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Questions and Answers
What is the term for a unique set of alleles that always occur together within a linkage block?
What is the term for a unique set of alleles that always occur together within a linkage block?
How are haplotypes identified within linkage blocks?
How are haplotypes identified within linkage blocks?
What is the term for the association of alleles from different loci because they are on the same linkage block?
What is the term for the association of alleles from different loci because they are on the same linkage block?
In the multiplicative inheritance model, how is disease risk affected by each additional 'A' allele?
In the multiplicative inheritance model, how is disease risk affected by each additional 'A' allele?
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What is the goal of Genome Wide Association Studies (GWAS)?
What is the goal of Genome Wide Association Studies (GWAS)?
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What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
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What does Linkage Disequilibrium (LD) measure?
What does Linkage Disequilibrium (LD) measure?
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What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
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What are haplotype blocks?
What are haplotype blocks?
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What is the difference between the frequency of gametes carrying the pair of alleles A and B at two loci (pAB) and the product of the frequencies of those alleles (pA and pB) called?
What is the difference between the frequency of gametes carrying the pair of alleles A and B at two loci (pAB) and the product of the frequencies of those alleles (pA and pB) called?
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What is the ramification of two loci being very close to each other on a chromosome?
What is the ramification of two loci being very close to each other on a chromosome?
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What is the main rationale for considering missense mutations as causal mutations?
What is the main rationale for considering missense mutations as causal mutations?
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What is the main challenge in understanding complex diseases with numerous subtle mutations?
What is the main challenge in understanding complex diseases with numerous subtle mutations?
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What did Hirschorn & Daly suggest as the most comprehensive approach towards understanding complex diseases?
What did Hirschorn & Daly suggest as the most comprehensive approach towards understanding complex diseases?
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What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
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What concept explains how phenotypes are associated with genotypes?
What concept explains how phenotypes are associated with genotypes?
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What is the main purpose of a Bonferroni correction in GWAS studies?
What is the main purpose of a Bonferroni correction in GWAS studies?
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What is the key challenge in performing a complete genome resequencing in a large population of cases and controls?
What is the key challenge in performing a complete genome resequencing in a large population of cases and controls?
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What is the purpose of haplotype blocks in GWAS?
What is the purpose of haplotype blocks in GWAS?
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What is the main reason for including low frequency SNPs (<5%) in human SNP chips for GWAS?
What is the main reason for including low frequency SNPs (<5%) in human SNP chips for GWAS?
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What is the purpose of Bonferroni correction in GWAS?
What is the purpose of Bonferroni correction in GWAS?
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What can lead to biased results in GWAS if not accounted for?
What can lead to biased results in GWAS if not accounted for?
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What is the purpose of a multistage approach in GWAS?
What is the purpose of a multistage approach in GWAS?
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What is the measure of effect size and strength of association in GWAS?
What is the measure of effect size and strength of association in GWAS?
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What is the term for the measure of effect size and strength of association in GWAS?
What is the term for the measure of effect size and strength of association in GWAS?
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In the context of inheritance patterns, what does 'penetrance' refer to?
In the context of inheritance patterns, what does 'penetrance' refer to?
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What is the main reason for including low frequency SNPs (<5%) in human SNP chips for GWAS?
What is the main reason for including low frequency SNPs (<5%) in human SNP chips for GWAS?
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What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
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What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
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Where does Linkage Disequilibrium (LD) come from?
Where does Linkage Disequilibrium (LD) come from?
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What is the purpose of haplotype blocks in GWAS?
What is the purpose of haplotype blocks in GWAS?
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What can lead to biased results in GWAS if not accounted for?
What can lead to biased results in GWAS if not accounted for?
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What is the measure of effect size and strength of association in GWAS?
What is the measure of effect size and strength of association in GWAS?
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What is the main rationale for considering missense mutations as causal mutations?
What is the main rationale for considering missense mutations as causal mutations?
