Genome-wide search for signatures of selection in three
... arithmetic mean of the maps from each breed. To assign the ancestral status at each marker, SNP genotyping was performed on animals from nine out-group species (Supplementary Table 1). Genotypes with GC score < 0.8 were discarded, before alleles were compared across species. A total of 35,008 SNP ha ...
... arithmetic mean of the maps from each breed. To assign the ancestral status at each marker, SNP genotyping was performed on animals from nine out-group species (Supplementary Table 1). Genotypes with GC score < 0.8 were discarded, before alleles were compared across species. A total of 35,008 SNP ha ...
Lecture 6: GWAS in Samples with Structure
... Genetic markers that are not influencing the disease but with significant differences in allele frequencies between the ...
... Genetic markers that are not influencing the disease but with significant differences in allele frequencies between the ...
A genome-wide scan in affected sibling pairs with
... LOD score .2) and were removed. The method we use for the linkage analysis is based on the assumption that there is no LD in the analyzed data. Therefore r 2 is set at a particularly low level of 0.1. A total of 18 379 SNPs remained after cleaning. Complying with the MIAME standards, raw data are av ...
... LOD score .2) and were removed. The method we use for the linkage analysis is based on the assumption that there is no LD in the analyzed data. Therefore r 2 is set at a particularly low level of 0.1. A total of 18 379 SNPs remained after cleaning. Complying with the MIAME standards, raw data are av ...
HST.161 Molecular Biology and Genetics in Modern Medicine
... the mutant allele will also have the SNP marker (SNP A in the case of beta globin, C in the case of cftr, etc.). In contrast, of mutants in the gene of interest are new, then presence of a mutant allele will not be strongly associated with a particular SNP in intron 2. With this simple logic, we can ...
... the mutant allele will also have the SNP marker (SNP A in the case of beta globin, C in the case of cftr, etc.). In contrast, of mutants in the gene of interest are new, then presence of a mutant allele will not be strongly associated with a particular SNP in intron 2. With this simple logic, we can ...
Multilocus Genetics
... mating in generation I and the first two matings in generation II are test cross. The third mating in generation II is not informative because it involves the A allele which we are not following. We have a total of 16 offspring that are informative. Of these three were recombinant. As with all test ...
... mating in generation I and the first two matings in generation II are test cross. The third mating in generation II is not informative because it involves the A allele which we are not following. We have a total of 16 offspring that are informative. Of these three were recombinant. As with all test ...
CHAPTER 1: Introduction During the past century some major
... Nucleotide polymorphism: proportion of nucleotide sites that are expected to be polymorphic in any suitable sample Multi-dimensional D ...
... Nucleotide polymorphism: proportion of nucleotide sites that are expected to be polymorphic in any suitable sample Multi-dimensional D ...
Bayesian Partition Models for Identifying Expression Quantitative
... multiple gene clusters into a module. Clustering of genes makes the computation faster and alleviates the dominance of the gene expression clustering effect in module determination. The aggregation of multiple gene clusters into a module allows the model to capture the complex dependence structure a ...
... multiple gene clusters into a module. Clustering of genes makes the computation faster and alleviates the dominance of the gene expression clustering effect in module determination. The aggregation of multiple gene clusters into a module allows the model to capture the complex dependence structure a ...
Relatedness in the post-genomic era: is it still
... Traditional measures of relatedness, which are based on probabilities of IBD (identity-by-descent) from common ancestors within a pedigree, depend on the choice of pedigree. However, in natural populations there is no complete pedigree or any optimal pedigree that could form the basis of a canonical ...
... Traditional measures of relatedness, which are based on probabilities of IBD (identity-by-descent) from common ancestors within a pedigree, depend on the choice of pedigree. However, in natural populations there is no complete pedigree or any optimal pedigree that could form the basis of a canonical ...
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... either a higher degree of vagility than expected for this species or similar selection pressures maintaining allele frequencies across the area sampled. Associations between patterns of variation at two loci and behavioural, morphological and environmental variables suggested that selection may be a ...
