Mapping Mendelian Disease

Question 1

What is a mendelian / monogenic disease?

Answer 1

disease that is caused by a single gene, with little or no impact from the environment (e.g. PKD)

Question 2

What is meant by a non-mendelian / polygenic disease?

Answer 2

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 3

What is a multifactorial disease?

Answer 3

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

Question 4

How is gene identifcation carried out with gene mapping?

Answer 4

Homozygosity mapping
Linkage analysis
GWAS

Question 5

What methods are used to prove certain genes cause disease?

Answer 5

We find disease causing mutations by sequencing

Using in silico, in vitro and in vivo tools we can prove they cause disease

Question 6

What is genetic linkage?

Answer 6

The tendency for alleles at neighbouring loci to segregate together at meiosis

Question 7

What causes gene linkage to occur?

Answer 7

To be linked, two loci must lie very close together

Question 8

What is a haplotype?

Answer 8

A haplotype defines multiple alleles at linked loci. Haplotypes mark chromosomal segments which can be tracked through pedigrees and populations

Question 9

Which loci are more susceptible to crossing over?

Answer 9

Cross-overs are more likely to occur between loci separated by some distance than those close together

Question 10

How can we use loci to identify disease genes?

Answer 10

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 - can use this to identify disease

Question 11

What is the effect of an unmarked loci in gene identification?

Answer 11

If the marker and the disease locus are unlinked (e.g. M5 – M8), affected relatives in a family are less likely to inherit the same marker alleles

Question 12

Outline the features of linkage analysis

Answer 12

Gene mapping

Family based design (from few large families to many small nuclear or subpairs)

Question 13

How is linkage analysis carried out?

Answer 13

Using an observed locus (marker) to draw inferences about an unobserved locus (disease gene)

Question 14

What is the aim of linkage analysis?

Answer 14

Find genomic region(s) linked to disease

Question 15

Summarise the method used for linkage analysis

Answer 15

1. Take a pedigree
2. Use a tool to generate genotyping data for your
   pedigree
   
   • E.g. Genome-Wide Human SNP Array 6.0
3. Physical and genetic distribution of markers on a
   genotyping array
4. Approx. 6000 SNP markers distributed uniformly across
   human genome
5. Run a linkage programme

Question 16

What is NPL?

Answer 16

Nonparametric Linkage Testing

Question 17

What is the significance of NPL?

Answer 17

No rules imposed in NPL –

looks for IBD (identity by descent)

Question 18

How does NPL testing identify genes?

Answer 18

Highlights regions (by high LOD scores) where:
all affected are equal, but different to unaffected.
Regardless of what inheritance pattern might be relevant

Question 19

How does parametric analysis differ from NPL?

Answer 19

Parametric imposes rules about inheritance and disease frequency

Question 20

How does parametric analysis identify disease genes?

Answer 20

Highlights regions (by high LOD scores) where:
all affected are equal, but different to unaffected
and the genotypes follow the imposed inheritance pattern

Question 21

What is a significant LOD score?

Answer 21

LOD scores > 3.0 are taken as significant evidence for linkage

LOD scores below -2.0 show significant non-linkage
LOD scores between -2 and 3 are inconclusive

Question 22

What are the functions of the lymphatic system?

Answer 22

• Fluid homeostasis
• Immune function
• Fatty acid transport

Question 23

What is primary lymphoedema?

Answer 23

Chronic oedema caused by a developmental abnormality of the lymphatic system

Question 24

How many people are affected by primary lymphoedema?

Answer 24

Affects 1 in 6,000

Often progressive

Question 25

What is the generic phenotype of lymphoedema patients?

Answer 25

Phenotypes vary: - age of onset - site - inheritance patterns - associated features - genetic causes

Question 26

Why is research in lymphoedema so significant?

Answer 26

Research is significant as lymphoedema is debilitating, causing recurrent infections, embarrassment and stress with no current medical cure

Question 27

What are the current treatments available for lymphoedema?

Answer 27

The only treatments available are: - Manual Lymph Drain (MLD) massage - Bandaging

Question 28

What is Hennekam Syndrome?

Answer 28

Generalised Lymphatic Dysplasia

Question 29

What are the effects of Hennekam syndrome?

Answer 29

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

Question 30

How would we go about mapping an autosomal recessive disease gene?

Answer 30

1. Generate genotyping data using Genome-Wide Human SNP Array 6.0 2. Run linkage analysis using an autosomal recessive model (parametric) 3. A LOD score > 3 translates to a p-value of approximately 0. 05 This means the genetic locus is significantly linked to disease LOD max = 2.0787 Result: Linkage to chromosome 18 (autosomal recessive model)

Question 31

Once you've established the significance of the GOIs what is the next step in mapping an autosomal recessive disease?`

Answer 31

Finding the disease causing mutation in one of the candidate genes

Question 32

How was the rare autosomal recessive disease identified?

Answer 32

100 candidate genes and 2 years later with lots of Sanger sequencing, mutations in CCBE1 was identified

Question 33

What is the final step in identifying the disease causing gene?

Answer 33

Proving that mutations in the gene identified are disease causing

Question 34

Outline the inheritance and onset of Limb lymphoedema

Answer 34

Autosomal dominant Pubertal/adult onset Associated with venous incompetence No other abnormalities

Question 35

Outline how an autosomal dominant model is used to identify GOI

Answer 35

1. Generate genotyping data e.g. using Genome WIde Human SNP Array 6.0 2. Run linkage analysis on the 2 families using an autosomal dominant model Result: the two families showed linkage to chr. 1 with an accumulative LOD max = 3.347

Question 36

What are the 2 methods used to prove disease-causing mutations?

Answer 36

Traditional Sanger sequencing - Candidate genes Next generation sequencing (NGS) - Whole genome sequencing (WGS) - Whole exome sequencing (WES)

Question 37

What is the benefit of NGS?

Answer 37

Next Generation Sequencing (NGS) makes us faster!

Question 38

What is the main cause of rare disease?

Answer 38

Rare disease is often caused by mutations in a single gene