S4: Genome Determinants of Learning Disability

Question 1

List prevelance of genetic conditions from birth

Answer 1

• 2-3% of all babies are born with a significant problems.
• Of this, genetic conditions are responsible for 50% of causes of deafness, blindness, childhood death, severe learning difficulty and 30% of hospital admissions.

Question 2

What is a learning disability?

Answer 2

A learning disability is defined as significantly reduced ability to understand new or complex information and to learn new skills. It also includes a reduce ability to cope independently which starts before adulthood with lasting effects on development. The incidence of learning disability is 1-2.5%.

Question 3

How can learning disability be defined?

Answer 3

The extent of the learning disability can be defined as mild, moderate, severe and profound.

• Mild = IQ of 50-70.
• Moderate = IQ of 35-50.
• Severe = IQ of 20-35.
• Profound = IQ <20.

Question 4

Describe autism

Answer 4

Autism (autism spectrum disorders) affects around 1% of the UK population, they are developmental conditions present from birth characterised typically by:
- Impaired social interaction.
- Impaired social communication.
- Impaired imagination.
- Repetitive and stereotyped mannerisms.
- Rigid patterns of behaviour.
They can occur in isolation or in combination with learning disabilities. However, learning disability and autism can occur independently e.g. High functioning autistic person.

Question 5

What is special educational needs (SEN)?

Answer 5

• SEN is a form of support given to children who find it more difficult to learn than their peers of the same age.
• About 20% of children in the UK have SEN.
• Of these about 3% have a statement.

Question 6

Describe causes of learning disability during pregnancy.

Answer 6

• Prenatal can include maternal infections and teratogens.
• Perinatal can include prematurity and pre/peri/postnatal trauma.
• Postnatal includes serious illness, head injury, poor nutrition and exposure to toxins. These are incidents after birth (anytime in your life!).

Question 7

Is there an overlap between genetic and environmental causes of disease (multifactorial)?

Answer 7

Yes. Some are purely genetic e.g. DMD, others purely environmental e.g. scurvy. However many do cross over. Rare conditions are generally single gene conditions such as phenylketonuria, the more common diseases are multifactorial!

Question 8

What is the role of an geneticist?

Answer 8

• Diagnosis.
• Explanation.
• Assessment of genetic risk.
• Predictive testing.
• Prenatal testing.

Question 9

Why make a diagnosis of LD?

Answer 9

• To help understand the aetiology of the condition.
• To advise family/patient if there are other investigations pertinent to the diagnosis e.g. physical problems.
• To advise patient and family about prognosis and suggest the therapeutic options.
• To discuss genetic aspects of the condition.
• To discuss the risk of recurrence in the family.
• To discuss if prenatal testing/preimplantation diagnosis is available if at risk.

Question 10

Describe general structure used to make a LD diagnosis

Answer 10

• Determine main concerns you have about the child.
• Observe the child during a consultation.
• Take a thorough history.
• Physical examination.
• Special investigations.

Question 11

What should a history for LD include?

Answer 11

• Family history.
• Pregnancy history. Consider drug/alcohol exposure, result of antenatal screening tests and scans.
• Developmental milestones.
• Vision, hearing, behaviour, sleep
• Seizures, developmental regression.

Question 12

What should a physical examination for LD include?

Answer 12

• Dysmorphic/non-dysmorphic (gestalt diagnosis?).
• Malformations -minor/major.
• Neurocutaneous stigmata.
• Neurological signs.

Question 13

What should special investigations for LD include?

Answer 13

• Biochemical tests.
• Imaging – brain + other organs?
• Genetic tests – array-CGH + targeted testing?

Question 14

What are cytogenetic abnormalities?

Answer 14

There are a variety of different types of cytogenetic abnormality these involve chromosomes so are defects on the macro level.

• Aneuploidy.
• Translocation.
• Deletions/Duplications.

Question 15

What are Aneuploidy?

