Clinical Genetics

Question 1

How are genetic disorders classified?

Answer 1

• Mendelian disorders - conditions caused by a single mutation; can be autosomal recessive, autosomal dominant or X-linked. Rare with a high recurrence rate.
• Chromosomal abnormalities - the inheritance pattern is not like Mendelian conditions - often empirical; in translations these abnormalities can be inherited. Usually de novo. Affects the overall gene balance. Account for the majority of spontaneous abortions. Multiple organ systems are affected.
• Multifactorial - caused by a combination of genes and environment. More common with a low recurrence rate.
• Mitochondrial disorders - Due to mutations in mitochondrial DNA which is past down from the mother. The mitochondrial genes mostly code for proteins involved in oxidative phosphorylation - and so cause issues in tissues with a high energy demand.
• Somatic mutations - mutations in somatic cells. usually de novo - can lead to mosaicism. Not passed down onto children.

Question 2

What is the difference between penetrance and expressivity?

Answer 2

Penetrance: The proportion of individuals with a genetic variant that also display phenotypic characteristics. A high penetrance is where everyone with the condition will have the symptoms. The condition is not effected by other genes or the environment.

Expressivity: variation in phenotypic expression when an allele is penetrant.

Question 3

What is the difference between autosomal dominant, autosomal recessive and X-linked patterns? What is the percentage of a child of a parent with each of these conditions having an affected child if with a normal parent?

Answer 3

Autosomal recessive: The individual must be homozygous for an allele in order to inherit the condition.
The chance is 25% with a 50% of being a carrier.

Autosomal dominant: The individual needs only to have one variant to have the disorder.
The chance is 50%.

X-Linked Patterns: The variant is found on the tail of the X-chromosome missing in the Y chromosome. As a result, it is expresses mainly in males.
The chance is 25% of having an an affected male if the mother is a carrier and the father is normal.

Question 4

Give an example of a multifactorial inheritance.

Answer 4

Multiple Sclerosis

Question 5

What is the genetic basis of dominantly inherited familial cancer syndromes?

Answer 5

A hereditary cancer syndrome is present when a person, because of an inherited mutation, has an increased risk of developing certain tumours. In most known hereditary malignant syndromes the elevated cancer risk is due to a mutation of a single gene. The affected genes concerned usually have a controlling function on the cell cycle or the repair of DNA damage. Sporadically occurring are also caused by an increased incidence of mutations in these genes.

Question 6

What are mitochondrial disorders? Give an example.

Answer 6

The mutation resides on the mitochondrial DNA – contains only 30-34 genes. These genes are usually related to oxidative phosphorylation. They are maternally inherited. Mitochondrial inheritance disorders usually are expresses in cells with a high energy demand.

Example: Leber hereditary optic neuropathy. degeneration of retinal ganglion cells (RGCs) and their axons that leads to an acute or subacute loss of central vision; this affects predominantly young adult males.

Question 7

What is the difference between mitosis and meiosis?

Answer 7

Meiosis is used only for the production of gametes. It is reduction division - it reduces the chromosome number to 23. It ensures every gamete is genetically unique through cross-over and independent assortment. Each homologue replicates to give two sister chromatids.

Mitosis: Normal cell division, produces daughter cells that are genetically identical to the parent cell.

Question 8

What is cross over?

Answer 8

In Prophase I, the homologous chromosomes pair together. They cross over enabling genes to shuffle between the chromosomes, thereby producing genetically unique chromosomes. This forms a chiasma.

Question 9

What is the structure of chromosomes?

Answer 9

Centromere - is the specialised DNA sequence of a chromosome that links a pair of sister chromatids

Telomere - is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes.

‘p’ arm - short arm
‘q’ arm - long arm

The chromosome is DNA wrapped tightly around histone proteins, RNA and non-histone proteins.

