Descriptive analysis and inference of Higher
... generation) genetic markers contains important information that can be used in genetic association studies (Gorelick and Laubichler [2004],Lewontin [1988],McPeek and Strahs [1999]) and population genetics. Deviation from probabilistic independence of alleles at two different markers (allelic associa ...
... generation) genetic markers contains important information that can be used in genetic association studies (Gorelick and Laubichler [2004],Lewontin [1988],McPeek and Strahs [1999]) and population genetics. Deviation from probabilistic independence of alleles at two different markers (allelic associa ...
gemini Documentation
... As version 0.12.2 of GEMINI it is required that your input VCF file undergo additional preprocessing such that multiallelic variants are decomposed and normalized using the vt toolset from the Abecasis lab. Note that we have also decomposed and normalized all of the VCF-based annotation files (e.g., ...
... As version 0.12.2 of GEMINI it is required that your input VCF file undergo additional preprocessing such that multiallelic variants are decomposed and normalized using the vt toolset from the Abecasis lab. Note that we have also decomposed and normalized all of the VCF-based annotation files (e.g., ...
Pest Control by the Introduction of a Conditional Lethal Trait on
... types and over 3 billion genotypes. With the rapid advance of gene technology, a release involving 10 Ð20 loci is conceivable. The multilocus problem is simple if the loci are in equilibrium. In this case the loci are in random association and gamete frequencies are simply the product of gene freque ...
... types and over 3 billion genotypes. With the rapid advance of gene technology, a release involving 10 Ð20 loci is conceivable. The multilocus problem is simple if the loci are in equilibrium. In this case the loci are in random association and gamete frequencies are simply the product of gene freque ...
TaqMan® SNP Genotyping Assays User Guide
... particular level of observation or actions as described below: Note: Provides information that may be of interest or help but is not critical to the use of the product. ...
... particular level of observation or actions as described below: Note: Provides information that may be of interest or help but is not critical to the use of the product. ...
Fulltext PDF - Indian Academy of Sciences
... to this topic: researchers concluded that only homozygous CYP2C19*17/*17 could be considered UMs and that they are likely at an increased risk to suffer therapeutic ineffectiveness, principally for drugs with a very narrow therapeutic window, such as Clopidogrel (Li-Wan-Po et al. 2009). We were able ...
... to this topic: researchers concluded that only homozygous CYP2C19*17/*17 could be considered UMs and that they are likely at an increased risk to suffer therapeutic ineffectiveness, principally for drugs with a very narrow therapeutic window, such as Clopidogrel (Li-Wan-Po et al. 2009). We were able ...
Tapanes-Castillo A, Weaver EJ, Smith RP, Kamei Y, Caspary T, Hamilton-Nelson KL, Slifer SH, Martin ER, Bixby JL, Lemmon VP. Neurogenetics. 2012 Feb;11(1):53-71. A modifier locus on chromosome 5 contributes to L1 cell adhesion molecule X-linked hydrocephalus in mice.
... knocked out using a Cre/lox approach [60]. L1-6D heterozygous females (L1-6D/+) were then bred to wild-type 129S2/ SvPasCrlf (129S2) or C57BL/6J (B6) males for at least 12 generations to generate congenic (Cg) mice. A twogeneration, outcross–intercross breeding scheme was next performed to generate ...
... knocked out using a Cre/lox approach [60]. L1-6D heterozygous females (L1-6D/+) were then bred to wild-type 129S2/ SvPasCrlf (129S2) or C57BL/6J (B6) males for at least 12 generations to generate congenic (Cg) mice. A twogeneration, outcross–intercross breeding scheme was next performed to generate ...
Time to asthma onset Asthma score Bivariate analysis - Hal-CEA
... to date have examined the variability of asthma age-of-onset using survival analysis concepts. Such approach can take into account age at onset for individuals who developed the disease and age at time of examination for those who were free of disease upon examination but were still at risk for the ...
... to date have examined the variability of asthma age-of-onset using survival analysis concepts. Such approach can take into account age at onset for individuals who developed the disease and age at time of examination for those who were free of disease upon examination but were still at risk for the ...
The importance of genetic influences in asthma REVIEW H. Los* , G.H. Koppelman*
... It has long been established that genetic factors are very important in the pathogenesis of asthma. Familial aggregation of asthma was probably first described by Sennertus in 1650 [26]. At the beginning of this century, R. Cooke performed two large studies on the inheritance of atopy, one in 1916 a ...
... It has long been established that genetic factors are very important in the pathogenesis of asthma. Familial aggregation of asthma was probably first described by Sennertus in 1650 [26]. At the beginning of this century, R. Cooke performed two large studies on the inheritance of atopy, one in 1916 a ...
Population Genetics - University of Evansville Faculty Web sites
... Polymorphism (P) - the proportion of polymorphic (e.g. variable) loci in a population We can also determine the average polymorphism by examining the degree of polymorphism in 3 or more populations ...
... Polymorphism (P) - the proportion of polymorphic (e.g. variable) loci in a population We can also determine the average polymorphism by examining the degree of polymorphism in 3 or more populations ...
