH1. Further analysis included a life-events composite as a co-variable, this lead to a stronger association of TPH1. To our knowledge, this is the first study to report an association of the 3' end of TPH1 with continuous measures of depression and anxiety.

Alleles↗
PubMed2005

Brain MRI abnormalities in schizophrenia: same genes or same environment?

BACKGROUND: Structural brain volume abnormalities are among the most extensively studied endophenotypes in schizophrenia. Bivariate genetic model fitting (adjusted to account for selection) was used to quantify the genetic relationship between schizophrenia and brain volumes and to estimate the heritability of these volumes. METHOD: We demonstrated by simulation that the adjusted genetic model produced unbiased estimates for endophenotype heritability and the genetic and environmental correlations. The model was applied to brain volumes (whole brain, hippocampus, third and lateral ventricles) in a sample of 14 monozygotic (MZ) twin pairs concordant for schizophrenia, 10 MZ discordant pairs, 17 MZ control pairs, 22 discordant sibling pairs, three concordant sibling pairs, and 114 healthy control subjects. RESULTS: Whole brain showed a substantial heritability (88%) and lateral ventricles substantial common environmental effects (67%). Whole brain showed a significant genetic correlation with schizophrenia, whereas lateral ventricles showed a significant individual specific correlation with schizophrenia. There were significant familial effects for hippocampus and third ventricle, but the analyses could not resolve whether these were genetic or environmental in origin (around 30%each). CONCLUSIONS: Using genetic model fitting on twin and sibling data we have demonstrated differential sources of covariation between schizophrenia and brain volumes, genetic in the case of whole brain volume and individual specific environment in the case of lateral ventricles.

Adolescent↗
PubMed2005

Identifying potential risk haplotypes for schizophrenia at the DTNBP1 locus in Han Chinese and Scottish populations.

The dystrobrevin-binding protein 1 (DTNBP1) gene on chromosome 6p has emerged as a potential susceptibility gene for schizophrenia. Although a number of attempts to replicate the original association finding have been successful, they have not identified any obvious pathogenic variants or a single at risk haplotype common to all populations studied. In the present study we attempted further replication in an independent sample of 638 nuclear families from the Han Chinese population of Sichuan Province, SW China. We also examined 580 Scottish schizophrenic cases and 620 controls. We genotyped 10 single-nucleotide polymorphisms (SNPs) in DTNBP1 that were used in the original report of association, plus rs2619538 (SNP 'A') in the putative promoter region, which has also been associated with schizophrenia. In the Chinese trios we found that two SNPs (P1635 and P1765) were significantly overtransmitted, but with alleles opposite to those reported in the original studies. SNPs P1757 and P1765 formed a common haplotype, which also showed significant overtransmission. In the Scottish cases and controls, no individual markers were significantly associated with schizophrenia. A single haplotype, which included rs2619538 and P1583, and one rare haplotype, composed of P1320 and P1757, were significantly associated with schizophrenia, but no previously reported haplotypes were associated. Based on the data from the Chinese population, our results provide statistical support for DTNBP1 as a susceptibility gene for schizophrenia, albeit with haplotypes different from those of the original study. However, our lack of replication in the Scottish samples also indicates that caution is warranted when evaluating the robustness of the evidence for DTNBP1 as genetic risk factor for schizophrenia.

Alleles↗
PubMed2005

Association analysis of the RGS4 gene in Han Chinese and Scottish populations with schizophrenia.

