Data Analysis Using GeneSpring.ppt
... arrays have been run in order to answer a specific scientific question. • Sample: can be data files or sample which is created within GeneSpring. • Exp. Grouping, Parameter: ie. Treat vs un-treat, age, gender, …. • Interpretation: defines a particular way of grouping samples into experimental condit ...
... arrays have been run in order to answer a specific scientific question. • Sample: can be data files or sample which is created within GeneSpring. • Exp. Grouping, Parameter: ie. Treat vs un-treat, age, gender, …. • Interpretation: defines a particular way of grouping samples into experimental condit ...
Solution
... 15. (4 points) QTL mapping muscle mass phenotypes in pigs identified the genomic region including the Insulin Growth Factor 2 gene. Further fine mapping studies suggested the phenotype maps to a non-‐codi ...
... 15. (4 points) QTL mapping muscle mass phenotypes in pigs identified the genomic region including the Insulin Growth Factor 2 gene. Further fine mapping studies suggested the phenotype maps to a non-‐codi ...
Identifying Signatures of Natural Selection in Tibetan Data
... hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in ge ...
... hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in ge ...
Mendelian Genetics
... The demonstration of Linkage disequilibrium in a particular disease suggests that the mutation which has caused the disease occurred relatively recently and that the marker locus being studied is very closely linked to the disease locus. It is counter-intuitive, but linkage does not require link ...
... The demonstration of Linkage disequilibrium in a particular disease suggests that the mutation which has caused the disease occurred relatively recently and that the marker locus being studied is very closely linked to the disease locus. It is counter-intuitive, but linkage does not require link ...
MQ (54) LIV 2 contents
... A prediction of polygenic selection is that “the traitincreasing alleles will tend to have greater frequencies in the population with higher trait values, compared to the population with lower trait values” (Turchin et al, 2012). Another prediction of the polygenic selection model (explicitly advanc ...
... A prediction of polygenic selection is that “the traitincreasing alleles will tend to have greater frequencies in the population with higher trait values, compared to the population with lower trait values” (Turchin et al, 2012). Another prediction of the polygenic selection model (explicitly advanc ...
Manual - Keinan Lab
... 2. Variants are filtered if their missingness is significantly correlated with phenotype (recommended P -value threshold is 0.05). Note: this step is only applied to case-control studies. 3. Individual samples are removed if they are inferred to be related based on the proportion of shared Identity- ...
... 2. Variants are filtered if their missingness is significantly correlated with phenotype (recommended P -value threshold is 0.05). Note: this step is only applied to case-control studies. 3. Individual samples are removed if they are inferred to be related based on the proportion of shared Identity- ...
WORKING WITH THE FIGURES
... observed outcomes would have to be relatively very large to reach significance. However, a chi-square can be calculated. Overall, there were 10 strains that survived high temperatures. If SNP 1 has no effect, these survivors should be distributed randomly between the A and G variants. Out of 18 stra ...
... observed outcomes would have to be relatively very large to reach significance. However, a chi-square can be calculated. Overall, there were 10 strains that survived high temperatures. If SNP 1 has no effect, these survivors should be distributed randomly between the A and G variants. Out of 18 stra ...
Association genetics of complex traits in conifers
... reason they will have extended linkage disequilibrium around the mutation [24]. In common diseases, the underlying loci might have smaller effects, and the alleles might be older [22,23]. Plant breeders are interested in genes that have been under strong selection during domestication, such as flowe ...
... reason they will have extended linkage disequilibrium around the mutation [24]. In common diseases, the underlying loci might have smaller effects, and the alleles might be older [22,23]. Plant breeders are interested in genes that have been under strong selection during domestication, such as flowe ...
an R interface to SOLAR for variance component analysis
... The motivation to develop the solarius software came from the extensive experience of the group that studies the Genetic Analysis of Idiopathic Thrombophilia (GAIT) project [3, 4]. Both GAIT1 and GAIT2 projects include individuals from a Spanish population in extended pedigrees, an extensive list of ...
... The motivation to develop the solarius software came from the extensive experience of the group that studies the Genetic Analysis of Idiopathic Thrombophilia (GAIT) project [3, 4]. Both GAIT1 and GAIT2 projects include individuals from a Spanish population in extended pedigrees, an extensive list of ...