Light band - replicate early in S phase; less condensed chromatin; transcriptionally active gene and GC-rich

Dark band - replicate late; contain condensed and chromatin AT-rich

Question 10

Give examples of Mendelian inheritance.

Answer 10

Autosomal dominant: Huntington’s disease

Autosomal recessive: 
Familial Hypercholesterolemia (common - major risk for CVD), Cystic Fibrosis (Quite common - recurrent infection and pulmonary disease), Centennial deafness  

X-Linked Disorder: Haemophilia
Duchenne Muscular Dystrophy (Weak muscles, causing the individual to stand using Gower’s manoeuvre)
Fragile X Syndrome

Question 11

How do you draw a family Pedigree?

Answer 11

1. Each generation is labelled by a roman numeral
   
   2. The children are order by number from left to right
   3. Write their date of birth also underneath
   4. Start from bottom and build up starting with the index child (proband) and their siblings
   5. Ask about miscarriages, still births or death in each partnership - important to see if there is the possibility of chromosomal abnormalities - often incompatible with life
      Ask awkward questions: Ask if there are other children with other partners. Ask about consanguinity - a feature of autosomal inheritance.

Question 12

What is Mendel’s I Law?

Answer 12

The Law of Segregation ‘The allele of a given locus segregate into separate gametes’

Question 13

What is Mendel’s II Law?

Answer 13

The Law of independent assortment ‘The alleles of a given locus segregate into separate gametes’
This is how we increase genetic diversity.

Question 14

What is Mendel’s III Law?

Answer 14

The Law of Dominance ‘One of the factors for a pair of inherited traits will be dominant, and the other recessive, or both recessive’

Question 15

What issue can occur with the pairing of homologous chromosomes?

Answer 15

There are regions on chromosomes that look very similar and so chromosomes that are not homologous can pair up causing translocation.

Question 16

What are Acrocentric chromosomes?

Answer 16

Chromosomes 13,14,15,21 and 22.
These chromosomes do not have a ‘p’ arm but instead have a short repetitive sequence - usually encoding rRNA and tRNA. Acrocentric chromosomes, can line up incorrectly such as 13 and 21 which is common translocation event.

Question 17

What is heterochromatin?

Answer 17

Tightly packed form of DNA that is genetically inactive. Chromosome 1,9 and 16 have heterochromatin at the top of their chromosome.

Question 18

What is the smallest chromosome?

Answer 18

21

Question 19

Explain common chromosomal abnormalities relating to number.

Answer 19

Aneuploidy: Aneuploidy is the presence of an abnormal number of chromosomes in a cell. e.g. Trisomy 21 is three copies of chromosome 21. Monosomy is a deletion of a chromosome and so there is only one copy of the chromosome e..g Turner’s Syndrome.

Polyploidy: When there is more than two copies of whole sets of chromosomes e.g. triploidy is 69 chromosomes. This is incompatible with life.

Mosaicism:
When there are cells in the body with different chromosome numbers. This is due to a disruption of meiosis I, meiosis II or mitosis. This is due to errors in the formation of the metaphase plate and so produces different populations of somatic cells e.g. Can produce a milder form of Down’s syndrome.

Question 20

What are the two types of chromosome translation?

Answer 20

Robertsoniain translation:
When the ‘q’ arm of a chromosome fuses with another chromosome, losing a ‘p’ arm. Since there is so much repetition of the RNA genes, there isn’t an overall change in gene dosage and so will not have an effect on the child. This is the most common form of chromosomal translocation - it does not usually cause health difficulties but can lead to an inherited form of Down’s syndrome and Patau’s Syndrome.

Reciprocal translocation:
Exchange fragments between non-homologous chromosomes.

Question 21

How are gametogenesis and non-disjunction linked?

Answer 21

Mitosis I of spermatogonia produces spermatocytes. Meiosis II produces spermatids which mature into spermatozoa. The incidence rate of de novo mutations increase with paternal age as higher mutation rates in males are related to the greater number of germ cell divisions.

