Biomedical subjects

Josephine Hoh

Publications and source records attributed to Josephine Hoh.

8 recordsLinked to original sources

PubMed2003

Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA.

The efficiency of single-nucleotide polymorphism haplotype analysis may be increased by DNA pooling, which can dramatically reduce the number of genotyping assays. We develop a method for obtaining maximum likelihood estimates of haplotype frequencies for different pool sizes, assess the accuracy of these estimates, and show that pooling DNA samples is efficient in estimating haplotype frequencies. Although pooling K individuals increases ambiguities, at least for small pool size K and small numbers of loci, the uncertainty of estimation increases <K times that of unpooled DNA. We also develop the asymptotic variance-covariance of maximum likelihood estimates and evaluate the accuracy of variance estimates by Monte Carlo methods. When the sample size of pools is moderately large, the asymptotic variance estimates are rather accurate. Completely or partially missing genotyping information is allowed for in our analysis. Finally, our methods are applied to single-nucleotide polymorphisms in the angiotensinogen gene.

Algorithms↗

PubMed2003

SNP haplotype tagging from DNA pools of two individuals.

BACKGROUND: DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers. RESULTS: We present an algorithm for reconstructing haplotypes (alleles for multiple SNPs on same chromosome) from pools of two individual DNAs, in which Hardy-Weinberg equilibrium conditions or other assumptions are not required. The program outputs, in addition to inferred haplotypes, a minimal number of haplotype-tagging SNPs that are identified after an exhaustive search procedure. CONCLUSION: Our method and algorithms lead to a significant reduction in genotyping effort, for example, in case-control disease association studies while maintaining the possibility of reconstructing haplotypes under very general conditions.

Algorithms↗

PubMed2003

Mathematical multi-locus approaches to localizing complex human trait genes.

Statistical analysis methods for gene mapping originated in counting recombinant and non-recombinant offspring, but have now progressed to sophisticated approaches for the mapping of complex trait genes. Here, we outline new statistical methods that capture the simultaneous effects of multiple gene loci and thereby achieve a more global view of gene action and interaction than is possible by traditional gene-by-gene analysis. We aim to show that the work of statisticians goes far beyond the running of computer programs.

Biometry↗

PubMed2003

Statistical methods for analyzing microarray feature data with replications.

Expression levels in oligonucleotide microarray experiments depend on a potentially large number of factors, for example, treatment conditions, different probes, different arrays, and so on. To dissect the effects of these factors on expression levels, fixed-effects ANOVA methods have previously been proposed. Because we are not necessarily interested in estimating the specific effects of different probes and arrays, we propose to treat these as random effects. Then we only need to estimate their means and variances but not the effect of each of their levels; that is, we can work with a much reduced number of parameters and, consequently, higher precision for estimating expression levels. Thus, we developed a mixed-effects ANOVA model with some random and some fixed effects. It automatically accounts for local normalization between different arrays and for background correction. The method was applied to each of the 6,584 genes investigated in a microarray experiment on two mouse cell lines, PA6/S and PA6/8, where PA6/S enhances proliferation of Pre B cells in vitro but PA6/8 does not. To detect a set of differentially expressed genes (multiple testing problem), we applied the method of controlling the false discovery rate (FDR), which successfully identified 207 genes with significantly different expression levels.

Algorithms↗

PubMed2003

Set association analysis of SNP case-control and microarray data.

Common heritable diseases ("complex traits") are assumed to be due to multiple underlying susceptibility genes. While genetic mapping methods for Mendelian disorders have been very successful, the search for genes underlying complex traits has been difficult and often disappointing. One of the reasons may be that most current gene-mapping approaches are still based on conventional methodology of testing one or a few SNPs at a time. Here, we demonstrate a simple strategy that allows for the joint analysis of multiple disease-associated SNPs in different genomic regions. Our set-association method combines information over SNPs by forming sums of relevant single-marker statistics. As previously hypothesized, we show here that this approach successfully addresses the "curse of dimensionality" problem--too many variables should be estimated with a comparatively small number of observations. We also report results of simulation studies showing that our method furnishes unbiased and accurate significance levels. Power calculations demonstrate good power even in the presence of large numbers of nondisease associated SNPs. We extended our method to microarray expression data, where expression levels for large numbers of genes should be compared between two tissue types. In applications to such data, our approach turned out to be highly efficient.

