Genetic Architecture of Maize Kernel Composition in the Nested
... NAM Joint QTL Linkage Analysis Joint stepwise regression identified 21 starch, 26 protein, and 22 oil QTL, which collectively explained 59%, 61%, and 70% of the total variation, respectively (Fig. 1; Table 1). All starch, protein, and oil QTL were shared among multiple families, with most QTL showin ...
... NAM Joint QTL Linkage Analysis Joint stepwise regression identified 21 starch, 26 protein, and 22 oil QTL, which collectively explained 59%, 61%, and 70% of the total variation, respectively (Fig. 1; Table 1). All starch, protein, and oil QTL were shared among multiple families, with most QTL showin ...
Comprehensive analysis of thiopurine S
... thiopurine drugs. However, the prerequisition for replacing phenotyping by genotyping strategy depends on two requirements: (i) all relevant mutations must be known to explain the different phenotypes and (ii) when genotyping is used in clinical practice, the correct prediction of molecular diagnost ...
... thiopurine drugs. However, the prerequisition for replacing phenotyping by genotyping strategy depends on two requirements: (i) all relevant mutations must be known to explain the different phenotypes and (ii) when genotyping is used in clinical practice, the correct prediction of molecular diagnost ...
A Genomic Imprinting Test for Ordinal Traits in Pedigree Data
... generated from N(0,1) that is shared by all family members, and a random noise eij was also generated from N(0,1) for each individual. For each founder in a pedigree, 20 highly polymorphic markers with 10 equally likely alleles [Speer et al., 1995], spaced 5 cM apart, were generated on one chromosom ...
... generated from N(0,1) that is shared by all family members, and a random noise eij was also generated from N(0,1) for each individual. For each founder in a pedigree, 20 highly polymorphic markers with 10 equally likely alleles [Speer et al., 1995], spaced 5 cM apart, were generated on one chromosom ...
Genetic variation at RYR1, IGF2, FUT1, MUC13, and KPL2
... RYR1. The desirable allele (C) at the RYR1 c.1843C>T locus conferring resistance to malignant hyperthermia was fixed in two Synthetic Lines and it was predominant in Duroc (0.917), Large White (0.981), and Landrace (0.972) pigs (Table 2). After the identification of the RYR1 c.1843C>T mutation in 19 ...
... RYR1. The desirable allele (C) at the RYR1 c.1843C>T locus conferring resistance to malignant hyperthermia was fixed in two Synthetic Lines and it was predominant in Duroc (0.917), Large White (0.981), and Landrace (0.972) pigs (Table 2). After the identification of the RYR1 c.1843C>T mutation in 19 ...
Population Genetics
... This can only occur if the population is sufficiently large to ensure that the chance of an offspring getting one allele or the other is purely random. When populations are small the principle of genetic drift enters and the equilibrium is not established or will be lost as population size dwindles ...
... This can only occur if the population is sufficiently large to ensure that the chance of an offspring getting one allele or the other is purely random. When populations are small the principle of genetic drift enters and the equilibrium is not established or will be lost as population size dwindles ...
Genome-wide search for signatures of selection in three
... present study was to identify genomic regions that may have been under selection and therefore may explain ecological and production differences observed among three important Brazilian locally adapted sheep breeds. Animals from the Brazilian Creole, Morada Nova and Santa Ines breeds were genotyped u ...
... present study was to identify genomic regions that may have been under selection and therefore may explain ecological and production differences observed among three important Brazilian locally adapted sheep breeds. Animals from the Brazilian Creole, Morada Nova and Santa Ines breeds were genotyped u ...
Benzimidazole resistance survey for Haemonchus - diss.fu
... codon F200Y (TTC to TAC) of isotype-1 b-tubulin of Haemonchus contortus, leading to the expression of tyrosine instead of phenylalanine (Kwa et al., 1994, 1995). Furthermore, two additional codons, codon F167Y (TTC to TAC) (Prichard, 2001) and codon E198A (GAA to GCA) (Ghisi et al., 2007) have also ...
... codon F200Y (TTC to TAC) of isotype-1 b-tubulin of Haemonchus contortus, leading to the expression of tyrosine instead of phenylalanine (Kwa et al., 1994, 1995). Furthermore, two additional codons, codon F167Y (TTC to TAC) (Prichard, 2001) and codon E198A (GAA to GCA) (Ghisi et al., 2007) have also ...
VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism
... CNV or SNP region. (Key Words: Copy Number Variation, Cytomap, Homozygosity, Single Nucleotide Polymorphism, Visualization) ...
... CNV or SNP region. (Key Words: Copy Number Variation, Cytomap, Homozygosity, Single Nucleotide Polymorphism, Visualization) ...
Math of Genetics - College of William & Mary
... This will not alter genotypic ratios, but it will alter ...
... This will not alter genotypic ratios, but it will alter ...
Proof-of-principle rapid noninvasive prenatal diagnosis
... SNP panel. Six of these homoallelic patients with type I Gaucher disease were homozygotic for all 490 SNPs on our initial sequencing panel. The seventh sample shared the same haplotype within and 3′ to GBA, but a heterozygous region was clearly identified 144,388 nucleotides 5′ to the gene and beyon ...
... SNP panel. Six of these homoallelic patients with type I Gaucher disease were homozygotic for all 490 SNPs on our initial sequencing panel. The seventh sample shared the same haplotype within and 3′ to GBA, but a heterozygous region was clearly identified 144,388 nucleotides 5′ to the gene and beyon ...
Short Tandem Repeat Polymorphism and Cancer Risk: Influence of
... in CA repeats between the two methods, including 5 samples with two-repeat difference, 3 with three-repeat difference, 3 with four-repeat difference, and 1 with fiverepeat difference. Of the 12 samples that had the same allelic difference in CA repeats, only 8 had exactly the same number of repeats ...
... in CA repeats between the two methods, including 5 samples with two-repeat difference, 3 with three-repeat difference, 3 with four-repeat difference, and 1 with fiverepeat difference. Of the 12 samples that had the same allelic difference in CA repeats, only 8 had exactly the same number of repeats ...
Genetic Etiologies for Phenotypic Diversity in Sickle Cell Anemia
... could be computed[1], When this likelihood was used as a severity score in a candidate gene-based genetic association study, genes involved in oxidative and vascular biology, fatty acid oxidation, and inflammation were associated with severity. Second, one-SNP-at-a-time (SNP, single nucleotide polym ...
... could be computed[1], When this likelihood was used as a severity score in a candidate gene-based genetic association study, genes involved in oxidative and vascular biology, fatty acid oxidation, and inflammation were associated with severity. Second, one-SNP-at-a-time (SNP, single nucleotide polym ...
Simple Algorithms to Calculate Asymptotic Null Distributions of
... trend test with a data-driven score, which was also noticed by Zheng et al. (2009). Based on this finding, Yamada and Okada (2009) proposed an optimal dose-effect mode trend test where the genetic effect of the heterozygous genotype is restricted between two homozygous genotypes. The performance of ...
... trend test with a data-driven score, which was also noticed by Zheng et al. (2009). Based on this finding, Yamada and Okada (2009) proposed an optimal dose-effect mode trend test where the genetic effect of the heterozygous genotype is restricted between two homozygous genotypes. The performance of ...
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 ...
Genetic linkage studies in the pseudoautosomal
... marker and the disease-causing gene are said to be linked, and are assumed to be very close together. After using linkage to get an idea where risk genes may be located, association studies allow to test candidate genes, or very small genetic regions, to see if they are associated with having the di ...
... marker and the disease-causing gene are said to be linked, and are assumed to be very close together. After using linkage to get an idea where risk genes may be located, association studies allow to test candidate genes, or very small genetic regions, to see if they are associated with having the di ...
Molecular Genetics of Bipolar Disorder and Related Traits
... majority of the population. This provides excellent opportunities for special study designs for the identification not only of rare disease genes but also of major loci, which contribute to complex diseases. The genome-wide scan strategy using family material from the isolated Finnish population has ...
... majority of the population. This provides excellent opportunities for special study designs for the identification not only of rare disease genes but also of major loci, which contribute to complex diseases. The genome-wide scan strategy using family material from the isolated Finnish population has ...
Disease and Trait Information for IDB Genotyped Animals in
... The cattle genome has approximate 3 billion DNA bases, the same number as found in the human genome. To help store all this information DNA are packaged in chromosomes. These chromosomes can be broken down into 3 categories: autosomes, sex determining chromosomes- X and Y, and mitochondria. While mo ...