CYP2C19 phenotype in a South African cohort
... represent the demographics of the South African population. This included 70 Black African, 10 White Caucasian, 10 South African Coloured, and 10 Indian volunteers. The sample was not chosen to compare inter-ethnic differences, but to represent that which could potentially be seen in South African c ...
... represent the demographics of the South African population. This included 70 Black African, 10 White Caucasian, 10 South African Coloured, and 10 Indian volunteers. The sample was not chosen to compare inter-ethnic differences, but to represent that which could potentially be seen in South African c ...
Health consequences of adult hypolactasia
... th lactase l t persistence i t phenotype • it was suggested that C/T-13910 might not be the causing variant in these groups. • possibility that another variant may underlie the lactase persistence in those populations; however, more studies on the issue are warranted ...
... th lactase l t persistence i t phenotype • it was suggested that C/T-13910 might not be the causing variant in these groups. • possibility that another variant may underlie the lactase persistence in those populations; however, more studies on the issue are warranted ...
Ingenuity Variant Analysis
... mutation, but does not show the same single nucleotide base change. We only check exact nucleotides for SNVs, any insertions/deletions are by default checked only by coords. Base matching variants are more interesting than ones just overlapping, but one really has to look at each case. HGMD Disease: ...
... mutation, but does not show the same single nucleotide base change. We only check exact nucleotides for SNVs, any insertions/deletions are by default checked only by coords. Base matching variants are more interesting than ones just overlapping, but one really has to look at each case. HGMD Disease: ...
Hardy-Weinberg Proportions Methods Manual
... As well as individual genotype deviations from HWP, specific sets of genotypes may overall show deviations from HWP. This may occur in MSAT genotyping as a result of preferential amplification or allelic dropout (alleles that cannot be distinguished from background noise). Similarly, with null MSAT ...
... As well as individual genotype deviations from HWP, specific sets of genotypes may overall show deviations from HWP. This may occur in MSAT genotyping as a result of preferential amplification or allelic dropout (alleles that cannot be distinguished from background noise). Similarly, with null MSAT ...
Publication - The University of Texas Health Science Center at
... risk, w1.5–2.0) and that multiple loci are involved. In this light, interpretation of genetic-association studies in an uncommon and phenotypically heterogeneous disease, such as scleroderma, must be performed using strict guidelines. Such studies often are limited by lack of sufficient statistical po ...
... risk, w1.5–2.0) and that multiple loci are involved. In this light, interpretation of genetic-association studies in an uncommon and phenotypically heterogeneous disease, such as scleroderma, must be performed using strict guidelines. Such studies often are limited by lack of sufficient statistical po ...
IBS Methods for Affected Pairs Linkage
... “Allows one to find where a gene is, without knowing what it is.” ...
... “Allows one to find where a gene is, without knowing what it is.” ...
Genetic Analysis of Variation in Human Meiotic Recombination
... [14] collections to determine recombination phenotypes. For our analysis, we used the genotype data from members of twogeneration families that have two or more children to infer recombination phenotypes of the parents in these families. The 511 AGRE families have an average of 2.26 children (median ...
... [14] collections to determine recombination phenotypes. For our analysis, we used the genotype data from members of twogeneration families that have two or more children to infer recombination phenotypes of the parents in these families. The 511 AGRE families have an average of 2.26 children (median ...
Mapping Mendelian Factors Underlying Quantitative ... Using RFLP Linkage Maps Eric
... 1923; SOLLERand BRODY1976) involves studying single genetic markers one-at-a-time. In general, the drawbacks of the method include that (a) the phenotypic effects of QTLs are systematically underestimated, (b) the geneticlocations of QTLs are not well resolved because distant linkage cannot be disti ...
... 1923; SOLLERand BRODY1976) involves studying single genetic markers one-at-a-time. In general, the drawbacks of the method include that (a) the phenotypic effects of QTLs are systematically underestimated, (b) the geneticlocations of QTLs are not well resolved because distant linkage cannot be disti ...
PDF - Blood Journal
... range combined with a pronounced interindividual variability in the dose required for adequate anticoagulation.1 Clinical use of warfarin is further complicated by a substantial risk for hemorrhagic side effects, which is increased in patients with low-dose requirements.2 A minor part of the variabi ...
... range combined with a pronounced interindividual variability in the dose required for adequate anticoagulation.1 Clinical use of warfarin is further complicated by a substantial risk for hemorrhagic side effects, which is increased in patients with low-dose requirements.2 A minor part of the variabi ...
Variant Effect Predictor Web interface Documentation
... CCDS - add the Consensus CDS transcript identifier where available. Equivalent to --ccds Protein - add the Ensembl protein identifer (ENSP). Equivalent to --protein Uniprot - add identifiers for translated protein products from three UniProt -related databases (SWISSPROT, TREMBL and UniParc). Equiva ...
