A5066249678- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Genetic Dynamics
- Geochemistry and Geologic Mapping
- Genetic and phenotypic traits in livestock
- Sensory Analysis and Statistical Methods
- Spectroscopy and Chemometric Analyses
- Genetics and Plant Breeding
- Gene expression and cancer classification
- Leaf Properties and Growth Measurement
- Hydrocarbon exploration and reservoir analysis
- Bayesian Methods and Mixture Models
- Bioinformatics and Genomic Networks
- Statistical Methods and Applications
- Neural Networks and Applications
- Ecology and Vegetation Dynamics Studies
- Genomic variations and chromosomal abnormalities
- Mental Health Research Topics
- Biomedical Text Mining and Ontologies
- Mineral Processing and Grinding
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Data-Driven Disease Surveillance
- Species Distribution and Climate Change
- Advanced Statistical Methods and Models
University of Washington
2017-2025
Polytechnic University of Puerto Rico
2025
Universitat Politècnica de Catalunya
2015-2024
University of California, Los Angeles
2022
Seattle University
2018
Universitat Pompeu Fabra
2000
Genetics and IVF Institute
1999
Testing genetic markers for Hardy-Weinberg equilibrium is an important issue in association studies. The HardyWeinberg package offers the classical tests equilibrium, functions power computation and simulation of marker data under disequilibrium. Functions testing presence missing by using multiple imputation are provided. also supplies various graphical tools such as ternary plots with acceptance regions, log-ratio Q-Q exploring status a large set diallelic markers. Classical...
Statistical tests for Hardy–Weinberg equilibrium have been an important tool detecting genotyping errors in the past, and remain quality control of next generation sequence data. In this paper, we analyze complete chromosomes 1000 genomes project by using exact test procedures autosomal X-chromosomal variants. We find that rate disequilibrium largely exceeds what might be expected chance alone all chromosomes. Observed is, about 60% cases, due to heterozygote excess. suggest most excess can...
Testing genetic markers for Hardy–Weinberg equilibrium (HWE) is an important tool detecting genotyping errors in large-scale studies. For at the X chromosome, typically χ2 or exact test applied to females only, and hemizygous males are considered be uninformative. In this paper we show that relevant, because a difference allele frequency between may indicate HWE not hold. The testing of on chromosome has received little attention, lay down foundation biallelic X-chromosomal HWE. We develop...
Genotype-phenotype association studies often combine phenotype data from multiple to increase statistical power. Harmonization of the usually requires substantial effort due heterogeneity in definitions, study design, collection procedures, and data-set organization. Here we describe a centralized system for harmonization that includes input domain experts, quality control, documentation, reproducible results, data-sharing mechanisms. This was developed National Heart, Lung, Blood...
Objective: Exact tests for Hardy-Weinberg equilibrium are widely used in genetic association studies. We evaluate the mid p-value, unknown genetics literature, as an alternative standard p-value exact test.
We design a graphical test for Hardy-Weinberg equilibrium. This can circumvent the calculation of p values and statistical (non)significance large number bi-allelic markers be inferred from their position in graph.By rewriting expressions chi(2) statistic (with without continuity correction) terms heterozygote frequency an acceptance region equilibrium is obtained that depicted ternary plot.We obtain equations curves plot separate are out those The depend on chosen significance level, sample...
The graphical representation of the correlation matrix by means different multivariate statistical methods is reviewed, a comparison procedures presented with use an example data set, and improved better fit proposed. Principal component analysis widely used for making pictures structure, though as shown weighted alternating least squares approach that avoids fitting diagonal outperforms both principal factor in approximating matrix. Weighted very strong competitor analysis, particular if...
John Aitchison has shown that the logratio principal component analysis of multiple samples a biallelic polymorphism can evidentiate Hardy-Weinberg law. This article extends Aitchison's work to multiallelic polymorphisms showing how law manifests itself in based statistical larger genotypic compositions. Some fundamental relationships between allelic and compositions are derived, close corresponding compositional biplots established. We perform simulations practical genetic data explore...
The visualization of the correlation matrix by means biplots is considered. classical centering operations, either overall mean, column means, or row and are shown to be problematic for visualisation matrix, sub-optimal in terms goodness-of-fit. More flexible adjustments possible using a single scalar adjustment, set scalars both row–and–column weighted alternating least squares algorithm. Recently, with adjustment have been advocated outperform usual made principal component analysis. This...
