Mapping Mendelian Disease

Question 1

What are the 3 classification of genetic disease?

Answer 1

• Mendelian/Monogenic
• Non-Mendelian/Polygeneic
• Multifactorial

Question 2

What is a mendelian/monogenic disease?

Answer 2

Disease caused by a single gene, with little or no impact from the environment

Question 3

What is a non-mendelian/monogenic disease?

Answer 3

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)

Question 4

What is a multifactorial disease?

Answer 4

Diseases or traits resulting from an interaction between multiple genes and often multiple environmental factors (e.g. heart disease)

Question 5

How is mendelian genetic disease studied?

Answer 5

In the lab through gene identification and functional studies

Question 6

What are the ways genes are identifed by gene mapping?

Answer 6

• Homozygosity mapping
• Linkage analysis
• GWAS

Question 7

How do we find disease-causing mutations?

Answer 7

Through sequencing

Question 8

How do we prove they cause disease?

Answer 8

Using in silico, in vitro and in vivo tools

Question 9

What is genetic linkage? What is required for a gene to be linked?

Answer 9

The tendency for alleles at neighbouring loci to segregate together at meiosis. Therefore to be linked, two loci must lie very close together.

Question 10

What is a haplotype?

Answer 10

Multiple alleles at linked loci.

Question 11

How can haplotypes benefit population and pedigree tracking?

Answer 11

They mark chromosomal segments

Question 12

When does cross-overs occur?

Answer 12

During meiosis when the loci is separated by some distance rather than closer together

Question 13

How can genetic linkage be used to identify disease causing genes?

Answer 13

• If a marker is linked to a disease locus, 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, the affected individuals in a family are less likely to inherit the same marker alleles.

Question 14

What is linkage analysis?

Answer 14

• Gene mapping
• Using an observed locus (marker) to draw inferences about an unobserved locus (disease gene).
• Family based design
• To find genomic regions linked to the disease

Question 15

Summarise the method of linkage analysis

Answer 15

1. Take a pedigree
2. Use a tool to generate genotyping data for the pedigree
   
   • > Physical and genetic distribution of markers on a genotyping array
3. Generate a file with the pedigree information plus the genotyping data from the microarray
4. Run a linkage programme

Question 16

What is non parametric linkage testing?

Answer 16

There is no “rules” imposed, rather it looks for identity by descent. It highlights regions with high LOD scores and all affected are equal, but different to unaffected. This is regardless of what inheritance pattern might be relevant.

Question 17

What is parametric linkage testing?

Answer 17

• Imposes rules about inheritance and disease frequency
• It highlights regions with high LOD scores where all affected are equal, but different to unaffected. The genotypes follow the imposed inheritance pattern.

Question 18

What do LOD scores show about linkage?

Answer 18

LOD scores below -2.0 show significant non-linkage
LOD scores between -2 and 3 are inconclusive
Disease gene is likely to be located the two markers defining the linkage peak

Question 19

Function of the lymphatic system

Answer 19

• Fluid homeostasis
• Immune function
• Fatty acid transport

Question 20

What causes chronic oedema (primary lymphoedema)?

Answer 20

Caused by a developmental abnormality of the lymphatic system

Question 21

How many people does primary lymphoedema affect?

Answer 21

1 in 6,000

Often progressive

Question 22

What do phenotypes affect in primary lymphoedema?

Answer 22

Age of onset 
Site 
Inheritance Patterns 
Associated features 
Genetic causes

Question 23

Why is lymphoedema research important?

Answer 23

It is debilitating, embrassing, stressful and causes recurrent infections. But there is no known medical cure.

Question 24

What is the current treatment for primary lymphoedema?

Answer 24

• Manual Lymph Drain (MLD) massage

- Bandaging

Question 25

What is Hennekam syndrome?

Answer 25

Generalised Lymphatic dysplasia

• Antenatal hydrops with ascites and pleural effusions
• Oedematous at birth
• Intestinal lymphangiectasia
• Peripheral lymphoedema: arms, legs, face
• Mild developmental delay

Question 26

How are families for primary lymphoedema studied - explain using an autosomal recessive model

Answer 26

1. Genotype data is generated
2. Run linkage analysis using an autosomal recessive model
3. Result will show if ther is a linkage - looking at the LOD score
4. They found approx. 130 candidate genes. They completed sanger sequencing to find the gene responsible for the mutations in CCBE1.
5. To prove the mutation identified was disease causing, they inserted the gene into a zebrafish and it had an absence of trunk lymphatic vessels and was full of fluid.

Question 27

Describe how primary lymphoedema was investigated in an autosomal dominant model

Answer 27

1. Generated genotyping data found that 4 samples all where affected.
2. Ran a linkage analysis on the 2 families using an autosomal dominant model
3. The results found that two families showed linkage to chromosome 1 with a cumulative LODmax = 3.347
4. They found 173 candidate genes.
5. A different technique rather than sanger sequencing was used - Next Gen sequencing. This is faster. They did the WGS and WES.
6. WES found NOVEL changes in the linkage region on chromosome 1.
7. Sanger sequencing found the rest of the family, showing the only GJC2 co-segregated with the disease status, thereby excluding NVL as a candidate.
8. Sanger sequencing of GJC2 in additional individuals with 4-limb lymphoedema identified further mutations associated with the phenotype.
9. Prove that this mutation caused the lymphoedema:
   - > In vitro work showed that GJC2 protein function was disrupted
   
   • > In vivo work showed that knock out of GJC2 in mice cause lymphatic problems