Answer 15

Having an incorrect/abnormal number of chromosomes.

e.g. trisomy 21, turners

Question 16

3 types of translocation

Answer 16

Reciprocal translocation = when chromosomal segments are exchanged between two non- homologous chromosome.
Non-reciprocal translocations = one-way transfer of a chromosomal segment to another chromosome.
Robertsonian = Occurs between acrocentric chromosomes.
- Translocation can be balanced (all genetic material present) or unbalanced.

Question 17

What are acrocentric chromosomes?

Answer 17

Most chromosomes are long length of genetic material made up of a short arm (“p arm”) and a long arm (“q arm”), which are joined by a centromere. All the chromosomes have different lengths and the lengths of the q and p arm are also different. Acrocentric chromosomes have a very short p arm and a very long q arm.
- Acrocentric chromosome pairs are 13, 14, 15, 21 and 22.

Question 18

Describe robertsonian translocation of chromosome 13 and 14

Answer 18

• Chromosome 13 and 14 may get too close and exchange genetic material, where the long arm of chromosome 13 joins to the long arm of chromosome 14 giving a long chromosome. This is called a Robertsonian 13:14 translocation!
• The p-arms are so short they get lost, this isn’t a real issue as the p-arms just code for repetitive sequences.
  So overall, two acrocentric chromsomes get close together, there is a breakage and rejoining and the two q arms join together. This is the robertsonian translocation.
• Just like a balanced translocation, this person will also not have any problems because they still contain the right amount of genetic material, it’s just arranged differently.
• The children however, due to the formation of the gametes by meiosis and the very synchronised and specific division method of the DNA/chromosomes. It can produce gametes with a wide variation in the genetic material as the cell gets confused.

Question 19

Describe robertsonian translocation in Down’s

Answer 19

• Initially we would see the two 21 chromosomes side by side and the two chromosome 14 side by side. Their centromere’s at the top because they have long q arm and very small p arm.
• They have the Robertsonian translocation however (possibly due to mosacism) and the two q arms of chromosome 21 and 14 join together. We now have one chromosome 21, one chromosome 14 and a Robertsonian 21:14 chromosome.
• All the genetic material is still there. However as we can see that it does affect the gametes which need to be haploid (4 outcomes). The two are haploid (one normal and one balanced translocation carrier) and two contain two copies of chromosome 14 and two copies of chromosome 21. Unbalanced trisomy 21 is Down’s and unbalanced trisomy 14 is lethal in foetus.
• This will produce problems if they fertilise with the other gamete.

Question 20

What happens to balanced reciprocal translocation offspring?

Answer 20

A balanced reciprocal translocation in an individual will not have any effect on them. But it can cause an unbalanced translocation in their offspring, due to the affected persons gametes containing more/less genetic material.

Question 21

List microdeletion syndromes

Answer 21

• Wolf-hirschhorn (4p16) this is a microscopic deletion which is viewed on a karyotype where the p arm is missing on chromosome 4.
• Velocardiofacial/DiGeorge/Shprintzen (22q11).
• Williams (7q11).
• Smith-Magenis (17p11).
• Angelman (15q11-12(mat)).
• Prader-willi (15q11-13 (pat)).

Question 22

What test can detect deletions/duplications?

Answer 22

Karyotype

Question 23

Describe new deletion/duplication syndromes associated with LD

Answer 23

• 16p11.2 – 12.2 deletion/duplication.
• Deletion identified in children with developmental delay and dysmorphism.
• Later found in children with autism/ASD (~1%) +/- dysmorphism.
• Associated with obesity in some individuals.
• Also found in asymptomatic individuals.

Question 24

Describe 22q11 microdeletion

Answer 24

This is DiGeorge/Velocardiofacial/ Shprintzen syndrome.
- This is too small to be seen on a karyotype. It is usually antenatally detected with ventricular septal defect (VSD) which is usually repaired at birth. Detected with FISH.
- 90% arise de-novo, this means 90% of the parents of a individual with DiGeorge won’t have this deletion.
- Individuals with 22q11del have significant speech and language difficulties and moderate LD.
- They also tend to have cleft palate/nasal speech, congenital heart disease, hypocalcaemia, mild to moderate LD and renal abnormalities.