The scatter plot is a well known and easily applicable graphical tool to explore relationships between two quantitative variables. For the exploration of relations multiple variables, generalisations are useful. We present an overview multivariate plots focussing on following situations. Firstly, we look at for portraying variables within one data matrix. Secondly, discuss similar case qualitative Thirdly, describe sets where focus correlations. Finally, treat response predictor matrix...
The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism equilibrium will retain its status if any allele together with corresponding genotypes deleted from population. Similarly, transitivity principle also applies alleles are joined, which leads summation of frequencies and their genotype frequencies. These basic properties intuitive, but they have apparently not been formalized or investigated. This article provides straightforward proof principle,...
Abstract Statistical tests for Hardy–Weinberg equilibrium are important elementary tools in genetic data analysis. X‐chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing equilibrium. Recently, we proposed specific exact bi‐allelic that include the hemizygous males, as well consider gender. In this study, present extension of previous work with multiple alleles. A full enumeration algorithm used...
Objective To analyse the correlation between implementation of tobacco control policies and consumption, particularly rolling tobacco, electronic cigarettes (e-cigarettes) users intent to quit smoking in 27 countries European Union. Design Ecological study with country as unit analysis. Data sources We used data from activities, measured by Tobacco Control Scale (TCS), countries, 2010, prevalence consumption Eurobarometer 2012. Analysis Spearman coefficients (r sp ) their 95% CIs. Results...
This paper addresses the issue of exact-test based statistical inference for Hardy-Weinberg equilibrium in presence missing genotype data. Missing genotypes often are discarded when markers tested equilibrium, which can lead to bias about equilibrium. Single and multiple imputation improve on We develop tests missingness by using both inbreeding coefficients (or, equivalently, χ(2) statistics) exact p-values. The analysis a set with high rate from GENEVA project prematurity shows that be...
The human secondary sex ratio is compared with the percentage of Y-chromosome bearing spermatozoa in semen. Live birth about 51.3%, whereas overall our study samples was 50.3%, i.e. 1% closer to proportion expected by Mendelian segregation. observed difference between live and sperm–sex ratios significant (P < 0.0001). A possible effect male age on Y-bearing found be non-significant.
It is well known that the pattern of linkage disequilibrium varies between human populations, with remarkable geographical stratification. Indirect association studies routinely exploit around genes, particularly in isolated populations where it assumed to be higher. Here, we explore both amount and decay physical distance along 211 gene regions, most them related complex diseases, across 39 HGDP-CEPH population samples, focusing on defined as isolates. Within each region use r2 all possible...
Recombination varies greatly among species, as illustrated by the poor conservation of recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand evolution recombination. Here, we analyze its recent in humans. We calculated rates adjacent pairs 636,933 common single-nucleotide polymorphism loci 28 worldwide human populations analyzed them relation genetic distances populations. found a strong highly significant correlation...
Abstract This paper treats the topic of representing supplementary variables in biplots obtained by principal component analysis (PCA) and correspondence (CA). We follow a geometrical approach where we minimize errors that are when scores PCA or CA solution projected onto vector represents variable. shows optimal directions for can be found solving regression problem, justifies earlier formulae from Gabriel least squares sense. derive new results regarding properties, goodness fit statistics...
ABSTRACT Standard statistical tests for equality of allele frequencies in males and females Hardy‐Weinberg equilibrium are tightly linked by their assumptions. Tests assume equilibrium, whereas the usual chi‐square or exact test sexes. In this paper, we propose ways to break interdependence assumptions two proposing an omnibus that can both hypotheses jointly, as well a likelihood ratio approach permits these phenomena be tested jointly separately. The illustrated with data from 1000 Genomes project.
In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking procedure. Missing genotypes typically discarded prior to testing. this paper we show that inference can be biased when missing values discarded. We propose use multiple imputation of in order improve proportions. For employ multinomial logit model uses information from allele intensities and/or neighbouring markers. Analysis an empirical data set single nucleotide...
Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction kinship RNA-seq would be useful for confirming the expected relationships family based studies highlighting samples case-control or population Currently, reconstruction pedigrees largely on SNPs microsatellites, obtained genotyping arrays, whole genome exome sequencing. Potential problems with using detection are low proportion that it covers, highly skewed...
The X chromosome is a relatively large chromosome, harboring lot of genetic information. Much the statistical analysis X-chromosomal information complicated by fact that males only have one copy. Recently, frequentist tests for Hardy–Weinberg equilibrium been proposed specifically dealing with markers on chromosome. Bayesian test procedures autosomes described, but work in this context lacking. This paper gives first approach testing biallelic at Marginal and joint posterior distributions...