Linkage Analysis Flashcards
What is genetic variation and what are the different effects it can have?
Genetic variation refers to differences in the DNA sequence between individuals in a population
Genetic variation can have different effects:
Alteration of the amino acid sequence (protein) that is encoded by a gene
Changes in gene regulation (where and when a gene is expressed)
Physical appearance of an individual (e.g. eye colour, genetic disease risk)
Silent or no apparent effect
Why is genetic variation so important?
- Genetic variation underlies phenotypic differences among different individuals
- Genetic variations determine our predisposition to complex diseases and responses to drugs and environmental factors
- Genetic variation reveals clues of ancestral human migration history
What are the three different types of mutations?
Germline mutations: present in germ cells, passed on to descendants
Somatic mutations: present in somatic cells, not transmitted to descendants, can cause cancers
de novo mutations: new mutation not inherited from either parent, in early development but can then be passed on to next generation
What is homologous recombination?
Homologous recombination: shuffling of chromosomal segments between partner (homologous) chromosomes of a pair
What is gene flow?
Gene flow: the movement of genes from one population to another (e.g. migration) is an important source of genetic variation
What is the difference between a mutation and polymorphism?
A mutation is a rare change in the DNA sequence that is different to the normal (reference) sequence.
- The ‘normal’ allele is prevalent in the population and the mutation changes this to a rare ‘abnormal’ variant
By contrast, a polymorphism is a DNA sequence variant that is common in the population. In this case no single allele is regarded as the ‘normal’ allele.
- Instead there are two or more equally acceptable alternatives
The arbitrary cut-off point between a mutation and a polymorphism is a minor allele frequency (MAF) of 1% (i.e. for a variant to be classed as a polymorphism, the least common (minor) allele must be present in ≥1% of the population)
When does recombination happen?
The creation of haploid gametes (i.e. sperm and eggs)
Genetic recombination takes place during prophase 1 where the crossing over of homologous arms of chromosome happens
This is completely random
What is the classification of genetic disease?
Mendelian / Monogenic: disease that is caused by a single gene, with little or no impact from the environment (e.g. PKD)
Linkage analysis can only be applied to Mendelian/Monogenic diseases
Non-Mendelian / Polygenic: diseases or traits caused by the impact of many different genes, each having only a small individual impact on the final condition (e.g. psoriasis)
Multifactorial: diseases or traits resulting from an interaction between multiple genes and often multiple environmental factors (e.g. heart disease)
What is linkage analysis?
Linkage analysis is a method used to map the location of a disease gene in the genome
The term ‘linkage’ refers to the assumption of two things being physically linked to each other
What are the principles of genetic linkage?
Genetic linkage is the tendency for alleles at neighbouring loci to segregate together at meiosis
Cross-overs are more likely to occur between loci separated by some distance than between loci close together on the chromosome
Therefore to be linked, two loci must lie very close together
A haplotype defines multiple alleles at linked loci. These chromosomal segments can be tracked through pedigrees and populations
What is the method for detecting genetic linkage?
Genotype multiple genetic markers across the genome
Genotype multiple family members from families with the genetic trait
Identify which genetic markers co-segregate with the disease (phenotype)
(i.e. which haplotypes are the same in all affected family members)
These genetic markers are therefore ‘linked’ to the disease gene
–> This indicates where in the genome the disease gene is likely to be located
NB: further work is needed to identify the gene and disease-causing mutation!
What are the two different types of genetic markers?
Microsatellite markers
Single nucleotide polymorphism (SNP)
What are the features of microsatellite markers?
Less common now. Highly polymorphic short tandem repeats of 2 to 6 bp
Microsatellites may differ in length between chromosomes (heterozygous)
Are relatively widely spaced apart
To do a genome linkage analysis you'd be looking at: 400 (200) microsatellite markers Average spacing 9 cM (20 cM) PCR-based system Fluorescently-labelled primers Manual assignment of genotypes Labour intensive Whole genome scan >2-3 months
What are the features of SNP markers?
Now the genetic marker of choice. Biallelic (a SNP will be one of two possible bases)
Lower heterozygosity than microsatellites, but spaced much closer together
More informative
To do a genome linkage analysis you'd be looking at: ~6,000 SNPs Spaced throughout the genome Microarray-based system Genotypes assigned automatically Highly automated Data returned within <1-2 months
What is microsatellite genotyping used for?
Typically used for:
DNA fingerprinting from very small amounts of material
Standard test uses 13 core loci making the likelihood of a chance match 1 in three trillion
Paternity testing
Linkage analysis for disease gene identification
