1. Linkage and Genetic Mapping
Lecture 1
Human Molecular Genetics (Strachan and Read) Chapters 4, 13, 14

2. What are genetic diseases? There are two basic types
1. Simple Mendelian (easy to analyse)
e.g. Huntington's disease, cystic fibrosis, Duchenne muscular dystrophy follow a simple pattern of inheritance (e.g. autosomal dominant, autosomal recessive, X-linked recessive).
There is a complete correlation between genotype and phenotype. If you've got the mutant gene, you'll get the disease.
2. Complex or multifactorial (hard to analyse)
e.g. many common diseases, such as cancer, asthma, schizophrenia, hypertension, heart disease.The risk of getting the disease is modified by individual's genotype.
Evidence for "genetic-ness" of a disease is expressed as l = (risk to 1st degree relatives of patient)/(population risk). For type I diabetes, l = 15 (6%/0.4%).
Other factors, especially other genes and environment, also influence risk of getting disease.

3. Strategies for cloning a disease gene
If you know the biochemical basis of the disease, e.g. there is an enzyme missing from a biochemical pathway, you can go straight to the gene that codes for the enzyme/protein. This called functional cloning
If you have some idea of the pathological basis of the disease, or if there is a similar animal or human disease for whose basis is known, you might be able to guess what the gene might be and test that gene directly in patients: the candidate gene approach
If the only thing you know about the disease gene is its location in the genome from linkage studies, the approach used is called positional cloning
Positional cloning can be based on translocations or deletions that disrupt the gene and cause the phenotype (rare), or on linkage mapping in families

4. The main questions that have to be answered when planning the strategy
What type of inheritance? Simple (which mode?) or complex?
How to search? Can you guess at a candidate gene? If so, test it directly in patients and controls to see if a mutation is associated with disease state
Are families available? If so can use the genetic linkage approach - study the inheritance of polymorphic DNA sequences, see if any segregate with the disease. This identifies candidate region of genome.

5. Positional cloning

6. Mendelian Inheritance
Autosomal dominant
Autosomal recessive
X-linked recessive

7. Linkage and recombination
Mapping disease genes in humans is done by using DNA polymorphisms,
These polymorphisms can be genotyped using simple laboratory techniques, mostly based on PCR.
In a simple genetic disease polymorphisms are studied in family members to find genetic linkage.
If the polymorphism is close to the disease gene on the chromosome there is a low chance of recombination at meiosis and linkage is observed.
If the polymorphism and disease gene are far apart or on different chromosomes, linkage is not observed.

9. Recombination fractions
A recombination event gives ½ parental type (P) and ½ recombinant type (R) offspring
Recombination fraction RF = R/R+P
RF is between 0 and 0.5 (0 and 50%)
The closer together the genes are, the smaller is RF
RF = 0.5 for unlinked genes (very far apart or on different chromosomes)

12. Lod scores
Experimental animals such as mice or fruit-flies produce large numbers of offspring, so can estimate RF very accurately.
Human families only produce small numbers of children.
To get statistically significant evidence for linkage, combine evidence from many families
A complex mathematical procedure, implemented by computer software, is used to generate "Lod scores".
Lod score is a statistic that describes the strength of evidence for linkage, at any chosen value of the RF, given the family data available.

14. A lod score of 3 or more is considered good evidence for linkage.
A lod score of -2 or less is evidence against linkage.
Values between -2 and 3 are inconclusive and indicate that more data must be obtained.

15. Multipoint linkage mapping
Using 1000s of markers, genetic maps have been constructed across the whole genome
Multipoint mapping uses several markers at once to localise a disease gene relative to the other markers in the map
More efficient process than using one marker at a time

16. Multipoint linkage mapping
Fig 13.8 from Strachan and Read (3rd edition)