2011_InstructorSlidesR
... Objectives of Group Research Projects • Enable participants to use the polymerase chain reaction (PCR) and DNA sequence analyses to discover something new about themselves or the surrounding microbial environment • Run 2-3 different projects, to keep group number to a manageable size and so differe ...
... Objectives of Group Research Projects • Enable participants to use the polymerase chain reaction (PCR) and DNA sequence analyses to discover something new about themselves or the surrounding microbial environment • Run 2-3 different projects, to keep group number to a manageable size and so differe ...
Package 'MatrixEQTL'
... The testing procedure accounts for extra covariates in cvrt parameter. The errorCovariance parameter can be set to the error variance-covariance matrix to account for heteroskedastic and/or correlated errors. Associations significant at pvOutputThreshold (pvOutputThreshold.cis) levels are saved to o ...
... The testing procedure accounts for extra covariates in cvrt parameter. The errorCovariance parameter can be set to the error variance-covariance matrix to account for heteroskedastic and/or correlated errors. Associations significant at pvOutputThreshold (pvOutputThreshold.cis) levels are saved to o ...
ORIGINAL ARTICLES Genetic, Functional, and Phenotypic Diversity
... DNA samples were extracted from whole blood, drawn during each subject’s first visit for taste testing, by the Human Genetics Clinical Laboratory (HGCL) core facility at the University of Texas Southwestern Medical Center. To comprehensively ascertain mutational polymorphism, the TAS2R38 gene was se ...
... DNA samples were extracted from whole blood, drawn during each subject’s first visit for taste testing, by the Human Genetics Clinical Laboratory (HGCL) core facility at the University of Texas Southwestern Medical Center. To comprehensively ascertain mutational polymorphism, the TAS2R38 gene was se ...
Basic Concepts in the Study of Diseases with Complex Genetics
... quite unlikely to be linked. In fact, with a LOD score of 3.0, our chance to be wrong is about 9%—assuming a simple Mendelian disease (Lander and Schork 1994). To model the traditional threshold of claiming significance, i.e., p 5 .05, a LOD score of 3.3 needs to be achieved (Lander and Schork 1994) ...
... quite unlikely to be linked. In fact, with a LOD score of 3.0, our chance to be wrong is about 9%—assuming a simple Mendelian disease (Lander and Schork 1994). To model the traditional threshold of claiming significance, i.e., p 5 .05, a LOD score of 3.3 needs to be achieved (Lander and Schork 1994) ...
Genomics of Dyslipidemia → Trends in Cardiovascular Medicine
... Population variation in genes can be studied to look for effects of new drugs on specific mechanisms of disease Can be used to show causality WE CAN FOCUS ON the random genetic variation assigned at birth via processes of meiosis and chromosomal assortment Mimics randomization during clinical trials ...
... Population variation in genes can be studied to look for effects of new drugs on specific mechanisms of disease Can be used to show causality WE CAN FOCUS ON the random genetic variation assigned at birth via processes of meiosis and chromosomal assortment Mimics randomization during clinical trials ...
Document
... Kaplan, Hudson, and Langley (1989) showed that the distance d at which a neutral site can be influenced by a sweep is a function of the strength of selection s and the recombination fraction c, with d = 0.01 s/c. ...
... Kaplan, Hudson, and Langley (1989) showed that the distance d at which a neutral site can be influenced by a sweep is a function of the strength of selection s and the recombination fraction c, with d = 0.01 s/c. ...
Genomic scans for selective sweeps using SNP data
... Access the most recent version at doi:10.1101/gr.4252305 ...
... Access the most recent version at doi:10.1101/gr.4252305 ...
Applications of Genomics
... as mutations. Classic examples include hypertrophic cardiomyopathy and Marfan syndrome. There are common variants (>1% of the general population) that have a small effect on the function of a gene. These variants do not change gene activity enough to cause disease by themselves but instead need to b ...
... as mutations. Classic examples include hypertrophic cardiomyopathy and Marfan syndrome. There are common variants (>1% of the general population) that have a small effect on the function of a gene. These variants do not change gene activity enough to cause disease by themselves but instead need to b ...
