Using linear predictors to impute allele frequencies from summary or pooled genotype data

Using Linear Predictors to Impute Allele Frequencies from Summary or Pooled Genotype Data.

Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level genotype data, whereas in practice it is often the case that only summary data are available. For example this may occur because, for reasons of privacy or politi...

Allele Frequencies and Genotype Frequencies

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection ...

A computer program to simulate multilocus genotype data with spatially autocorrelated allele frequencies.

Many models for inference of population genetic parameters are based on the assumption that the data set at hand consists of groups displaying within-group Hardy-Weinberg equilibrium at individual loci and linkage equilibrium between loci. This assumption is commonly violated by the presence of within-group spatial structure arising from nonrandom mating of individuals due to isolation by dista...

Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation

Next-generation sequencing (NGS) technology has provided researchers with opportunities to study the genome in unprecedented detail. In particular, NGS is applied to disease association studies. Unlike genotyping chips, NGS is not limited to a fixed set of SNPs. Prices for NGS are now comparable to the SNP chip, although for large studies the cost can be substantial. Pooling techniques are ofte...