We investigated the RGS4 as a susceptibility gene for schizophrenia in Chinese Han (184 trios and 138 sibling pairs, a total of 322 families) and Scottish (580 cases and 620 controls) populations using both a family trio and case-control design. Both the samples had statistical power greater than 70% to detect a heterozygote genotype relative risk of >1.2 for frequent RGS4-risk alleles. We genotyped four single nucleotide polymorphisms (SNPs) which have previously been associated with schizophrenia as either individually or part of haplotypes. Allele frequencies and linkage disequilibrium between the SNPs was similar in the two populations. In the Chinese sample, no individual SNPs or any of their haplotypes were associated with schizophrenia. In the Scottish population, one SNP (SNP7) was significantly over-represented in the cases compared with the controls (0.44 vs. 0.38; A allele; chi(2) 7.08, P = 0.011 after correction for correlation between markers by permutation testing). One two-marker haplotype, composed of alleles T and A of SNP4 and SNP7, respectively, showed individual significance after correction by permutation testing (chi(2) 6.8; P = 0.04). None of the full four-marker haplotypes showed association, including the G-G-G-G haplotype previously associated with schizophrenia in more than one sample and the A-T-A-A haplotype. Thus, our data do not directly replicate previous associations of RGS4, but association with SNP 7 in the Scottish population provides some support for a role in schizophrenia susceptibility. We cannot conclusively exclude RGS4, as associated haplotypes are likely to be surrogates for unknown causative alleles, whose relationship with overlying haplotypes may differ between the population groups. Differences in the association seen across the two populations could result from methodological factors such as diagnostic differences but most likely result from ethnic differences in haplotype structures within RGS4.

Case-Control Studies↗
PubMed2004

Haplotype association analysis of discrete and continuous traits using mixture of regression models.

We present a regression-based method of haplotype association analysis for quantitative and dichotomous traits in samples consisting of unrelated individuals. The method takes account of uncertain phase by initially estimating haplotype frequencies and obtaining the posterior probabilities of all possible haplotype combinations in each individual, then using these as weights in a finite mixture of regression models. Using this method, different combinations of marker loci can be modeled, to find a parsimonious set of marker loci that are most predictive and therefore most likely to be closely associated with the a quantitative trait locus. The method has the additional advantage of being able to use individuals with some missing genotype data, by considering all possible genotypes at the missing markers. We have implemented this method using the SNPHAP and Mx programs and illustrated its use on published data on idiopathic generalized epilepsy.

Chromosome Mapping↗
PubMed2004

Further investigation of linkage disequilibrium SNPs and their ability to identify associated susceptibility loci.

There is currently considerable interest in the use of single-nucleotide polymorphisms (SNPs) to map disease susceptibility genes. The success of this method will depend on a number of factors including the strength of linkage disequilibrium (LD) between marker and disease loci. We used a data set of SNP genotypings in the region of the APOE disease susceptibility locus to investigate the likely usefulness of SNPs in case-control studies. Using the estimated haplotype structure surrounding and including the APOE locus, and assuming a codominant disease model, we treated each SNP in turn as if it were a disease susceptibility locus and obtained, for each disease locus and markers, the expected likelihood ratio test (LRT) to assess disease association. We were particularly interested in the power to detect association with the susceptibility polymorphism itself, the power of nearby markers to detect association, and the ability to distinguish between the susceptibility polymorphism and marker loci also showing association. We found that the expected LRT depended critically on disease allele frequencies. For disease loci with a reasonably common allele we were usually able to detect association. However, for only a subset of markers in the close neighbourhood of the disease locus was association detectable. In these cases we were usually, but not always, able to distinguish the disease locus from nearby associated marker loci. For some disease loci, no other loci demonstrated detectable association with the disease phenotype. We conclude that one may need to use very dense SNP maps in order to avoid overlooking polymorphisms affecting susceptibility to a common phenotype.

Alzheimer Disease↗
PubMed2003

A quantitative genetic analysis of schizotypal personality traits.

BACKGROUND: Previous twin studies investigating the heritability of schizotypy have often had limited power and have failed to measure the disorganization/social anxiety component. METHOD: Seven hundred and thirty-three female twin pairs, drawn from the Institute of Psychiatry Volunteer Twin Register, completed the Oxford-Liverpool Inventory of Feelings and Experiences and the Peters et al. Delusions Inventory. Structural equation modelling was carried out on scores for MZ and DZ twin pairs. RESULTS: The best fitting models for all scales comprised additive genetic and unique environmental effects. Heritability was estimated at approximately 50% for most scales, although it was lower at 37% for the PDI scale. Multivariate structural equation model fitting revealed a best-fitting model in which additive genetic and unique environmental influences act through a single common pathway for Cognitive Disorganization, Unusual Experiences and the PDI, and through a separate common pathway for Cognitive Disorganization and Introvertive Anhedonia. CONCLUSIONS: The various components of schizotypy are moderately heritable. Multivariate model fitting indicates that at least two latent factor structures are required to account for the covariation between the various components of schizotypy. The positive and negative components of schizotypy are relatively genetically independent, although each in turn may be related to Cognitive Disorganization.