Fifteen years of genomewide scans for selection: trends, lessons
... mutational events occurs span several orders of magnitude. In humans, single-nucleotide mutations happen at a rate of 10 8–10 9/site/generation (Nachman & Crowell 2000; Roach et al. 2010), microsatellite mutation rates range from 10 2 to 10 6 (Weber & Wong 1993; Sun et al. 2012), and large-scale cop ...
... mutational events occurs span several orders of magnitude. In humans, single-nucleotide mutations happen at a rate of 10 8–10 9/site/generation (Nachman & Crowell 2000; Roach et al. 2010), microsatellite mutation rates range from 10 2 to 10 6 (Weber & Wong 1993; Sun et al. 2012), and large-scale cop ...
Directional selection
... together on the chromosome forming a tight linkage group a “supergene”. ...
... together on the chromosome forming a tight linkage group a “supergene”. ...
Amelioration of Sardinian 0 thalassemia by genetic
... Interestingly, the contribution of BCL11A variation appeared to be greater than that of the HBS1L-MYB locus variants (OR ⫽ 5.15 and 4.61, respectively), whereas both were appreciably larger than the effect attributable to the coinheritance of ␣-thalassemia (OR ⫽ 3.32, Table 1). A more definitive est ...
... Interestingly, the contribution of BCL11A variation appeared to be greater than that of the HBS1L-MYB locus variants (OR ⫽ 5.15 and 4.61, respectively), whereas both were appreciably larger than the effect attributable to the coinheritance of ␣-thalassemia (OR ⫽ 3.32, Table 1). A more definitive est ...
mdr1-1 - Salamander Genome Project
... • Loci were selected based on proximity to MDR1 • Primers were produced for 4 markers and MDR1 for PCR • Haplotypes reconstructed with PHASE program (assumes all haplotypes from a pop. were created in that population) ...
... • Loci were selected based on proximity to MDR1 • Primers were produced for 4 markers and MDR1 for PCR • Haplotypes reconstructed with PHASE program (assumes all haplotypes from a pop. were created in that population) ...
Divergent evolution of lifespan associated with mitochondrial DNA
... several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected ...
... several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected ...
Diversity of Lactase Persistence Alleles in Ethiopia
... method. Ethical approval was obtained from the University of Addis Ababa and UCLH (ref 01/0236). Each volunteer provided fully informed consent for the project and completed a questionnaire relating to their self-declared ethnicity, ancestry, language (also language and ethnicity of parents and gran ...
... method. Ethical approval was obtained from the University of Addis Ababa and UCLH (ref 01/0236). Each volunteer provided fully informed consent for the project and completed a questionnaire relating to their self-declared ethnicity, ancestry, language (also language and ethnicity of parents and gran ...
Suggestive Association With Ocular Phoria at Chromosome 6p22
... quantitative phenotype using the software PLINK.31 To control for any population stratification that remained in our sample, we used EIGENSOFT32 to extract the top three principal components (PC) accounting for genetic variation. The three PCs were entered, along with sex, as covariates in the regre ...
... quantitative phenotype using the software PLINK.31 To control for any population stratification that remained in our sample, we used EIGENSOFT32 to extract the top three principal components (PC) accounting for genetic variation. The three PCs were entered, along with sex, as covariates in the regre ...
Genetic diversity in Northern Spain (Basque Country and Cantabria
... the main ethnic groups, GM haplotypes have been shown to be a powerful tool in human population genetics due to their high frequency variation between populations. Furthermore, since several haploptypes are specific to certain groups4,5 they allow the possibility to evaluate gene flow and admixtures ...
... the main ethnic groups, GM haplotypes have been shown to be a powerful tool in human population genetics due to their high frequency variation between populations. Furthermore, since several haploptypes are specific to certain groups4,5 they allow the possibility to evaluate gene flow and admixtures ...
GenomeBrowser - CBS
... Basic functionalities • Finding a gene • by name • by sequence • Gene structure • Sequence orthologues • Single Nucleotide Polymorphisms • Gene Sorter - sort according to expression, homology ... • Custom tracks ...
