A robust method to estimate regional polygenic correlation under misspecified linkage disequilibrium structure

2018 ◽  
Vol 42 (7) ◽  
pp. 636-647 ◽  
Author(s):  
Guillaume Paré ◽  
Shihong Mao ◽  
Wei Q. Deng
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Disequilibrium Structure ◽  
Robust Method

scholarly journals Linkage disequilibrium structure of the 5q31-33 region in a Thai population

2008 ◽  
Vol 53 (9) ◽  
pp. 850-856 ◽  
Author(s):  
Pornlada Nuchnoi ◽  
Jun Ohashi ◽  
Izumi Naka ◽  
Duangporn Nacapunchai ◽  
Katsushi Tokunaga ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Disequilibrium Structure ◽  
Thai Population

Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens

2005 ◽  
Vol 33 (4) ◽  
pp. 582-585 ◽  
Author(s):  
J. Hardy ◽  
A. Pittman ◽  
A. Myers ◽  
K. Gwinn-Hardy ◽  
H.C. Fung ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Neurodegenerative Disease ◽  
Sequence Comparison ◽  
Selection Pressure ◽  
Homo Sapiens ◽  
Linkage Disequilibrium Structure ◽  
Homo Neanderthalensis ◽  
Common Founder ◽  
The Common

The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the co-existence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.

scholarly journals Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Reuben J. Pengelly ◽  
William Tapper ◽  
Jane Gibson ◽  
Marcin Knut ◽  
Rick Tearle ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Human Populations ◽  
Whole Genome ◽  
Linkage Disequilibrium Structure ◽  
Genome Sequences

scholarly journals The nonlinear structure of linkage disequilibrium

2019 ◽  
Author(s):  
Reginald D. Smith
Keyword(s):  
Linkage Disequilibrium ◽  
Frequency Dependence ◽  
Allele Frequency ◽  
Allele Frequencies ◽  
Nonlinear Dependence ◽  
Mathematical Framework ◽  
Linkage Disequilibrium Structure ◽  
Nonlinear Structure ◽  
Linear And Nonlinear ◽  
Fundamental Shift

AbstractThe allele frequency dependence of the ranges of all measures of linkage disequilibrium is well-known. The maximum values of commonly used parameters such as r2 and D vary depending on the allele frequencies at each locus. However, though this phenomenon is recognized and accounted for in many studies, the comprehensive mathematical framework underlying the limits of linkage disequilibrium measures at various frequency combinations is often heuristic or empirical. Here, it is demonstrated that underlying this behavior is the fundamental shift between linear and nonlinear dependence in the linkage disequilibrium structure between loci. The proportion of linear and nonlinear dependence can be estimated and it demonstrates how even the same values of r2 can have different implications for the nature of the overall dependence. One result of this is the value of D′, when defined as only a positive number, has a minimum value of |r|. Understanding this dependence is crucial to making correct inferences about the relationships between two loci in linkage disequilibrium.

scholarly journals Linkage disequilibrium structure of KIAA0319 and DCDC2, two candidate susceptibility genes for developmental dyslexia

2006 ◽  
Vol 11 (12) ◽  
pp. 1061-1061 ◽  
Author(s):  
D Harold ◽  
S Paracchini ◽  
T Scerri ◽  
M Dennis ◽  
N Cope ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Developmental Dyslexia ◽  
Susceptibility Genes ◽  
Linkage Disequilibrium Structure

scholarly journals P4-084: THE APOLIPOPROTEIN E2 CODING POLYMORPHISM AND LINKAGE DISEQUILIBRIUM STRUCTURE IN ALZHEIMER'S DISEASE IN THE APOE REGION

2019 ◽  
Vol 15 ◽  
pp. P1306-P1307
Author(s):  
Alexander M. Kulminski ◽  
Leonardo Shu ◽  
Yury Loika ◽  
Liang He ◽  
Alireza Nazarian ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Linkage Disequilibrium ◽  
Linkage Disequilibrium Structure

Characterization of linkage disequilibrium structure, mutation history, and tagging SNPs, and their use in association analyses:ELAC2 and familial early-onset prostate cancer

2005 ◽  
Vol 28 (3) ◽  
pp. 232-243 ◽  
Author(s):  
Nicola J. Camp ◽  
Jeff Swensen ◽  
Benjamin D. Horne ◽  
James M. Farnham ◽  
Alun Thomas ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Linkage Disequilibrium ◽  
Early Onset ◽  
Linkage Disequilibrium Structure
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