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At least 307 records · Page 17Linked to original sources
PubMed2006

Testing for association in the presence of population stratification: a simulation study comparing the S-TDT, STRAT and the GC.

A novel approach for association testing in the presence of population stratification has been introduced by Pritchard et al. (2000a) and Pritchard et al. (2000b). The structured association approach is a two-tiered procedure that first estimates the population structure and then tests the null hypothesis H0: 'no association within subpopulations' in the second step. A power comparison of the stratified test for association (STRAT) (Pritchard et al., 2000b) and the Transmission-Disequilibrium-Test (TDT) (Spielman and Ewens, 1993a) in a simulation framework showed superiority of STRAT if allele frequencies or associations between allele and disease differ strongly in subpopulations. In more homogeneous situations, the TDT had greater power than STRAT. However, the TDT, based on family trios,that uses population controls, needs 50% more genotyping compared to STRAT. The Sib-Transmission-Disequilibrium-Test (S-TDT) needs the same amount of genotyping since it relays in its minimal configuration on pairs of siblings. This raises the question how the S-TDT (Spielman and Ewens, 1998a) performs compared to the population based methods STRAT and Genomic Controls (GC). In this paper, we present a simulation study accounting for two different models of population stratification in different settings of allele frequencies and under different risk models. The results showed that under a discrete as well as under an admixed population model, STRAT strongly outperformed the S-TDT and the GC when different alleles were associated in different subpopulations. In contrast, the S-TDT had greater power than STRAT when the same allele was associated in both subpopulations. Here, the GC was sometimes even more powerful than the S-TDT, depending on the population model and the allele frequency differences. A general recommendation for the use of one of the tests can therefore not be given.

Algorithms↗
PubMed2003

Power evaluations for family-based tests of association with incomplete parental genotypes.

While a variety of methods have been developed to deal with incomplete parental genotype information in family-based association tests, sampling design issues with incomplete parental genotype data still have not received much attention. In this article, we present simulation studies with four genetic models and various sampling designs and evaluate power in family-based association studies. Efficiency depends heavily on disease prevalence. With rare diseases, sampling affecteds and their parents is preferred, and three sibs will be required to have close power if parents are unavailable. With more common diseases, sampling affecteds and two sibs will generally be more efficient than trios. When parents are unavailable, siblings need not be phenotyped if the disease is rare, but a loss of power will result with common diseases. Finally, for a class of complex traits where other genetic and environmental factors also cause phenotypic correlation among siblings, little loss of efficiency occurs to rare disease, but substantial loss of efficiency occurs to common disease.

Data Interpretation, Statistical↗
PubMed2000

Implementing a unified approach to family-based tests of association.

We describe a broad class of family-based association tests that are adjusted for admixture; use either dichotomous or measured phenotypes; accommodate phenotype-unknown subjects; use nuclear families, sibships or a combination of the two, permit multiple nuclear families from a single pedigree; incorporate di- or multi-allelic marker data; allow additive, dominant or recessive models; and permit adjustment for covariates and gene-by-environment interactions. The test statistic is basically the covariance between a user-specified function of the genotype and a user-specified function of the trait. The distribution of the statistic is computed using the appropriate conditional distribution of offspring genotypes that adjusts for admixture.

Genotype↗
PubMed1996

Assessing declarative memory in schizophrenia using Wisconsin Card Sorting Test stimuli: the Paired Associate Recognition Test.

The Paired Associate Recognition Test (PART) was developed to measure declarative memory using Wisconsin Card Sorting Test (WCST) stimuli, so that both tasks could be administered during functional neuroimaging to differentiate memory and executive function, and associated frontal and temporal lobe activation in schizophrenia. The current study was designed to compare PART and WCST performance in schizophrenic patients and to examine effects of medication and symptomatology. The PART, WCST, and standard declarative memory tasks were administered to 30 chronic schizophrenic patients and 30 matched healthy control subjects. Supporting task validity was the finding that patients were equally impaired on the PART and the WCST. Neuroleptics did not appear to affect performance. The effect of anticholinergic medication correlated negatively with WCST performance in a small subsample. Severity of schizophrenia-specific symptoms measured at intake on the Brief Psychiatric Rating Scale correlated negatively with performance on the WCST. These results support the application of the PART and WCST in future functional neuroimaging studies.