Question 25

How are microdeletions detected?

Answer 25

Microdeletions such as DiGeorge syndrome is diagnosed using Fluorescent In Situ Hybridisation (FISH). This utilises a probe that we have specifically designed for that region of the genome where the deletion could be. If it anneals with the DNA we see the fluorescence, if it doesn’t anneal and we see no fluorescence this means that region has been deleted.

Question 26

How are microdeletions/microduplications and CNVs diagnosed?

Answer 26

Array CGH

Question 27

Describe array-CGH process

Answer 27

1. The patient and control DNA are labelled with different fluorescent dyes and applied to a microasssay
2. The patient and control ssDNA compete to attach/anneal to the probes on microassay slide
3. Now what should happen is that there should be equal binding to the slide probes, there should be two copies of each DNA in a normal person because the control DNA and normal person DNA is diploid. So that the relative fluorescence comes out as being equal. If there is deviation and the fluorescence of the microassay is different, then it indicates that there has been a duplication or deletion causing this change in fluorescence.
   - The array is looking at little bits throughout the chromosomes, in the fluorescence graph above we see that certain bits of the DNA are showing up more than others, this indicates it is appearing more.

Question 28

Describe William’s syndrome

Answer 28

• Caused by 7q11.2 microdeletion.
• History often shows a normal pregnancy and birth history, but children have hypermobility, global developmental delay and moderate LD (also CVS, GIT problems).
• Can be diagnosed through array-CGH.

Question 29

Some LD are caused by single gene disorders (not just big cytogenetic deletions and duplications). What 4 sequencing can be done to diagnose?

Answer 29

• Sanger sequencing.
• Next generation panel -> a sequencing panel that looks at a series of genes, e.g. cardiac generation panel looks at specific genes related to cardiac pathology. This allows us to just look at the genes that could be too blame.
• Whole exome sequencing -> Looking just at coding DNA.
• Whole genome sequencing -> Often highlights variants of unknown significance.

Question 30

What are the two major studies in the UK that have have led to implementation of new technologies into routine clinical care?

Answer 30

• DDD (deciphering developmental disorder) study.

- 100,000 genomes project.

Question 31

Describe DDD study

Answer 31

This is an exome study. They identified that when they were looking at exome, there are 20,00 variants per exome.
- Most single gene causes of LD are caused by de novo dominant mutations (DNMs). Generally speaking, if you have a child with a LD and you are not a consanguineous family, having a risk of another child with a LD is low.

Question 32

How is autosomal dominant related to LD?

Answer 32

Typically in autosomal dominant disease we see every generation being affected with around half in each generation being affected. However, note that many autosomal dominant causes of LD are new genetic events and affect reproductive fitness.

Question 33

Describe tuberous sclerosis (TSC)

Answer 33

• Example of an autosomal dominant disorder associated with LD.
• High rate of new mutation roughly 60% de novo.
• Variable expression.
• Two genes: TSC1 chromosome 9 and TSC2 chromosome 16. TSC1 more likely to be familial, and overall milder while TSC1/2 form a complex that inhibits mTOR.
• Such individuals also often have adenoma sebaceum, shargreen patches, ungula fibromas. They often have seizures that can contribute to LD.

Question 34

How is autosomal recessive related to LD?

Answer 34

• Both parents need to be carriers in order for children to be affected. Both copies of mutated gene required in order for condition to be expressed. Typically we see two unaffected parents (but carriers) have an affected child and one generation affected due to individuals who are carriers come together and have children.
• Consanguinity increases the risk of recessive alleles coming together
• There aren’t many autosomal recessive conditions associated with LD, but one example is phenylketonuria.

