Chapter 6 Multiple choice questions

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What is a genome wide association study? Select correct answer.

A study that tests whether a disease or trait is heritable correct incorrect

A study that tests association between a disease and every gene in the genome correct incorrect

A genetic association study between all genetic variants in the genome and disease correct incorrect

A genetic association study between a disease or trait and sufficient genetic markers to capture almost all common genetic variation correct incorrect

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What does the success of GWAS depend upon? Select all correct answers.

A thorough understanding of linkage disequilibrium in the population in which it is being conducted correct incorrect

About a million single nucleotide polymorphisms correct incorrect

A set of variants distributed across the genome that is in sufficient linkage disequilibrium to capture information from nearly every other polymorphic locus correct incorrect

A method to genotype large numbers of markers cheaply and quickly correct incorrect

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What is a Manhattan plot? Select all correct answers.

A comparison between New York's skyline and the degree of significance for SNPs in a genome wide association study correct incorrect

A plot of the distribution of significance of SNPs from a genome wide association study correct incorrect

On the vertical axis the negative logarithm of the P-value for association, and on the horizontal axis the position in the genome for every SNP in a genome wide association study correct incorrect

An effective and commonly used way to visualize the results of a genome wide association study correct incorrect

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What does it mean if a variant in a GWAS of schizophrenia exceeds the accepted significance threshold? Select all correct answers.

It could be a false positive finding correct incorrect

The variant may directly increase the risk of the schizophrenia correct incorrect

The variant could be in linkage disequilibrium with another variant that directly increases the risk of the schizophrenia correct incorrect

The variant is in a gene that causes schizophrenia correct incorrect

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What is the purpose of a quantile-quantile plot in GWAS? Select correct answer.

To show whether a GWAS has been successful correct incorrect

To identify the most significant results from a GWAS correct incorrect

To see if the distribution of test statistics is consistent with the null hypothesis correct incorrect

To detect inflation in the P-values of a GWAS correct incorrect

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What is genotype imputation? Select all correct answers.

A way to increase the significance of GWAS correct incorrect

A method of filling in missing data correct incorrect

A method that uses linkage disequilibrium and reference haplotypes to estimate genotypes at markers that have not been genotyped correct incorrect

A way to extend the reach of GWAS so that information can be obtained from ungenotyped markers correct incorrect

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What have we learnt from GWAS? Select correct answer.

GWAS has identified associations between allelic variants at loci that increase the risk of psychiatric disease correct incorrect

GWAS has identified genes involved in behavior and psychiatric disease correct incorrect

GWAS findings explain a significant proportion of the heritability of psychiatric diseases correct incorrect

GWAS variants are usually in portions of the genome that encode genes (the exome) correct incorrect

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What methods turn GWAS loci into genes? Select all correct answers.

Take the closest gene to each locus found by GWAS correct incorrect

Sequence genes close to a genome-wide significant marker to find a coding mutation correct incorrect

Find the causative variant and determine what it does correct incorrect

Use chromosome conformation capture to relate enhancer to promoter elements and use that information to relate GWAS variants within enhancers to the genes they regulate correct incorrect

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What is TWAS? Select correct answer.

A type of GWAS that uses expression data to identify genes correct incorrect

A method that unequivocally identifies the genes involved in psychiatric disease correct incorrect

A method that uses a set of genotypes known to affect transcription to estimate transcript levels in a group of genotyped people in which transcripts were not directly measured correct incorrect

An way of estimating how many transcripts are causal for a psychiatric disease correct incorrect