... either a higher degree of vagility than expected for this species or similar selection pressures maintaining allele frequencies across the area sampled. Associations between patterns of variation at two loci and behavioural, morphological and environmental variables suggested that selection may be a ...
Genome-wide association studies for complex traits: consensus
... The phenomenon whereby a single allele can affect several distinct aspects of the phenotype of an organism, often traits not previously thought to be mechanistically related. ...
... The phenomenon whereby a single allele can affect several distinct aspects of the phenotype of an organism, often traits not previously thought to be mechanistically related. ...
Resolving Individuals Contributing Trace Amounts of DNA to Highly
... modifications for known factors including homogeneity of the mixture and accuracy of our reference populations. We then proceed to simulate the effects of three combinations of variables when using SNP microarrays, including probe measurement noise, fraction of the person of interest’s DNA in the mi ...
... modifications for known factors including homogeneity of the mixture and accuracy of our reference populations. We then proceed to simulate the effects of three combinations of variables when using SNP microarrays, including probe measurement noise, fraction of the person of interest’s DNA in the mi ...
Complex Signatures of Natural Selection at the Duffy Blood Group
... (Hamblin and Di Rienzo 2000). The low level of variation in such a common allele, coupled with its unusually high FST value, prompted the question of whether a previously unrecognized selective pressure on the FY*A allele (or one tightly linked to it) underlies the observed patterns. Unlike the FY*O ...
... (Hamblin and Di Rienzo 2000). The low level of variation in such a common allele, coupled with its unusually high FST value, prompted the question of whether a previously unrecognized selective pressure on the FY*A allele (or one tightly linked to it) underlies the observed patterns. Unlike the FY*O ...
Natural selection
... the composition of a gene pool increases the probability favorable alleles will come together in the same individual. ...
... the composition of a gene pool increases the probability favorable alleles will come together in the same individual. ...
Blood pressure and human genetic variation in the
... The first few GWASs published by us and others in 2007, including the Wellcome Trust Case Control Consortium [68] (2000 hypertensive cases, 3000 population-based controls), the Diabetics Genetics Initiative [69] (1464 cases with type 2 diabetes and 1467 matched controls) and the Framingham Heart Stu ...
... The first few GWASs published by us and others in 2007, including the Wellcome Trust Case Control Consortium [68] (2000 hypertensive cases, 3000 population-based controls), the Diabetics Genetics Initiative [69] (1464 cases with type 2 diabetes and 1467 matched controls) and the Framingham Heart Stu ...
gene linkage probs
... Chapter 12.2 - Gene Linkage Different alleles exist because any gene is subject to mutation Wild type is a term used for the most common allele in the population. (+) Other alleles, often called mutant alleles, may produce a different phenotype An alternate form of designating alleles. Alleles that ...
... Chapter 12.2 - Gene Linkage Different alleles exist because any gene is subject to mutation Wild type is a term used for the most common allele in the population. (+) Other alleles, often called mutant alleles, may produce a different phenotype An alternate form of designating alleles. Alleles that ...
Quantitative Genetics
... Make 2 lines differing in both marker loci and the quantitative trait in loci. Cross the two lines. Cross F1 to itself or backcrossed with parental line. Measure offspring for quantitative phenotype. Characterize genotype and marker loci. ...
... Make 2 lines differing in both marker loci and the quantitative trait in loci. Cross the two lines. Cross F1 to itself or backcrossed with parental line. Measure offspring for quantitative phenotype. Characterize genotype and marker loci. ...
The Genome of a Mongolian Individual Reveals
... and population data are lacking. They are increasingly necessary to explore characteristics of population evolution, disease, and personal healthcare. In this study, we sequenced the genome of a representative Mongolian male individual with high coverage (>100) by using the next sequencing technolo ...
... and population data are lacking. They are increasingly necessary to explore characteristics of population evolution, disease, and personal healthcare. In this study, we sequenced the genome of a representative Mongolian male individual with high coverage (>100) by using the next sequencing technolo ...
