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Principal components analysis corrects for stratification in genome-wide association studies
TLDR
This work describes a method that enables explicit detection and correction of population stratification on a genome-wide scale and uses principal components analysis to explicitly model ancestry differences between cases and controls. Expand
PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
TLDR
An analytical strategy is introduced, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes, which identifies a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expand
Population Structure and Eigenanalysis
TLDR
An approach to studying population structure (principal components analysis) is discussed that was first applied to genetic data by Cavalli-Sforza and colleagues, and results from modern statistics are used to develop formal significance tests for population differentiation. Expand
A Draft Sequence of the Neandertal Genome
TLDR
The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other. Expand
A second generation human haplotype map of over 3.1 million SNPs
TLDR
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated. Expand
Sequencing and comparison of yeast species to identify genes and regulatory elements
TLDR
A comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species, which inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. Expand
Detecting recent positive selection in the human genome from haplotype structure
TLDR
A framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations is introduced, and the core haplotypes carrying the proposed protective mutation stand out and show significant evidence of selection. Expand
Ancient Admixture in Human History
TLDR
A suite of methods for learning about population mixtures are presented, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. Expand
Reconstructing Indian Population History
TLDR
It is predicted that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically and is higher in traditionally upper caste and Indo-European speakers. Expand
Testing for ancient admixture between closely related populations.
TLDR
This paper presents a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree, and derives the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. Expand
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