Linkage and association analyses (QTL/GWAS) Flashcards
What will be the typical content of a Biobank?
A Bio bank is a collection of genetic material from different animal and plant species.
How would you define a genetic marker?
A genetic marker is a DNA sequence with a known physical location on a chromosome. DNA segments close to each-other on a chromosome tend to be inherited together. Microsatellites and SNP are commonly used as genetic markers.
- A genetic marker must represent a unique location in the genome.
- A genetic marker must be polymorphic (have more than one allele)
What are the main differences between microsatellites and SNPs considered as genetic markers?
SNPs are far more abundant in the genome compared to microsatellites and can occur both within
and outside protein coding regions.
Microsatellites is usually not found in coding regions.
A SNP marker usually have two alleles, while microsatellites can have many alleles (only two alleles
per individual, but many in a population). Each microsatellite marker is therefore more informative
than a SNP-marker.
Genotyping of SNPs can be automated more easily than genotyping of microsatellites.
What do we mean by qualitative traits and what do we mean by quantitative traits?
Quantitative traits are traits such as hight or weight, can be measured on a continues scale and the traits are influenced by the environment. It is controlled by several genes and each gene contributing some variation to the trait in question
Qualitative traits are traits such as black or white, horns or no horns. These traits are usually controlled by one single or few genes. Not affected by environmental factors.
Why are qualitative traits more frequently mapped with success, compared to quantitative traits?
Qualitative traits are controlled by a single or few genes and is therefore easier to map with success. In addition,
environmental factors may also contribute to camouflage the genetic effect in quantitative traits.
What is the difference between linkage and linkage disequilibrium?
Linkage is calculated in a family structure (parents-offspring, one generation of recombination),
based on observed recombination rates that takes place during meiosis. Linkage can be used for
estimating genetic distance in centiMorgan (cM).
Linkage Disequilibrium (LD) is based on observed associations between alleles at different loci.
Individuals used for estimating linkage disequilibrium can be non-related (no need for family
structure). These associations have “survived” over many generations without being broken of
recombination.
Linkage disequilibrium can only be observed over shorter distances compared to linkage and is therefore a more precise mapping strategy compared to linkage. Linkage
disequilibrium can not be used for calculating genetic distance in cM.
What does the acronym GWAS stand for?
Genome-Wide Association Study help scientists identify genes associated with a particular disease (or another trait). This method studies the entire set of DNA (the genome) of a large group of people, searching for small variations, called single nucleotide polymorphisms or SNPs.
What are SNPs?
SNPs code for Genetic variation among individuals, as each SNPs represent a difference in a single nucleotide in a DNA sequences.