Advanced Twin Workshop 2001
... • Possible interactions between genes • Possible interactions between genes and environment • Relatively low frequencies of individual risk factors • Functional form of genotype-phenotype relations not known • Sorting out signal from noise – minimizing errors within budget • Scaling of phenotype (co ...
... • Possible interactions between genes • Possible interactions between genes and environment • Relatively low frequencies of individual risk factors • Functional form of genotype-phenotype relations not known • Sorting out signal from noise – minimizing errors within budget • Scaling of phenotype (co ...
Christine – horse genetics
... instead of STRs to verify parentage in 95 randomly chosen thoroughbreds. It was hypothesized that SNPs would be better than STRS for use in parentage verification because they have lower mutation rates, and SNP assays are cost effective, able to be analyzed with automated technology, can be detected ...
... instead of STRs to verify parentage in 95 randomly chosen thoroughbreds. It was hypothesized that SNPs would be better than STRS for use in parentage verification because they have lower mutation rates, and SNP assays are cost effective, able to be analyzed with automated technology, can be detected ...
Supplementary Information (doc 7548K)
... Supplementary Table 1 | Clinical characteristics of CG-SH cell line and AML patients. Data include FAB, French-American-British classification of AML, and mutational status of nucleophosmin gene (NPM1), internal tandem duplications of FLT3 gene (FLT3-3-ITD) and point mutations in DNMT3A (R882H). Ave ...
... Supplementary Table 1 | Clinical characteristics of CG-SH cell line and AML patients. Data include FAB, French-American-British classification of AML, and mutational status of nucleophosmin gene (NPM1), internal tandem duplications of FLT3 gene (FLT3-3-ITD) and point mutations in DNMT3A (R882H). Ave ...
Identification of loci affecting teat number by
... deduce the 60K SNP genotypes of 815 F2 pigs using the genotyped 928 F2 pigs and their F0/F1 ancestor as the reference panel. The markers on sex chromosomes were not imputed for a lack of an appropriate algorithm [22]. This imputation approach allowed us to increase the sample size up to 1,743 animal ...
... deduce the 60K SNP genotypes of 815 F2 pigs using the genotyped 928 F2 pigs and their F0/F1 ancestor as the reference panel. The markers on sex chromosomes were not imputed for a lack of an appropriate algorithm [22]. This imputation approach allowed us to increase the sample size up to 1,743 animal ...
Slide 1
... by an enzyme called lactase. • Virtually all humans are born with ability to utilize lactose but many lose ability to digest lactose by 12 or 13 years old. • In lactose tolerant individuals, lactase gene is expressed into adulthood, so eating a milkshake is a pleasant experience. But in people who a ...
... by an enzyme called lactase. • Virtually all humans are born with ability to utilize lactose but many lose ability to digest lactose by 12 or 13 years old. • In lactose tolerant individuals, lactase gene is expressed into adulthood, so eating a milkshake is a pleasant experience. But in people who a ...
Document
... and erythropoiesis during periods of hypoxic stress. This factor is necessary for animals in aquatic environments where the dissolved oxygen levels are often variable. Aquaculture could be greatly benefitted if animals are developed that can withstand hypoxic stress. It would also be important to kn ...
... and erythropoiesis during periods of hypoxic stress. This factor is necessary for animals in aquatic environments where the dissolved oxygen levels are often variable. Aquaculture could be greatly benefitted if animals are developed that can withstand hypoxic stress. It would also be important to kn ...
Rich Probabilistic Models for Genomic Data
... Each haplotype has a frequency, which is the proportion of chromosomes of that type in the population ...
... Each haplotype has a frequency, which is the proportion of chromosomes of that type in the population ...
Phenotypic variability of osteogenesis imperfecta is not accounted
... A father and his three sons had blue sclera, dentinogenesis imperfecta, and joint laxity (Fig. 1). Two sons (II-1 and II-3) had histories of more than 10 fractures before age 13 years, but three other members experienced no fracture. One son (II-1) had hearing loss from age 10 years and hip joint de ...
... A father and his three sons had blue sclera, dentinogenesis imperfecta, and joint laxity (Fig. 1). Two sons (II-1 and II-3) had histories of more than 10 fractures before age 13 years, but three other members experienced no fracture. One son (II-1) had hearing loss from age 10 years and hip joint de ...