Bio-session package - Social Science Genetic Association Consortium
... In this review we will briefly give the history of GWASs and then focus on the discoveries made through this experimental design, what those discoveries tell us and do not tell us about the genetics and biology of complex traits, and what immediate utility has come out of these studies. We will focu ...
... In this review we will briefly give the history of GWASs and then focus on the discoveries made through this experimental design, what those discoveries tell us and do not tell us about the genetics and biology of complex traits, and what immediate utility has come out of these studies. We will focu ...
Further genetic evidence suggesting a role for the
... proportion of permuted datasets in which the minimum P-value was at least as small as that seen in the observed data. This approach was used to correct for tests of multiple SNPs within each phenotype, and also for tests of multiple SNPs across multiple phenotypes. For the latter, correlation betwee ...
... proportion of permuted datasets in which the minimum P-value was at least as small as that seen in the observed data. This approach was used to correct for tests of multiple SNPs within each phenotype, and also for tests of multiple SNPs across multiple phenotypes. For the latter, correlation betwee ...
Two RANTES gene polymorphisms and their - dr
... conformity to the Hardy-Weinberg equilibrium. Multiple variable logistic regression model with adjustment for conventional risk factors was used. Haplotypes were estimated by maximum likehood (software ARLEQUIN, v.3.000). ...
... conformity to the Hardy-Weinberg equilibrium. Multiple variable logistic regression model with adjustment for conventional risk factors was used. Haplotypes were estimated by maximum likehood (software ARLEQUIN, v.3.000). ...
Masters_Thesis_Final - JScholarship
... analyze the correlation of sequence variation to human genetic traits and diseases. Genome-wide association studies (GWAS) have been performed ...
... analyze the correlation of sequence variation to human genetic traits and diseases. Genome-wide association studies (GWAS) have been performed ...
Numbering the hairs on our heads: The shared
... rare variants in the diseased population, followed by verification that the function of the candidate gene is altered, indicates that altered function increases disease. Typical rare variants have ORs between 2 and 10 , but individually explain little of the variance in disease susceptibility becaus ...
... rare variants in the diseased population, followed by verification that the function of the candidate gene is altered, indicates that altered function increases disease. Typical rare variants have ORs between 2 and 10 , but individually explain little of the variance in disease susceptibility becaus ...
Quantitative Genetics: Traits controlled my many loci Quantitative
... measured phenotypes in a population of F2 plants from parents that differ in kernel colour. We can see that more than two or three phenotypes are seen in the F2. This pattern is explained by the action of ...
... measured phenotypes in a population of F2 plants from parents that differ in kernel colour. We can see that more than two or three phenotypes are seen in the F2. This pattern is explained by the action of ...
Selection Purpose change over a period of several generations the
... change in the phenotype. Results in a fairly constant mean possibly somewhat reduced variance for a trait from one generation to the next. It is done by selecting those individuals for the trait that are near the average for the trait. It may occur with or without knowledge or intent of the breeder. ...
... change in the phenotype. Results in a fairly constant mean possibly somewhat reduced variance for a trait from one generation to the next. It is done by selecting those individuals for the trait that are near the average for the trait. It may occur with or without knowledge or intent of the breeder. ...
PopGen2: Linkage Disequilibrium
... markers are located in a genome. You look for markers that exhibit strong disequilibrium of alleles with the disease trait. Association studies have their limitations as well. If the disease is influenced by rare alleles at many loci this approach will have low power. The recombination rate and the ...
... markers are located in a genome. You look for markers that exhibit strong disequilibrium of alleles with the disease trait. Association studies have their limitations as well. If the disease is influenced by rare alleles at many loci this approach will have low power. The recombination rate and the ...
Tag SNP
A tag SNP is a representative single nucleotide polymorphism (SNP) in a region of the genome with high linkage disequilibrium that represents a group of SNPs called a haplotype. It is possible to identify genetic variation and association to phenotypes without genotyping every SNP in a chromosomal region. This reduces the expense and time of mapping genome areas associated with disease, since it eliminates the need to study every individual SNP. Tag SNPs are useful in whole-genome SNP association studies in which hundreds of thousands of SNPs across the entire genome are genotyped.