Mapping Mendelian Disease Flashcards
As a recap, what are the different classifications of genetic diseases?
MENDELIAN/MONOGENIC: disease that is caused by a single gene, with little or no impact from the environment (e.g. PKD)
NON-MEDELIAN/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)
How do we study Medelian genetic diseases?
Gene identification by gene mapping:
- Homozygosity mapping
- Linkage analysis
- GWAS
How do we fine disease-causing mutations?
We find them by sequencing.
How do we prove that certain sequences cause disease?
We do this using in silico, in vitro and in vivo tools.
As a recap, list the principles of genetic linkage.
Genetic linkage is the tendency for alleles at neighbouring loci to segregate together at meiosis. Therefore to be linked, two loci must lie very close together.
A haplotype defines multiple alleles at linked loci. Haplotypes mark chromosomal segments which can be tracked through pedigrees and populations.
Cross-overs are more likely to occur between loci separated by some distance than those close together.
How can we use the principles of genetic linkage to identify disease-causing genes?
If a marker is linked to a disease locus (i.e. M3 and M4), the same marker alleles will be inherited by two affected relatives more often than expected by chance.
If the marker and the disease locus are unlinked (e.g. M5 – M8), the affected relatives in a family are less likely to inherit the same marker alleles.
The markers are usually SNP markers chosen from databases and we know exactly where they are. You will then zoom into the diseased gene region and find out what genes lie in that region and which ones could be the disease-causing gene.
As a recap, what is linkage analysis?
It is used for gene mapping.
It’s done using an observed locus (marker) to draw inferences about an unobserved locus (disease gene).
It has a family based design (from few large families to many small nuclear or sibpairs).
Our goal is to find the genomic regions linked to a disease.
Give a quick summary of linkage analysis.
- first, take a pedigree
- use some kind of tool to generate genotyping data for your pedigree
- graph the physical and genetic distribution of markers on a genotyping array
- run a linkage programme (can choose to run it in a parametric or non-parametric way)
- figure out LOD score
What is the main difference between running a linkage programme in a parametric and non-parametric way?
NON-PARAMETRIC:
- this doesn’t assume anything about inheritance patterns
- in some graphs, there are peaks and in some there is linkage (this gives us a rough idea of what could happen in you start applying the model)
- there are no rules imposed in NPL, it looks for IBD (identity by descent)
PARAMETRIC:
- imposes rules about inheritance and disease frequency
What are the functions of the lymphatic system?
- fluid homeostasis
- immune function
- fatty acid transport
It’s a branched system that circulates antibodies and immune mediators.
Whatever fluid leaks out of the CVS goes into the lymphatic system and is brought back into the CVS.
Describe primary lymphoedema.
Here, the lymphatic system has not developed properly or is not functioning properly.
It’s a chronic oedema caused by a developmental abnormality of the lymphatic system. It affects 1 in 6,000, and is often progressive.
The phenotypes vary based on:
- age of onset
- site
- inheritance patterns
- associated features
- genetic causes
Why is research into lymphoedema important?
Lymphoedema is:
- debilitating
- embarassing
- stressful
- comes with recurrent infections
- there is no medical cure!
What is the treatment available for lymphoedema?
- manual lymph drain (MLD) massage
- bandaging
Describe lymphatic dysplasia?
It’s a severe form of dysplasia, and it’s also known as Hennekam syndrome.
It’s antenatal hydrops (swelling) with ascites and pleural effusions.
The child is oedematous at birth. They get intestinal lymphangiectasia.
It also comes with peripheral lymphoedema of the arms, legs, and face.
Additionally, it causes a mild developmental delay.
Using the example of lymphoedema, how would we go about finding the gene responsible for the disease?
First, we would generate genotyping data. This can be done using the Genome-Wide Human SNP Array 6.0.
Then, we would run linkage analysis using an autosomal recessive model. The result of this showed linkage to chromosome 18. They couldn’t prioritise the candidate gene enough, so we would work our way through them.
Next, you would go about finding the disease causing mutation in one of the candidate genes. You would design a primer for each of the exons of the candidate genes and carry out the Sanger sequencing.
The final step would be proving that the mutations in the gene are identified as disease-causing. They knocked the suspected in zebra-fish, and the fish ended up filling with fluid.
