Complex High-Resolution Linkage Disequilibrium and Haplotype Patterns of Single-Nucleotide Polymorphisms in 2.5 Mb of Sequence on Human Chromosome 21

Genomics ◽  
2001 ◽  
Vol 78 (1-2) ◽  
pp. 64-72 ◽  
Author(s):  
Michael Olivier ◽  
Valerie I Bustos ◽  
Michelle R Levy ◽  
Geoff A Smick ◽  
Ismael Moreno ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
High Resolution ◽  
Single Nucleotide Polymorphisms ◽  
Human Chromosome ◽  
Chromosome 21 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Chromosome 21

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

The effect of linkage disequilibrium on the estimates of Single Nucleotide Polymorphic effects

2009 ◽  
Vol 2009 ◽  
pp. 44-44
Author(s):  
K Moore ◽  
J Gibson ◽  
D Johnston
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Improvement ◽  
Dairy Herd ◽  
Physical Distance ◽  
Causative Mutation ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide Polymorphic ◽  
Single Nucleotide

The identification and exploitation of single nucleotide polymorphisms (SNP) associated with production traits present new opportunities for livestock genetic improvement. Often the identified SNP is not the causative mutation but rather is in some degree of linkage disequilibrium (LD). LD markers within 5cM can be considered as direct markers for the causative mutation because they are located close to the causative mutation (Dekkers, 2004). In a dairy herd, Farnir et al., (2000) estimated that the average LD, measured as D′ was 0.5 for loci pairs positioned within 5cM. Goddard et al., (2006) estimated that LD measured as r2 decreased rapidly as the physical distance between loci increased; at a separating distance of 0.5Mb the LD (r2) was only approximately 0.2. The aim of this work was to use stochastic simulation to investigate the effect that the distance between the SNP and causative mutation had on the accuracy of estimating additive and dominance effects of the causative mutation.

scholarly journals Susceptibility to Heart Defects in Down Syndrome Is Associated with Single Nucleotide Polymorphisms in HAS 21 Interferon Receptor Cluster and VEGFA Genes

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1428
Author(s):  
Carmela Rita Balistreri ◽  
Claudia Leonarda Ammoscato ◽  
Letizia Scola ◽  
Tiziana Fragapane ◽  
Rosa Maria Giarratana ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Single Nucleotide Polymorphisms ◽  
Heart Defects ◽  
Chromosome 21 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cardiac Defects ◽  
Risk Alleles ◽  
And Gender ◽  
Heart Disorders

Background: Congenital heart defects (CHDs) are present in about 40–60% of newborns with Down syndrome (DS). Patients with DS can also develop acquired cardiac disorders. Mouse models suggest that a critical 3.7 Mb region located on human chromosome 21 (HSA21) could explain the association with CHDs. This region includes a cluster of genes (IFNAR1, IFNAR2, IFNGR2, IL10RB) encoding for interferon receptors (IFN-Rs). Other genes located on different chromosomes, such as the vascular endothelial growth factor A (VEGFA), have been shown to be involved in cardiac defects. So, we investigated the association between single nucleotide polymorphisms (SNPs) in IFNAR2, IFNGR2, IL10RB and VEGFA genes, and the presence of CHDs or acquired cardiac defects in patients with DS. Methods: Individuals (n = 102) with DS, and age- and gender-matched controls (n = 96), were genotyped for four SNPs (rs2229207, rs2834213, rs2834167 and rs3025039) using KASPar assays. Results: We found that the IFNGR2 rs2834213 G homozygous genotype and IL10RB rs2834167G-positive genotypes were more common in patients with DSand significantly associated with heart disorders, while VEGFA rs3025039T-positive genotypes (T/*) were less prevalent in patients with CHDs. Conclusions: We identified some candidate risk SNPs for CHDs and acquired heart defects in DS. Our data suggest that a complex architecture of risk alleles with interplay effects may contribute to the high variability of DS phenotypes.

scholarly journals Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S73 ◽  
Author(s):  
Priya Duggal ◽  
Elizabeth M Gillanders ◽  
Rasika A Mathias ◽  
Grace P Ibay ◽  
Alison P Klein ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
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