Genetics Linkage Disequilibrium and GWAS

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Questions and Answers

What are microsatellites also known as?

Complex Genetic Markers

Long Sequence Variations

Simple Sequence Repeats (correct)

Mutation Sites

Why do microsatellites have greater resolution compared to SNPs when comparing genetic differences?

SNPs are more prevalent in the genome than microsatellites.

Microsatellites can show more variation due to multiple alleles. (correct)

Microsatellites are less stable than SNPs.

SNPs are located in non-coding regions only.

What is a significant characteristic of SNPs compared to microsatellites?

SNPs are more widely used in pedigree analysis.

SNPs can exhibit multiple types of variation.

SNPs have a single base variation. (correct)

SNPs contain repetitive sequences.

In the context of genetic research, what is a key advantage of using microsatellites?

They allow for higher density mapping of genetic traits. Signup and view all the answers

Which term is synonymous with microsatellites?

Sequence Tagged Sites Signup and view all the answers

What does the LOD score represent in genetic studies?

The probability of genetic markers being located near each other Signup and view all the answers

Which statement best differentiates linkage from association in genetic studies?

Linkage studies identify chromosome paths in families. Signup and view all the answers

In a genome-wide association study (GWAS), the results can show associations between variants and traits. What do the dots in these results typically represent?

Single nucleotide polymorphisms (SNPs) across the genome Signup and view all the answers

Which type of disease is most appropriately studied using linkage analysis?

Mendelian diseases Signup and view all the answers

What is the primary assumption behind association studies?

Common genetic variants are linked to causal variants. Signup and view all the answers

What type of data do DNA microarrays primarily use in genetic studies?

SINGLE nucleotide polymorphisms (SNPs) Signup and view all the answers

Which of the following best describes the goal of a genome-wide association study?

To identify genetic variants that associate with specific traits Signup and view all the answers

What is implied by the use of 'imputed' SNPs in association studies?

They are predicted from existing genetic data. Signup and view all the answers

What contributes to higher genetic diversity among African populations?

Founder effect leading to smaller haplotype blocks Signup and view all the answers

How can SNPs be inferred within a haplotype block without genotyping every SNP?

By genotyping a set of tag SNPs Signup and view all the answers

What is the function of recombination hotspots in the genome?

They are the primary sites for increased recombination activity. Signup and view all the answers

What percentage of haplotypes are shared across all populations studied?

51% Signup and view all the answers

What is characteristic of Mendelian traits?

They are caused by a single genetic locus. Signup and view all the answers

What does linkage disequilibrium (LD) refer to?

Non-random association of alleles at different loci. Signup and view all the answers

Which step is NOT part of the traditional method for cloning a disease gene?

Conduct epigenetic analysis on sample tissues Signup and view all the answers

How does PRDM9 contribute to recombination?

It binds to a specific motif at recombination hotspots. Signup and view all the answers

What indicates that a particular allele is linked to a disease phenotype?

It is common among diseased individuals. Signup and view all the answers

Which of the following haplotypes indicate alleles G and C are in linkage disequilibrium?

GC and GT in consistent pairs. Signup and view all the answers

Which of the following best describes the new haplotypes generated through recombination?

They can be a mix of maternal and paternal alleles. Signup and view all the answers

What technique can help identify which polymorphisms follow a disease?

Genotyping individuals from established families Signup and view all the answers

Recombination hotspots are important because they:

Facilitate genetic diversity between populations. Signup and view all the answers

Which statement is true regarding recombination outside of hotspots?

Recombination can occur but less frequently. Signup and view all the answers

How many possible haplotypes can be formed from two SNP loci each with two alleles?

4 possible haplotypes. Signup and view all the answers

What is the relationship between decreased recombination and linkage disequilibrium?

Decreased recombination causes increased linkage disequilibrium. Signup and view all the answers

Why are rare events not well captured in GWAS?

The study population size is too small. Signup and view all the answers

What is a common limitation of GWAS identified in the content?

It cannot capture structural variations effectively. Signup and view all the answers

Which explanation suggests a reason for the small proportion of risk explained in GWAS?

Only common variants are analyzed. Signup and view all the answers

What is proposed as a solution to finding missing heritability in complex diseases?

Sequencing personal genomes. Signup and view all the answers

Which statement about haplotype blocks is true?

Recombination rates within them are typically high. Signup and view all the answers

Which statement is true about linkage and association studies?

GWAS can link variants to specific traits like asparagus anosmia. Signup and view all the answers

Which continental group is believed to have the greatest number of variant sites?

Africa Signup and view all the answers

What is one of the challenges in understanding genetic variation's phenotypic consequences?

The consequences of genetic variation remain mostly unknown. Signup and view all the answers

Study Notes

Linkage Disequilibrium

Linkage disequilibrium (LD) refers to the non-random association of alleles at two or more loci within a general population.
LD is a result of decreased recombination between alleles.

Haplotype Blocks

Higher genetic diversity is found in African populations due to a founder effect.
This leads to smaller haplotype blocks with more possible haplotypes within those blocks.
Recombination hotspots exist between these haplotype blocks.
51% of haplotypes are found in all populations, and 72% are found in 2 of 3 populations.
Tag SNPs can be used to infer SNPs within haplotype blocks.

Mapping Mendelian Traits

Mendelian traits are characteristics caused by a single genetic locus.
Over 5,000 known heritable diseases/traits can be found on "Online Mendelian Inheritance in Man" (OMIM).

Genome-Wide Association Studies (GWASs)

GWASs are used to identify genetic variants associated with a trait or disease in a population.
GWASs require two groups: cases (affected individuals) and controls (unaffected individuals).
This approach assumes that common genetic variants cause phenotypes in a population, or are linked to the causal variants.
They are particularly useful for studying common and polygenic diseases.
GWASs can be used to find variants associated with asparagus anosmia.

Caveats of GWASs

GWASs primarily measure common SNPs and frequent haplotypes, making it difficult to capture rare events.
Structural variation (CNVs, inversions, etc.) may not be captured by GWASs.
It is difficult to pinpoint the specific responsible genes using GWASs alone.
Validation using follow-up experiments is required.
GWASs can only explain a small proportion of risk associated with complex diseases.
The missing heritability might be due to unknown genetic variants or complex interactions among known variants.

Solutions For Understanding The Missing Heritability

Sequencing personal genomes can help understand less frequent polymorphisms and expand our understanding of human genetic variation.

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Description

This quiz explores crucial concepts in genetics, including linkage disequilibrium, haplotype blocks, and mapping Mendelian traits. It also covers the methodology and significance of genome-wide association studies (GWAS). Test your understanding of these foundational topics in genetics and their implications in heritable diseases.