Transcript Linkage and Genetic Mapping

Linkage and Genetic Mapping
Lecture 1
Human Molecular Genetics (Strachan
and Read) Chapters 4, 13, 14
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.
Strategies for cloning a disease
gene
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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
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.
Positional cloning
Mendelian Inheritance
Autosomal dominant
Autosomal recessive
X-linked recessive
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.
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)
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.
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.
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
Multipoint linkage mapping
Fig 13.8 from Strachan and Read (3rd edition)