Linkage disequilibrium in humans: models and data.

By J. K. Pritchard, M. Przeworski. American Journal of Human Genetics, 2001

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Citations in the corpus

Development and Characterization of a High Density SNP Genotyping Assay for Cattle (2009, background): “We consider this density to represent a practical starting point for GWA studies in Bos taurus, and at this density, a set of approximately 30,000 variable markers would be sufficient to represent the 3 billion bases of sequence in the bovine genome [6] at an average LD of r(2)$0.”
LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms (2006, background): “The user can specify either the squared allelic correlation r 2 (Pritchard and Przeworski 2001) or Lewontin’s | D (cid:48) | (Lewontin 1964) as the measure of LD to be plotted.”
The future of association studies: gene-based analysis and replication. (2004, background): “This may be particularly relevant under a common-disease-common-variant (CDCV) hypothesis (Chakravarti 1999; Weiss and Clark 2002), in which the age of the mutation allows for differential recombination histories in different populations (Pritchard and Przeworski 2001).”
Haplotype tagging for the identification of common disease genes (2001, background): “Although different metrics that measure the extent of LD have been evaluate”
Calibrating a coalescent simulation of human genome sequence variation. (2005, background): “Perhaps the most obvious discrepancy occurs in predictions of linkage disequilibrium, the nonrandom association of nearby alleles (Frisse et al. 2001; Pritchard and Przeworski 2001; Ardlie et al. 2002).”
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets (2007, background): “…of pathogens (Awadalla 2003; Moya et al. 2004; Wilson et al. 2005) and the characterization of linkage disequilibrium in large genomes (Pritchard and Przeworski 2001; Ardlie et al. 2002; Gabriel et al. 2002) to theoretical questions about clonality and the definitions of clonal and nearly…”
A random forest approach to the detection of epistatic interactions in case-control studies (2009, methodology): “In the second stage, statistical tests on the basis of the B statistics are applied to detect significant one, two-, and three-way epistatic interactions. between the unobserved disease locus and a genotyped locus ( r 2 ) [31].”
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. (2004, background): “The power to detect the disease-associated polymorphism indirectly in N samples is equivalent to power to detect it directly in Nr 2 samples (Pritchard and Przeworski 2001).”
Association analysis using SSR markers to find QTL for seed protein content in soybean (2008, background): “Association studies have been effectively used to identify the genetic causes of several human diseases (Pritchard and Przeworski 2001; Reich et al. 2001; Goedde et al. 2002; Weiss and Clark 2002; Twells et al. 2003).”
A coalescent-based method for detecting and estimating recombination from gene sequences. (2002, background): “…the population recombination rate and test for recombinalinkage disequilibrium while population structure tends tion are available within the LDhat package, which can be downloaded from http:/ /www.stats.ox.ac.uk/‫ف‬mcvean. to increase linkage disequilibrium (e.g., Pritchard and Przeworski 2001).”
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms (2002, methodology): “Coalescent-based simulations have been used to explore the properties of LD in the human genom”