Case-Control Studies↗

PubMed2002

A protein kinase A-dependent molecular switch in synapsins regulates neurite outgrowth.

Cyclic AMP (cAMP) promotes neurite outgrowth in a variety of neuronal cell lines through the activation of protein kinase A (PKA). We show here, using both Xenopus laevis embryonic neuronal culture and intact X. laevis embryos, that the nerve growth-promoting action of cAMP/PKA is mediated in part by the phosphorylation of synapsins at a single amino acid residue. Expression of a mutated form of synapsin that prevents phosphorylation at this site, or introduction of phospho-specific antibodies directed against this site, decreased basal and dibutyryl cAMP-stimulated neurite outgrowth. Expression of a mutation mimicking constitutive phosphorylation at this site increased neurite outgrowth, both under basal conditions and in the presence of a PKA inhibitor. These results provide a potential molecular approach for stimulating neuron regeneration, after injury and in neurodegenerative diseases.

Animals↗

PubMed2002

Pharmacogenetic analysis of adverse drug effect reveals genetic variant for susceptibility to liver toxicity.

A retrospective pharmacogenetic study was conducted to identify possible genetic susceptibility factors in patients in whom the administration of the anti-Parkinson drug, tolcapone (TASMAR), was associated with hepatic toxicity. We studied 135 cases of patients with elevated liver transaminase levels (ELT) of >/=1.5 times above the upper limit of normal, in comparison with matched controls that had also received the drug but had not experienced ELT. DNA samples were genotyped for 30 previously described or newly characterized bi-allelic single nucleotide polymorphisms (SNPs), representing 12 candidate genes selected based on the known metabolic pathways involved in the tolcapone elimination. SNPs located within the UDP-glucuronosyl transferase 1A gene complex, which codes for the enzymes involved in the main elimination pathway of the drug, were found to be significantly associated with the occurrence of tolcapone-associated ELTs.

Benzophenones↗

PubMed2002

Asthma, allergy, and airway hyperresponsiveness are not linked to the beta(2)-adrenoceptor gene.

STUDY OBJECTIVES: To exclude genetic linkage between the beta(2)-adrenoceptor gene and asthma, allergy, and methacholine airway hyperresponsiveness. DESIGN: The current study used six distinct intragene markers within the beta(2)-adrenoceptor gene, and evaluated genetic linkage between the beta(2)-adrenoceptor and asthma, allergy, or methacholine airway hyperresponsiveness in eight multiplex families. PATIENTS: Forty-nine members of eight multiplex families with a high incidence of asthma. INTERVENTIONS: Phenotypes were characterized by history, physical examination, skin testing, pulmonary function tests, and methacholine inhalational challenge. Genetic loci were identified using restriction fragment length polymorphisms, denaturing gradient gel electrophoresis, and restriction enzyme digest of polymerase chain reaction-amplified fragments of the beta(2)-adrenoceptor gene. MEASUREMENTS AND RESULTS: Nonparametric analysis using computer analysis software found no evidence for linkage between these markers within the beta(2)-adrenoceptor gene and asthma. Parametric exclusion analysis using a dominant inheritance model resulted in large negative lod scores (- 6.74, - 19.44, and - 49.9, respectively) for tight linkage between asthma, allergy, or methacholine airway hyperresponsiveness and these polymorphic markers. CONCLUSIONS: These results indicate that asthma, allergy, and methacholine airway hyperresponsiveness are not linked to a dominant beta(2)-adrenoceptor gene with strong effect in these eight families with an inherited pattern of asthma.

Adolescent↗