... Basic functionalities • Finding a gene • by name • by sequence • Gene structure • Sequence orthologues • Single Nucleotide Polymorphisms • Gene Sorter - sort according to expression, homology ... • Custom tracks ...
PDF hosted at the Radboud Repository of the Radboud University
... procedures for the Illumina and Affymetrix data can be found elsewhere [24]. Imputation to the European reference dataset (HapMap 1+2, Release 22 Build 36) was undertaken by means of MACH [25] using a set of Single Nucleotide Polymorphisms (SNPSs) common across all genotyping platforms. SNPs charact ...
... procedures for the Illumina and Affymetrix data can be found elsewhere [24]. Imputation to the European reference dataset (HapMap 1+2, Release 22 Build 36) was undertaken by means of MACH [25] using a set of Single Nucleotide Polymorphisms (SNPSs) common across all genotyping platforms. SNPs charact ...
Unraveling the Genetic Etiology of Adult Antisocial
... procedures for the Illumina and Affymetrix data can be found elsewhere [24]. Imputation to the European reference dataset (HapMap 1+2, Release 22 Build 36) was undertaken by means of MACH [25] using a set of Single Nucleotide Polymorphisms (SNPSs) common across all genotyping platforms. SNPs charact ...
... procedures for the Illumina and Affymetrix data can be found elsewhere [24]. Imputation to the European reference dataset (HapMap 1+2, Release 22 Build 36) was undertaken by means of MACH [25] using a set of Single Nucleotide Polymorphisms (SNPSs) common across all genotyping platforms. SNPs charact ...
Notes
... Suffix tree Suffix tree is data structure, which allows one to find, extremely efficiently, all distinct subsequences in a given sequence. There are efficient algorithms to construct suffix trees given by Weiner (1973) and McCreight (1976) (in linear time) For the task of comparing two DNA se ...
... Suffix tree Suffix tree is data structure, which allows one to find, extremely efficiently, all distinct subsequences in a given sequence. There are efficient algorithms to construct suffix trees given by Weiner (1973) and McCreight (1976) (in linear time) For the task of comparing two DNA se ...
Remarkably Little Variation in Proteins Encoded
... We sought to answer several questions. Worldwide, what common coding differences exist among the X-degenerate ...
... We sought to answer several questions. Worldwide, what common coding differences exist among the X-degenerate ...
Self-incompatibility: How to Stay Incompatible
... haplotypes, particularly in the regions outside the Slocus [7,8] and the haplotypes have different gene arrangements (Figure 1). On the other hand, analyses of patterns of diversity in S-locus sequence data, particularly the observation that linkage disequilibrium between polymorphic sites decays wi ...
... haplotypes, particularly in the regions outside the Slocus [7,8] and the haplotypes have different gene arrangements (Figure 1). On the other hand, analyses of patterns of diversity in S-locus sequence data, particularly the observation that linkage disequilibrium between polymorphic sites decays wi ...
What is linkage disequilibrium
... - it also has been found to vary among individuals of a species. - if some of this variation is genetically controlled, then we would expect that recombination is a process that can evolve over time. - there are many studies known from Drosophila in which recombination rates have changed over the co ...
... - it also has been found to vary among individuals of a species. - if some of this variation is genetically controlled, then we would expect that recombination is a process that can evolve over time. - there are many studies known from Drosophila in which recombination rates have changed over the co ...
rs6445975 SNPedia tehranchi
... that in a pool of 9 SLE SNPs including rs6445975, an increase in genetic susceptibility to SLE was associated with early disease onset. [PMID 20881011]. Other studies have shown no association of rs6445975 to SLE. A study using 804 patients with SLE and 667 healthy controls, mainly of Mexican ancest ...
... that in a pool of 9 SLE SNPs including rs6445975, an increase in genetic susceptibility to SLE was associated with early disease onset. [PMID 20881011]. Other studies have shown no association of rs6445975 to SLE. A study using 804 patients with SLE and 667 healthy controls, mainly of Mexican ancest ...
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.