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Open AccessJournal ArticleDOI

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

TLDR
This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
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Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

TL;DR: The main innovations of the new version of the Arlequin program include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans.
Journal ArticleDOI

Second-generation PLINK: rising to the challenge of larger and richer datasets

TL;DR: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility, and for the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.
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GCTA: a tool for genome-wide complex trait analysis.

TL;DR: The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets and focuses on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation.
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Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

Shaun Purcell, +81 more
- 06 Aug 2009 - 
TL;DR: The extent to which common genetic variation underlies the risk of schizophrenia is shown, using two analytic approaches, and the major histocompatibility complex is implicate, which is shown to involve thousands of common alleles of very small effect.
Journal ArticleDOI

A second generation human haplotype map of over 3.1 million SNPs

Kelly A. Frazer, +237 more
- 18 Oct 2007 - 
TL;DR: 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.
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A general test of association for quantitative traits in nuclear families.

TL;DR: A general approach that can accommodate nuclear families of any size, with or without parental information, is constructed, and it is shown that, when siblings are available, the total number of genotypes required in order to achieve comparable power is smaller if parents are not genotyped.
Journal ArticleDOI

Permutation Tests for Multiple Loci Affecting a Quantitative Character

TL;DR: Two extensions of the permutation-based method for estimating empirical threshold values are presented, which yield critical values that can be used to construct tests for the presence of minor QTL effects while accounting for effects of known major QTL.
Journal ArticleDOI

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome

TL;DR: A high-resolution genetic map of the human genome is presented, based on statistical analyses of genetic variation data, and more than 25,000 recombination hotspots are identified, together with motifs and sequence contexts that play a role in hotspot activity.

Categorical Data Analysis

Agresti
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