L7: Emerging technology and genomic databases--genotyping

1. What is the International HapMap Project?

It is a catalog of common human genetic variants, including SNPs and indels, that occur in both coding and non-coding regions and are distributed within and across populations.

2. What does Hap stand for in HapMap?

It stands for haplotype, which refers to a combination of alleles located closely together on the same chromosome and tend to be inherited together.

3. What is linkage disequilibrium (LD)?

It is the phenomenon where genetic variants close in distance segregate together and the genotypes are correlated. LD is delayed by genetic distance as the chance of recombination increases.

4. How is a haplotype block defined?

A haplotype block is a region of high LD between alleles.

5. What are the types of genetic variation?

They include single nucleotide variation, insertion/deletion, copy number variation, and structural variation.

6. How is minor allele frequency (MAF) defined?

MAF is the frequency of the less common allele in a population. Mutations or rare DNA variations have MAF

7. What does the HapMap Project study?

It studies population-specific variants, allele frequencies, linkage disequilibrium patterns, haplotype information, and identifies tag SNPs.

8. What is the role of tag SNPs in the HapMap Project?

Tag SNPs are single nucleotide polymorphisms used to represent other SNPs in a region. They help identify genetic variations across populations efficiently.

9. How does the HapMap Project contribute to genetic research?

It provides LD patterns that reduce the need for genotyping and analysis of SNPs, helps design high-density SNP arrays for GWAS, and facilitates the selection of tag SNPs for genotyping.

10. What is the aim of a genome-wide association study (GWAS)?

The aim is to identify associations between genetic variants and traits or diseases through indirect tagging of causal variants in linkage disequilibrium.

11. How do linkage/association studies work in GWAS?

SNPs that are physically linked or in linkage disequilibrium with the disease gene are used as markers to identify mutations or variants that cause the disease or affect other traits through indirect association.

12. What does GWAS compare between patients and controls?

It compares the frequency of genetic markers between patients and controls. Markers that are more frequent in patients than in controls are considered "associated with the disease."

13. What is the GTEx Project?

The GTEx Project, or Genotype-Tissue Expression Project, aims to study how genetic variation influences gene expression across different human tissues.

14. How does the GTEx Project collect samples?

Samples are collected from deceased donors across multiple tissues.

15. What methods are used to analyze data in the GTEx Project?

The collected data is analyzed via genotyping, RNA sequencing, and analysis of gene expression patterns.

16. What are the findings of the GTEx Project?

It has revealed tissue-specific gene expression patterns and how genetic variants impact gene regulation.

17. What are SNPs?

SNPs are single nucleotide polymorphisms, which are variations in a single nucleotide base in the DNA sequence.

18. What are indels?

Indels refer to insertions or deletions of one or more nucleotides in the DNA sequence.

19. How do copy number variations (CNVs) differ from SNPs and indels?

CNVs involve duplications or deletions of larger segments of DNA, whereas SNPs and indels involve changes in single nucleotides.

20. What does MAF stand for?

MAF stands for minor allele frequency, which is the frequency of the less common allele in a population.

21. What is the purpose of analyzing gene expression patterns in the GTEx Project?

It helps understand how genetic variation influences gene expression in different tissues.

22. How are tag SNPs selected in the HapMap Project?

Tag SNPs are selected based on their ability to represent other SNPs in a region and efficiently identify genetic variations across populations.

23. How can LD patterns in the HapMap Project reduce the need for genotyping?

LD patterns allow researchers to identify a smaller number of SNPs that can represent a larger number of SNPs in a region, reducing the need for genotyping.

24. How does GWAS help locate DNA variants associated with diseases?

By comparing the frequency of genetic markers between patients and controls, GWAS can identify markers that are more frequent in patients, indicating an association with the disease. These markers are physically linked to the functional DNA variant that may lead to the disease.

25. What is the significance of the HapMap Project for designing high-density SNP arrays for GWAS?

The HapMap Project provides population-specific LD maps, which help select tag SNPs for genotyping and reduce thenumber of SNPs that need to be genotyped and tested in a GWAS, accelerating the research process.