... CCDS - add the Consensus CDS transcript identifier where available. Equivalent to --ccds Protein - add the Ensembl protein identifer (ENSP). Equivalent to --protein Uniprot - add identifiers for translated protein products from three UniProt -related databases (SWISSPROT, TREMBL and UniParc). Equiva ...
documentation in PDF format
... CCDS - add the Consensus CDS transcript identifier where available. Equivalent to --ccds Protein - add the Ensembl protein identifer (ENSP). Equivalent to --protein Uniprot - add identifiers for translated protein products from three UniProt -related databases (SWISSPROT, TREMBL and UniParc). Equivale ...
... CCDS - add the Consensus CDS transcript identifier where available. Equivalent to --ccds Protein - add the Ensembl protein identifer (ENSP). Equivalent to --protein Uniprot - add identifiers for translated protein products from three UniProt -related databases (SWISSPROT, TREMBL and UniParc). Equivale ...
Introduction of the AmpliChip CYP450 Test to a prospective cohort study
... CYP2D6*5 more reliably and could correctly distinguish between CYP2D6*2 and *41 in the Black African individuals. Alleles not covered by the AmpliChip were identified and four novel CYP2D6 alleles were also detected. CYP2C19 PCR-RFLP identified CYP2C19*9,*15, *17 and *27 in the Black African individ ...
... CYP2D6*5 more reliably and could correctly distinguish between CYP2D6*2 and *41 in the Black African individuals. Alleles not covered by the AmpliChip were identified and four novel CYP2D6 alleles were also detected. CYP2C19 PCR-RFLP identified CYP2C19*9,*15, *17 and *27 in the Black African individ ...
Genome-Wide Association Mapping Reveals Novel QTL for
... approach. More recently, advances in genomics have made it feasible to genotype a large collection of germplasm lines with thousands of SNP markers. As a result, the GWAS approach, based on the principle of linkage disequilibrium (LD), has been effectively used to exploit existing allelic diversity ...
... approach. More recently, advances in genomics have made it feasible to genotype a large collection of germplasm lines with thousands of SNP markers. As a result, the GWAS approach, based on the principle of linkage disequilibrium (LD), has been effectively used to exploit existing allelic diversity ...
Genotype C of hepatitis B virus can be classified into at least two
... southern end of Japan) and two from China. Two databasederived isolates found in Australian Aborigines and New Caledonia formed an outgroup of the genotype. Phylogenetic analysis based on full genomic sequences of 10 HBV isolates from Vietnam (3), Myanmar (3), Thailand (2) and Okinawa (2) also confi ...
... southern end of Japan) and two from China. Two databasederived isolates found in Australian Aborigines and New Caledonia formed an outgroup of the genotype. Phylogenetic analysis based on full genomic sequences of 10 HBV isolates from Vietnam (3), Myanmar (3), Thailand (2) and Okinawa (2) also confi ...
Genetic factors affecting dental caries risk
... disease model of caries. The scope is genetic aspects of various dental factors affecting dental caries. The PubMed database was searched for articles with keywords ‘caries’, ‘genetics’, ‘taste’, ‘diet’ and ‘twins’. This was followed by extensive handsearching using reference lists from relevant art ...
... disease model of caries. The scope is genetic aspects of various dental factors affecting dental caries. The PubMed database was searched for articles with keywords ‘caries’, ‘genetics’, ‘taste’, ‘diet’ and ‘twins’. This was followed by extensive handsearching using reference lists from relevant art ...
PDF - NIMH Genetics
... less significant than the parametric linkage results. Model-free linkage analysis can be a favorable method of analysis for complex disease traits since there are no assumptions about mode of inheritance, disease allele frequencies, and penetrance. However, even without specifying models correctly, ...
... less significant than the parametric linkage results. Model-free linkage analysis can be a favorable method of analysis for complex disease traits since there are no assumptions about mode of inheritance, disease allele frequencies, and penetrance. However, even without specifying models correctly, ...
Genome-wide association study
In genetic epidemiology, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS) or common-variant association study (CVAS), is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases.These studies normally compare the DNA of two groups of participants: people with the disease (cases) and similar people without (controls). This approach is known as phenotype-first, in which the participants are classified first by their clinical manifestation(s), as opposed to genotype-first. Each person gives a sample of DNA, from which millions of genetic variants are read using SNP arrays. If one type of the variant (one allele) is more frequent in people with the disease, the SNP is said to be ""associated"" with the disease. The associated SNPs are then considered to mark a region of the human genome which influences the risk of disease. In contrast to methods which specifically test one or a few genetic regions, the GWA studies investigate the entire genome. The approach is therefore said to be non-candidate-driven in contrast to gene-specific candidate-driven studies. GWA studies identify SNPs and other variants in DNA which are associated with a disease, but cannot on their own specify which genes are causal.The first successful GWAS was published in 2005 and investigated patients with age-related macular degeneration. It found two SNPs which had significantly altered allele frequency when comparing with healthy controls. As of 2011, hundreds or thousands of individuals are tested, over 1,200 human GWA studies have examined over 200 diseases and traits, and almost 4,000 SNP associations have been found. Several GWA studies have received criticism for omitting important quality control steps, rendering the findings invalid, but modern publications address these issues. However, the methodology itself still has opponents.