W3 - Linkage Analysis Flashcards
What are germline mutations?
Passed onto descendants - present on all cells.
What are somatic mutations?
They are not transmitted to descendants and present in some cells of the body. Occurs due to external insult like radiation, smoking etc - causes cancers.
What are de novo mutations?
New mutations often in the embryonic stage of development. Not inherited from either parent. Can be passed onto descents.
What is homologous recombination?
Shuffling of chromosomal segments between partner (homologous) chromosomes of a pair.
Crossing over: Breaking and rejoining of the homologous chromosomes during meiosis. Results in exchange of chromosome segments and new allele combinations.
Crossovers are more likely to occur between Loci separated by some distance than between loci close together on the chromosome.
What is gene flow?
The movement of genes from one population to a number (eg. Migration) is an important source of genetic variation.
What is the difference between mutations and polymorphism?
- Mutation = Rare change. Normal allele is prevalent in the population - the mutation changes this to a rare abnormal variant.
- polymorphism = DNA variant common in the population. No allele is the normal allele. Instead or two or more equal acceptable alternatives.
The arbitrary cut-off point between mutations on a polymorphism as a minor allele frequency of 1%. Ie. For variant to be classified as a polymorphism, the least common allele must be present in less than 1% of the population.
What is a haplotype?
It is a group of alleles that are inherited together from a single parent.
Multiple alleles at linked loci. These chromosomal segments can be tracked through pedigree and population.
What are the three classification of genetic disease?
- Mendelian/ Monogenic
- Non-Mendelian/ Polygenic
- Multifactorial
What is a Mendelian/Monogenic disease?
Disease that is caused by a single gene with little or no impact on the environment. Eg. Polycystic kidney disease. 
What is non-Mendelian/ polygenic disease?
Disease or trait caused by the impact of many different genes each having only a small individual impact on the final condition. Eg. Psoriasis
What is a multifactorial disease?
Disease or traits resulting from interaction between multiple genes and of multiple environmental factors eg heart disease.
What is linkage analysis?
Linkage analysis is a method used to map the location of the disease gene into Genome.
The term linkage refers to the assumption of two things being physically linked to each other
Assumption made= can use genetic markers to identify the location of a disease gene based on the physical proximity.
What is the difference between genetic maps and physical maps of Genome?
Maps allow orientation and calculation of distance.
Genetic: looks at information in blocks or regions. Used before 2001. Used CentiMorgans.
Physical: provide information on the physical distance between landmarks. Used after 2001 and uses Megabase.
What are the two types of genetic markers?
- Microsatellite Markers
- Single nucleotide polymorphisms 
What are Microsatellite markers?
Less common now – highly polymorphic short tandem repeats of 2 to 6bp.
Microsatellites my different length between chromosomes (heterozygous)
A relatively widely spaced apart 
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 single nucleotide polymorphism Markers?
No the genetic marker of choice- Biallelic (a SNP will be one of two possible bases).
Lower heterozygosity than Microsatellites, but space to much closer together.
More informative
~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
How is microsatellite genotyping done?
There are lots of polymorphic repeat units.
You can amplify it across the region using PCR.
Can we run on a gel.
Smaller repeat units = shorter fragments.
How is fluorescent genotyping done?
- Fluorescently tagged PCR primers
- allows for multiplexing of PCR products with different colours and fragment lengths.
- fragment sizes separated down to 1bp resolution. 
The peaks and numbers of the charts can be used to identify maternal and paternal inheritance.
What are Single nucleotide polymorphism (SNP)?
- Single base change
- most common type of variation
-Go to occur approximately one per 1000 bases - Human genome is 3 billion base pairs
What are SNP genotyping microarrays?
Provides genome-wide coverage of SNP markers
SNPs are proxy markers; NOT the causal disease variants
Can amplify thousands of markers in a single experiment
Alleles are identified by relative fluorescence
homozygous for allele 1 = green signal
homozygous for allele 2 = red signal
heterozygous (1/2) = yellow signal
What are SNP genotyping microarrays used for?
Typically used for:
Linkage analysis in families (affected vs unaffected relatives)
homozygosity mapping (autosomal recessive) and mapping of
Mendelian traits
GWAS in populations (unrelated cases vs matched controls)
non-Mendelian disorders and multifactorial traits
What can you tell with linkage mapping using genetic markers?
If a marker is linked to disease Locus, the same marker alleles will be inherited by two affected relatives more often than expected by chance.
If the market and the disease locus of unlinked, the infected relatives and family are less likely to inherit the same marker alleles.
How do we build haplotypes?
Haplotypes are half the genetics.
We look at the markers of both parents and affected individual to figure out the haplotypes from the mother and father.
We look at the affected members eg, mother and you and work out which regions are the same.
If your brother is affected too, we can do the same for him and see the similarities and differences to narrow down the location of the affected gene.
Can build up pedigrees.
What is the statistical analysis of linkage?
Creating the haplotypes genomes would be laborious individually. We use software instead.
The probability of linkage can be assessed using a LOD score.
LOD = logarithm of the odds score
Assesses the probability of obtaining the test data if the two loci are linked,
to the likelihood of observing the same data purely by chance
(Refer to Power point slides for the formula)
Recombination fraction is the proportion of recombinant births (i.e. R / NR+R)
Maximum recombination fraction = 0.5, which is equivalent to independent assortment
The higher the LOD score, the higher the likelihood of linkage
What is parametric analysis?
Specifies the pedigree structure and inheritance pattern (model)
What is non-parametric analysis?
Detects allele sharing between affected individuals.
How old is LOD scores additive?
Different families linked to the same disease Locus will increase the overall score.
What are LOD scores indicative of?
A LOD score ≥ 3 is considered evidence for linkage
Equivalent to odds of 1000:1 that the observed linkage occurred by chance
Translates to a p-value of approximately 0.05
A LOD score ≤ -2 is considered evidence against linkage