... The cattle genome has approximate 3 billion DNA bases, the same number as found in the human genome. To help store all this information DNA are packaged in chromosomes. These chromosomes can be broken down into 3 categories: autosomes, sex determining chromosomes- X and Y, and mitochondria. While mo ...
Tumour necrosis factor and lymphotoxin A progression? EDITORIAL
... different, usually lower, prevalences of the polymorphisms under study in Caucasian subjects. However, this explanation might be too simple. If the decision to study a particular gene is based on biological plausibility or homology with other diseases, one would expect that the majority of positive ...
... different, usually lower, prevalences of the polymorphisms under study in Caucasian subjects. However, this explanation might be too simple. If the decision to study a particular gene is based on biological plausibility or homology with other diseases, one would expect that the majority of positive ...
Farmer_Genetic-Disea..
... The cattle genome has approximate 3 billion DNA bases, the same number as found in the human genome. To help store all this information DNA are packaged in chromosomes. These chromosomes can be broken down into 3 categories: autosomes, sex determining chromosomes- X and Y, and mitochondria. While mo ...
... The cattle genome has approximate 3 billion DNA bases, the same number as found in the human genome. To help store all this information DNA are packaged in chromosomes. These chromosomes can be broken down into 3 categories: autosomes, sex determining chromosomes- X and Y, and mitochondria. While mo ...
twin studies - Institute for Behavioral Genetics
... (PHENOTYPE)30,31. For example, a family might contain one or more individuals who inherit a high-risk genotype but do not develop problems (cases of incomplete PENETRANCE). Conversely, there might be subjects who are clearly affected, even though they have a low-risk genotype (PHENOCOPIES). Genotype ...
... (PHENOTYPE)30,31. For example, a family might contain one or more individuals who inherit a high-risk genotype but do not develop problems (cases of incomplete PENETRANCE). Conversely, there might be subjects who are clearly affected, even though they have a low-risk genotype (PHENOCOPIES). Genotype ...
Association of estrogen receptor β gene polymorphisms with bulimic
... genetic variants. Only two of these appeared at an allele frequency over 1% for the less common allele. These SNPs, 1082 G-A and 1730 A-G, did not display association with the phenotypes under study. These SNPs have later been analyzed for association between ERb and ovulatory dysfunctions,19 includ ...
... genetic variants. Only two of these appeared at an allele frequency over 1% for the less common allele. These SNPs, 1082 G-A and 1730 A-G, did not display association with the phenotypes under study. These SNPs have later been analyzed for association between ERb and ovulatory dysfunctions,19 includ ...
genotype AND phenotype
... Brandy has one allele for being tall, and one allele for being short. Is this genotype or phenotype? Explain how you know. ...
... Brandy has one allele for being tall, and one allele for being short. Is this genotype or phenotype? Explain how you know. ...
Identifying Common Genetic Variants by High
... easiest to distinguish on difference plots (Fig. 1B). Although the identity of the sequence variants was initially not known, samples with melting curves identical to those in a normal population should be benign variants. To test this method of eliminating common variants, we analyzed a blinded pan ...
... easiest to distinguish on difference plots (Fig. 1B). Although the identity of the sequence variants was initially not known, samples with melting curves identical to those in a normal population should be benign variants. To test this method of eliminating common variants, we analyzed a blinded pan ...
1 shared allele
... Linkage analysis within pedigrees • Examines the coinheritance of a disease with chromosomal markers within multiple extended families • SNPs, mini- or “micro-satellites are often used as markers • Usually allows localization to only a general region of a particular chromosome (e.g. within several ...
... Linkage analysis within pedigrees • Examines the coinheritance of a disease with chromosomal markers within multiple extended families • SNPs, mini- or “micro-satellites are often used as markers • Usually allows localization to only a general region of a particular chromosome (e.g. within several ...
Base-pair neutral homozygotes can be discriminated by calibrated
... LCGreen Plus dye that stabilizes double-stranded DNA hybrids. A nonparametric Mann–Whitney U-test of the uncalibrated and calibrated mean Tm values for the alternate homozygotes indicated significant differences (P < 0.001) for all six variants. The Tm variation was lower by 37–90% after calibration. ...
... LCGreen Plus dye that stabilizes double-stranded DNA hybrids. A nonparametric Mann–Whitney U-test of the uncalibrated and calibrated mean Tm values for the alternate homozygotes indicated significant differences (P < 0.001) for all six variants. The Tm variation was lower by 37–90% after calibration. ...
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.