Question 35

Describe Phenylketonuria (PKU)

Answer 35

Phenylketonuria (PKU) is a disease caused by an inability to break down phenylalanine. It is associated with a variety of problems such as: Developmental delay, Behavioural or social problems, Seizure, Hyperactivity, Growth retardation, Eczema, Microcephaly, A musty odor in childs breath, skin or urine and Fair skin and blue eyes.
- We nowadays rarely see adults presenting with this condition, as we screen for it at birth. If the child has it we then advise them to avoid foods containing phenylalanine and therefore they won’t have it build up and they won’t suffer toxic effects.

Question 36

Describe fragile X syndrome

Answer 36

• Fragile X Syndrome is an X-linked condition, affecting 5% of all males with LD. It is characterised by a particular physical phenotype, high forehead, long ears, long face, prominent jaw, macro-orchidism.
• Fragile X syndrome is caused by a triplet repeat expansion on the X chromosome.

Question 37

Describe triplet repeat expansions

Answer 37

• Are unstable/dynamic expansions and therefore can increase in size in the next generation leading to something called anticipation, where the next generation has more severe phenotype (developing condition earlier).
• Instability depends on parent of origin. There is general correlation between size of the expansion and severity of the disorder.
• Triplet repeat expansions are a type of mutation also seen in Huntington’s disease, myotonic dystrophy and spinobulbar muscular atrophy.
  e. g. CGGCGGCGG etc..

Question 38

Give an example of triplet repeat anticipation

Answer 38

Myotonic dystrophy anticipation. Condition worsening as generations go by due to no. of repeats increasing.

Question 39

Describe imprinting

Answer 39

• Genomic imprintingis anepigeneticphenomenon that causesgenesto beexpressedin a parent-of-origin-specific manner. Normally only one of the parental genes inherited will be expressed and the other will be silenced (imprinted).
• Imprinting is when the disease is present even though there is no apparent cytogenetic or molecular genetic abnormality.
• Whether or a not a gene is expressed can depend on markers on the DNA, certain parts of the genome are imprinted/methylated.
• If you happen to lack one of the genes and the other gets silenced you will not express the protein. This can lead to disease.

Question 40

Give examples of diseases that can be caused by imprinting problems

Answer 40

• Prader-willi syndrome.

- Angelman syndrome.

Question 41

Describe Prader-Willi Syndrome

Answer 41

Prader- Willi syndrome is an example of a genetic disease that can be caused by imprinting problems. It is characterised by: Short stature, Hypotonia, Obesity, Hypogonadism and Learning disability.

• Individuals with Prader-Willi have had a loss of paternally expressed SNRPN and adjacent genes (don’t work) and don’t have a maternal copy to compensate as it is imprinted.
• 75% caused by deletion of the paternal 15q11-13.
• 25% due to maternal uniparental disomy 15.
• 2% abnormalities of ICR.

Question 42

Describe Angelman syndrome

Answer 42

Angelman syndrome is another genetic condition caused by imprinting disorder, characterised by: Epilepsy, Severe learning difficulty, Ataxia and Happy affect.

• It is caused by loss of maternally expressed UBE3A.
• 70% due to maternal microdeletion of 15q11-13.
• 5% due to paternal uniparental disomy.
• 10% have a mutation in UBE3A.
• 5% abnormalities of ICR (imprinting control region) which is the regulation of imprinting.

Question 43

What method is used to investigate imprinting defects?

Answer 43

Methylation specific PCR.
In prader willi we see a loss of paternal gene (non-functional) while the maternal copy is imprinted (silenced). In angelman syndrome, the paternal copy is silenced and the maternal copy is lost (non-functional).

Question 44

LD diseases caused by enviroment/teratogens

Answer 44

• Foetal alcohol syndrome. Often severe LD, physical features (e.g. thin lip, attention deficit).
• Foetal valproate syndrome. This is caused by medicating with valproate (anti-seizure) during pregnancy, as it is a teratogen. Risk of 5-10% is for malformation but on top of that there is the risk of behavioural problems. Child will have LD, behavioural difficulties and characteristic facial features.