Adolescent↗
PubMed2003

Pre-morbid characteristics and co-morbidity of methamphetamine users with and without psychosis.

BACKGROUND: The long-term use of methamphetamine (MAMP) can result in psychosis but it is not clear why some individuals develop psychotic symptoms, while others use MAMP regularly over long periods and remain unscathed. We set out to characterize MAMP users and to examine the relationship of pre-morbid personality, pre-morbid social function and other psychiatric disorders to MAMP psychosis. METHOD: Four hundred and forty-five amphetamine users were recruited from a psychiatric hospital and a detention centre in Taipei, and were assessed with the Diagnostic Interview for Genetic Studies (DIGS). Their parents were interviewed with the Premorbid Schizoid and Schizotypal Traits (PSST) and the Premorbid Social Adjustment (PSA) schedules. Pre-morbid characteristics and psychiatric co-morbidity were compared between the MAMP users with a lifetime diagnosis of MAMP psychosis and those without. RESULTS: The MAMP users with psychosis presented a clinical picture which mimicked the positive symptoms of schizophrenia: 85% had auditory hallucinations; 71% persecutory delusions; 63% delusions of reference. Compared with their non-psychotic counterparts, these MAMP users were younger at first MAMP use, used larger amounts of MAMP, had a significantly higher mean PSST score, and higher rates of major depressive disorder, alcohol dependence and antisocial personality disorder. CONCLUSIONS: Earlier and larger use of MAMP was associated with increased risk of psychosis. Our data are also compatible with the view that pre-morbid schizoid/schizotypal personality predisposes MAMP users to develop psychosis, and that the greater the personality vulnerability, the longer the psychosis will persist.

Adolescent↗
PubMed2003

A model-fitting implementation of the DeFries-Fulker model for selected twin data.

In this research note, DeFries-Fulker (DF) regression analysis is reframed in model-fitting terms, where an individual's expected score is modeled as a function of their co-twin's proband status. This more flexible implementation of the DF model allows DZ-O twins to be incorporated in a sex-limitation model. Brief simulation results are presented along with the Mx scripts used.

Computer Simulation↗
PubMed2003

Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.

Biallelic markers, such as single nucleotide polymorphisms (SNPs), provide greater information for localising disease loci when treated as multilocus haplotypes, but often haplotypes are not immediately available from multilocus genotypes in case-control studies. An artificial neural network allows investigation of association between disease phenotype and tightly linked markers without requiring haplotype phase and without modelling any evolutionary history for the disease-related haplotypes. The network assesses whether marker haplotypes differ between cases and controls to the extent that classification of disease status based on multi-marker genotypes is achievable. The network is "trained" to "recognise" affection status based on supplied marker genotypes, and then for each multi-marker genotype it produces outputs which aim to approximate the associated affection status. Next, the genotypes are permuted relative to affection status to produce many random datasets and the process of training and recording of outputs is repeated. The extent to which the ability to predict affection for the real dataset exceeds that for the random datasets measures the statistical significance of the association between multi-marker genotype and affection. This permutation test performs well with simulated case-control datasets, particularly when major gene effects are present. We have explored the effects of systematically varying different network parameters in order to identify their optimal values. We have applied the permutation test to 4 SNPs of the calpain 10 (CAPN10) gene typed in a case-control sample of subjects with type 2 diabetes, impaired glucose tolerance, and controls. We show that the neural network produces more highly significant evidence for association than do single marker tests corrected for the number of markers genotyped. The use of a permutation test could potentially allow conditional analyses which could incorporate known risk factors alongside marker genotypes. Permuting only the marker genotypes relative to affection status and these risk factors would allow the contribution of the markers to disease risk to be independently assessed.

Calpain↗