linkage and genetic mapping lecture 1 human molecular genetics (strachan and read) chapters 4, 13,...
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Linkage and Genetic Mapping
Lecture 1Human Molecular Genetics (Strachan
and Read) Chapters 4, 13, 14
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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 = (risk to 1st degree relatives of patient)/(population risk). For type I diabetes, = 15 (6%/0.4%).
– Other factors, especially other genes and environment, also influence risk of getting disease.
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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
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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.
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Positional cloning
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Mendelian Inheritance
Autosomal dominant
Autosomal recessive
X-linked recessive
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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.
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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)
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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.
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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.
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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
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Multipoint linkage mappingFig 13.8 from Strachan and Read (3rd edition)