scholarly journals Homozygosity and Linkage Disequilibrium

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1707-1719
Author(s):  
Chiara Sabatti ◽  
Neil Risch
Keyword(s):  
Phase Equilibrium ◽  
Linkage Disequilibrium ◽  
Specific Form ◽  
Polymorphic Markers ◽  
Biological Interpretation ◽  
Gametic Phase

Abstract We illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure from the gametic phase equilibrium: We describe the specific form of dependence that is associated with high (low) homozygosity and derive various linkage disequilibrium measures. They feature a clear biological interpretation, can be used to construct tests, and are standardized to allow comparison across loci and populations. They are particularly advantageous to measure linkage disequilibrium between highly polymorphic markers.

scholarly journals Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

BMC Genetics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Luiz F. Brito ◽  
Mohsen Jafarikia ◽  
Daniela A. Grossi ◽  
James W. Kijas ◽  
Laercio R. Porto-Neto ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Consistency Of Gametic Phase ◽  
Gametic Phase

Haplotype Distribution of and Linkage Disequilibrium Between Four Polymorphic Markers Near the CFTR Locus in Brazilian Cystic Fibrosis Patients

Human Biology ◽  
2005 ◽  
Vol 77 (6) ◽  
pp. 853-865 ◽  
Author(s):  
Giselda M. K. Cabello ◽  
Pedro H. Cabello ◽  
Jorge S. Lopez-Camelo ◽  
Juan C. Llerena ◽  
Octavio Fernandes
Keyword(s):  
Cystic Fibrosis ◽  
Linkage Disequilibrium ◽  
Polymorphic Markers ◽  
Haplotype Distribution

scholarly journals Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Daniela A. Grossi ◽  
Mohsen Jafarikia ◽  
Luiz F. Brito ◽  
Marcos E. Buzanskas ◽  
Mehdi Sargolzaei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Gametic Phase

Adjacent genetic markers on chromosome 11p15.5 at or near the tyrosine hydroxylase locus that show population linkage disequilibrium with each other do not show allelic association with bipolar affective disorder

1999 ◽  
Vol 29 (6) ◽  
pp. 1449-1454 ◽  
Author(s):  
A. McQUILLIN ◽  
J. LAWRENCE ◽  
D. CURTIS ◽  
G. KALSI ◽  
C. SMYTH ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Tyrosine Hydroxylase ◽  
Affective Disorder ◽  
Association Studies ◽  
Bipolar Affective Disorder ◽  
Allelic Association ◽  
Polymorphic Markers ◽  
Chromosome 11 ◽  
Chromosome 11P15.5 ◽  
Control Association

Background. Linkage and association studies have suggested genetic susceptibility to bipolar affective disorder in a region of chromosome 11 around the tyrosine hydroxylase locus. We attempted to test the hypothesis that there was allelic association between polymorphisms around the tyrosine hydroxylase locus and bipolar affective disorder.Methods. A case–control association study was employed using four polymorphic markers, which span a region of approximately 2 cM across the tyrosine hydroxylase locus.Results. No evidence for allelic association between bipolar affective disorder and any of these markers was found. However, linkage disequilibrium between the markers was detected.Conclusions. This finding diminishes the probability that genes in this region influence susceptibility to bipolar affective disorder, at least in our sample.

scholarly journals Assumptions about frequency-dependent architectures of complex traits bias measures of functional enrichment

2020 ◽  
Author(s):  
Shadi Zabad ◽  
Aaron P. Ragsdale ◽  
Rosie Sun ◽  
Yue Li ◽  
Simon Gravel
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Variants ◽  
Complex Traits ◽  
Statistical Difference ◽  
Functional Enrichment ◽  
Frequency Effect ◽  
Summary Statistics ◽  
Biological Interpretation ◽  
Implicit And Explicit ◽  
The Relationship

AbstractLinkage-Disequilibrium Score Regression (LDSC) is a popular framework for analyzing GWAS summary statistics that allows for estimating SNP heritability, confounding, and functional enrichment of genetic variants with different annotations. Recent work has highlighted the influence of implicit and explicit assumptions of the model on the biological interpretation of the results. In this work, we explored a formulation of LDSC that replaces the r2 measure of LD with a recently-proposed unbiased estimator of the D2 statistic. In addition to modest statistical difference across estimators, this derivation highlighted implicit and unrealistic assumptions about the relationship between allele frequency, effect size, and annotation status. We carry out a systematic comparison of alternative LDSC formulations by applying them to summary statistics from 47 GWAS traits. Our results show that commonly used models likely underestimate functional enrichment. These results highlight the importance of calibrating the LDSC model to achieve a more robust understanding of polygenic traits.

The worldwide distribution of the VHL 598C>T mutation indicates a single founding event

Blood ◽  
2004 ◽  
Vol 103 (5) ◽  
pp. 1937-1940 ◽  
Author(s):  
Enli Liu ◽  
Melanie J. Percy ◽  
Christopher I. Amos ◽  
Yongli Guan ◽  
Sanjay Shete ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Human Evolution ◽  
Haplotype Analysis ◽  
Strong Linkage Disequilibrium ◽  
Healthy Controls ◽  
Polymorphic Markers ◽  
Strong Linkage ◽  
Vhl Gene ◽  
Worldwide Distribution ◽  
Common Defect

Abstract The first congenital defect of hypoxia-sensing homozygosity for VHL 598C>T mutation was recently identified in Chuvash polycythemia. Subsequently, we found this mutation in 11 unrelated individuals of diverse ethnic backgrounds. To address the question of whether the VHL 598C>T substitution occurred in a single founder or resulted from recurrent mutational events in human evolution, we performed haplotype analysis of 8 polymorphic markers covering 340 kb spanning the VHL gene on 101 subjects bearing the VHL 598C>T mutation, including 72 homozygotes (61 Chuvash and 11 non-Chuvash) and 29 heterozygotes (11 Chuvash and 18 non-Chuvash), and 447 healthy unrelated individuals from Chuvash and other ethnic groups. The differences in allele frequencies for each of the 8 markers between 447 healthy controls (598C) and 101 subjects bearing the 598T allele (P < 10–7) showed strong linkage disequilibrium. Haplotype analysis indicated a founder effect. We conclude that the VHL 598C>T mutation, the most common defect of congenital polycythemia yet found, was spread from a single founder 14 000 to 62 000 years ago.

Sign in / Sign up

Export Citation Format

Share Document