Adult↗
PubMed2001

Efficient use of siblings in testing for linkage and association.

Tests of linkage and association between a disease and either a candidate gene or marker allele can be based on sibships with at least one affected and one unaffected sibling. However, specialized techniques are required to account for within-sibship correlation if some sibships contain more than one affected or more than one unaffected sib. In this paper, we propose Within Sibship Paired Resampling (WSPR), a technique that is designed to test the null hypothesis of no linkage or no association, even when sibships contain variable numbers of sibs. One repeatedly generates data subsets based on randomly sampling one affected and one unaffected sibling from each sibship, and each subset is analyzed individually. Then, evidence is combined by averaging results across these resampled data sets, applying a variance expression that implicitly accounts for the correlation among siblings. While the general WSPR procedure allows for numerous testing strategies, we describe two in detail. Simulation results for scenarios with varying degrees of population stratification demonstrate good power for the WSPR testing methods compared to the sib TDT (S-TDT) and the sibship disequilibrium test (SDT).

Computer Simulation↗
PubMed2004

Syphilis testing in association with gonorrhea/chlamydia testing during a syphilis outbreak.

We used an electronic medical records system retrospectively to evaluate how frequently, in a public hospital and its clinics, combined gonorrhea/chlamydia tests were accompanied by a syphilis test before and during a syphilis outbreak. Among 70,330 gonorrhea/chlamydia tests (1996-2000), the proportion with a syphilis test increased from 13% (preoutbreak) to 50% (intervention period) for men and from 6% to 13% for nonpregnant women. The increased syphilis testing coincided with a multifaceted public health intervention.

Adult↗
PubMedDate not supplied

Factors associated with PAP testing in adolescents in northern Nova Scotia.

OBJECTIVE: To determine relationships of socio-economic factors and contraceptive behaviours with PAP testing in sexually active women aged 15-19 who had received physician services in northern Nova Scotia in the previous year. METHODS: A cross-sectional survey was completed by adolescents attending four high schools in three counties in northern Nova Scotia. Questions concerned contraceptive behaviours, socio-economic status and health services use, including PAP testing. Associations of socio-economic factors and contraceptive behaviours with receipt of a PAP test in the previous year were examined in women who were sexually active for at least one year, and who also had visited a physician during the previous year. RESULTS: One thousand and ninety adolescent women aged 15-19 completed surveys, with a response rate of 91%. Of the 396 (36.3%) who reported being sexually active and having visited a physician in the previous year, 393 provided information about PAP testing. Of these, 214 (54.5%) reported receiving a PAP test. Factors associated with PAP testing included viewing one's family as advantaged and living in a major town as opposed to a more rural area. Compared with using hormonal contraception, using either condom without other effective contraception or no effective contraception at last intercourse were negatively associated with PAP testing. CONCLUSIONS: These findings suggest that physicians use hormonal contraception as a cue for PAP testing in adolescent women. Guidelines call for regular PAP testing of sexually active adolescents, and efforts to increase adolescent PAP testing should include professional development to increase recognition of sexual activity.

Adolescent↗
PubMed2004

The role of haplotypes in candidate gene studies.

Human geneticists working on systems for which it is possible to make a strong case for a set of candidate genes face the problem of whether it is necessary to consider the variation in those genes as phased haplotypes, or whether the one-SNP-at-a-time approach might perform as well. There are three reasons why the phased haplotype route should be an improvement. First, the protein products of the candidate genes occur in polypeptide chains whose folding and other properties may depend on particular combinations of amino acids. Second, population genetic principles show us that variation in populations is inherently structured into haplotypes. Third, the statistical power of association tests with phased data is likely to be improved because of the reduction in dimension. However, in reality it takes a great deal of extra work to obtain valid haplotype phase information, and inferred phase information may simply compound the errors. In addition, if the causal connection between SNPs and a phenotype is truly driven by just a single SNP, then the haplotype-based approach may perform worse than the one-SNP-at-a-time approach. Here we examine some of the factors that affect haplotype patterns in genes, how haplotypes may be inferred, and how haplotypes have been useful in the context of testing association between candidate genes and complex traits.

Genetic Predisposition to Disease↗