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What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
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What is the purpose of Bonferroni correction in GWAS?
What is the purpose of Bonferroni correction in GWAS?
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What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
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What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
What does strong Linkage Disequilibrium (LD) on chromosomes indicate?
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What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
What is the coefficient of Linkage Disequilibrium (LD), D, defined as?
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What is the main rationale for considering missense mutations as causal mutations?
What is the main rationale for considering missense mutations as causal mutations?
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What is the purpose of Bonferroni correction in GWAS studies?
What is the purpose of Bonferroni correction in GWAS studies?
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Where does Linkage Disequilibrium (LD) come from?
Where does Linkage Disequilibrium (LD) come from?
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What is the measure of effect size and strength of association in GWAS?
What is the measure of effect size and strength of association in GWAS?
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What is the key challenge in performing a complete genome resequencing in a large population of cases and controls?
What is the key challenge in performing a complete genome resequencing in a large population of cases and controls?
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What is the purpose of haplotype blocks in GWAS?
What is the purpose of haplotype blocks in GWAS?
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What is the term for the association of alleles from different loci because they are on the same linkage block?
What is the term for the association of alleles from different loci because they are on the same linkage block?
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What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
What did Nik-Zainal et al. analyze to advance understanding of driver mutations in breast cancer?
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Study Notes
Genome Wide Association Studies (GWAS) in Medical News
- GWAS studies focus on the cumulative action of many genes and the environment for complex phenotypes and diseases
- GWAS surveys most of the genome for causal genetic variants and can be applied to quantitative and complex traits
- Haplotype blocks are used to find genes affecting phenotypes and enable large-scale GWAS
- Human SNP chips can assay >1 million SNPs and need to include low frequency SNPs (1-5%)
- Correcting for multiple-hypothesis testing is necessary in GWAS due to the large number of independent tests
- Odds ratio is a measure of effect size and strength of association in GWAS
- False positives in GWAS can result from random effects, systematic bias, population stratification, and missing data
- Population stratification due to admixture can lead to biased results in GWAS if not accounted for
- GWAS requires genotyping of thousands of individuals to have power, and a multistage approach can reduce genotyping cost while maintaining power
- Bonferroni correction is punitively conservative and permutation testing can find a more appropriate p-value threshold
- GWAS studies need to repeat with another set of samples and a subset can be retested with a denser SNP assay
- Critical to take population structure into account when doing GWAS to avoid biased results due to population stratification
Genome Wide Association Studies (GWAS) in Medical News
- GWAS studies focus on the cumulative action of many genes and the environment for complex phenotypes and diseases
- GWAS surveys most of the genome for causal genetic variants and can be applied to quantitative and complex traits
- Haplotype blocks are used to find genes affecting phenotypes and enable large-scale GWAS
- Human SNP chips can assay >1 million SNPs and need to include low frequency SNPs (1-5%)
- Correcting for multiple-hypothesis testing is necessary in GWAS due to the large number of independent tests
- Odds ratio is a measure of effect size and strength of association in GWAS
- False positives in GWAS can result from random effects, systematic bias, population stratification, and missing data
- Population stratification due to admixture can lead to biased results in GWAS if not accounted for
- GWAS requires genotyping of thousands of individuals to have power, and a multistage approach can reduce genotyping cost while maintaining power
- Bonferroni correction is punitively conservative and permutation testing can find a more appropriate p-value threshold
- GWAS studies need to repeat with another set of samples and a subset can be retested with a denser SNP assay
- Critical to take population structure into account when doing GWAS to avoid biased results due to population stratification
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Description
Test your knowledge of Genome Wide Association Studies (GWAS) with this quiz! Learn about the application of GWAS in understanding complex phenotypes and diseases, the use of haplotype blocks, SNP chips, and the necessity of correcting for multiple-hypothesis testing. Explore the challenges and considerations in GWAS, including population stratification and strategies to increase power while reducing genotyping cost.