20061121113012301-150349
... • Note, however, that a person's genotype, the measured risk factors and phenotype (time to event and event type) may all be statistically dependent of each other. Therefore the likelihood contribution from an individual who has not been genotyped involves an integration with respect to a (condition ...
... • Note, however, that a person's genotype, the measured risk factors and phenotype (time to event and event type) may all be statistically dependent of each other. Therefore the likelihood contribution from an individual who has not been genotyped involves an integration with respect to a (condition ...
Fernanda Appleton Biology 1615 Research Paper:” The Oxytricha
... genome is fragmented into at least 16,000 tiny (~3.2 kb mean length) chromosomes, most of which encode single actively transcribed genes and are differentially amplified to a few thousand copies each. The smallest chromosome is just 469 bp, while the largest is 66 kb and encodes a single enormous pr ...
... genome is fragmented into at least 16,000 tiny (~3.2 kb mean length) chromosomes, most of which encode single actively transcribed genes and are differentially amplified to a few thousand copies each. The smallest chromosome is just 469 bp, while the largest is 66 kb and encodes a single enormous pr ...
Platform: Affymetrix GeneChip System
... From set of SNPs in high LD with each other, select only one (the tag SNP) to genotype (others can be imputed, e.g. IMPUTE, MACH, PLINK) A systematic association analysis of a gene, a chromosome region, or the entire genome can be achieved by the appropriate choice of tag SNPs This requires a catalo ...
... From set of SNPs in high LD with each other, select only one (the tag SNP) to genotype (others can be imputed, e.g. IMPUTE, MACH, PLINK) A systematic association analysis of a gene, a chromosome region, or the entire genome can be achieved by the appropriate choice of tag SNPs This requires a catalo ...
PowerPoint
... 2. Response to artificial selection 3. Effects of inbreeding B. How much genetic variation is there? C. More direct measurement of genetic variation V. What maintains genetic variation in natural populations? ...
... 2. Response to artificial selection 3. Effects of inbreeding B. How much genetic variation is there? C. More direct measurement of genetic variation V. What maintains genetic variation in natural populations? ...
IV. Genetic Variation in Natural Populations A. Indirect evidence for
... 2. Response to artificial selection 3. Effects of inbreeding B. How much genetic variation is there? C. More direct measurement of genetic variation V. What maintains genetic variation in natural populations? ...
... 2. Response to artificial selection 3. Effects of inbreeding B. How much genetic variation is there? C. More direct measurement of genetic variation V. What maintains genetic variation in natural populations? ...
Statistical Power for Computational Mapping
... sizes are equal, the F statistics for samples with effect size 2 follows the noncentral F distribution F(k – 1, n – k, ) with the noncentrality parameter Therefore, the power of the one-way ANOVA test with significance level is given by: (2) where Fcrit = F(1 , k–1, n–k) is the (1 ) quantile o ...
... sizes are equal, the F statistics for samples with effect size 2 follows the noncentral F distribution F(k – 1, n – k, ) with the noncentrality parameter Therefore, the power of the one-way ANOVA test with significance level is given by: (2) where Fcrit = F(1 , k–1, n–k) is the (1 ) quantile o ...
STAAR REVIEW—GENETICS, NATURAL SELECTION
... Alleles: Genes that code for different versions of a trait (represented by capital and lower case letters) Chromosomes: Specific location of the inherited traits (genes) in our cells Phenotype: The physical appearance of an individual (ex: green eyes, tongue roller, hitchhikers thumb, blood ty ...
... Alleles: Genes that code for different versions of a trait (represented by capital and lower case letters) Chromosomes: Specific location of the inherited traits (genes) in our cells Phenotype: The physical appearance of an individual (ex: green eyes, tongue roller, hitchhikers thumb, blood ty ...
Slide 1
... • Bootstrap Aggregating (Bagged) Logic Regression is a new technique that may be useful in analyzing SNP associations. • Bagged Logic Regression identified “Worst-Least” CFS SNP genes consistent with exhaustive search by Goertzel, et al (2006). • “Interesting” SNPs did not show statistically signifi ...
... • Bootstrap Aggregating (Bagged) Logic Regression is a new technique that may be useful in analyzing SNP associations. • Bagged Logic Regression identified “Worst-Least” CFS SNP genes consistent with exhaustive search by Goertzel, et al (2006). • “Interesting” SNPs did not show statistically signifi ...
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.