There may be a lengthy interval between Meiosis I and Meiosis II as Meiosis II occurs when the oocyte is fertilised (this can be up to 50 years). This time means that there is a lot of opportunity for environmental factors to take effect. Damage to repair mechanisms of the primary oocyte increases the chance of non-disjunction.

Question 22

What is the Karyotype for:

a) Down’s syndrome
b) Turner’s Syndrome
c) Klinefelter’s Syndrome
d) Edward’s Syndrome
e) Patau’s Syndrome

Answer 22

a) 47, XX + 21
b) 46, X
c) 47, XXY
d) 47, XX, + 18
e) 47, XX, + 13

Question 23

Give examples of chromosomal structural abnormalities.

Answer 23

Translocations

Deletions

Question 24

Give examples of chromosomal structural abnormalities.

Answer 24

Most are de novo events occurring in meiosis - very low recurrence risk in future pregnancies.

Translocations
Deletions
Duplications
Inversions

Question 25

What are the symptoms of Down’s syndrome?

Answer 25

• Small, round face
• Up slanted eyes (palpebral fissure)
• Learning Disabilities
• Protruding tongue
• Epicanthic folds

Endophenotypes (characteristics of a disorder or illness that are not observable):

• Choroid plexus cyst
• Nuchal transparency (is the sonographic appearance of a collection of fluid under the skin behind the foetal neck in the first-trimester of pregnancy)
• Short femurs
• Sandal gap, single palmar crease

Question 26

What are the genetic causes of Down’s syndrome?

Answer 26

• Trisomy 21 (95%) Due to de novo non-disjunction.
• Robertsonain translocation (4%) can result in an inherited form of Down’s syndrome. This is if one of the parents has a translocation that results in chromosome 21 being attached to another chromosome, 14, when the other gamete fuses, there is 3 copies of chromosome 21. This is as these children have the usual copies of chromosome 21, but they also have additional genetic material from chromosome 21 on another chromosome. This can be passed from parent to child. However balanced translocations can occur in which the mother or father has rearranged genetic material form chromosome 21 on another chromosome but not extra genetic material. This means they will not have Down’s Syndrome, but can pass an unbalanced translocation onto children, causing Down’s Syndrome.
• Mosaicism (1%) non-disjunction occurs in mitosis; you can then have 2 populations of cells. There is a population that has trisomy and other cells that have monosomy (these cells die).

Question 27

What is Edward’s Syndrome?

Answer 27

Trisomy 18. 1 in 3000 births. Leads to multiple malformations, clenched hands with overlapping fingers.

Question 28

What is Patau’s Syndrome?

Answer 28

Trisomy 13. 1 in 5000 births. Multiple malformations, affects midline structures particularly; poor cognitive development; cleft lip; congenital heart disease.

Question 29

What is Klinefelter and Turner’s syndrome?

Answer 29

Klinefelter syndrome - Having 3 Sex chromosomes - 2 X chromosomes and one Y chromosome. The individual is phenotypically male due to the Y chromosome. Cause poor development of secondary sexual characteristics (pubic hair and facial hair, deepened voice due to lack of testosterone).

Turner’s Syndrome: Having only one X chromosome. The individual is phenotypically female. The individual may suffer from primary amenorrhoea and congenital heart disease (20%). Other characteristics include short stature, wide angle of arms, and other developmental defects.

Question 30

Give examples of conditions caused by micro deletions.

Answer 30

DiGeorge Syndrome: A small chromosomal region is lost. Caused by a micro deletion in chromosome 22.
Phenotypical features: Small mouth, comet nose, congenital heart defects, frequent infections, developmental delay, learning difficulties and cleft palate.

Williams-Beuren Syndrome Due to a microdeletion of chromosome 7 - also congenital heart defects. Also phenotypical characteristics: bright eyes, stellate irides (patch in the iris), wide mouth, upturned nose.

Question 31

What is FISH?

Answer 31

Fluorescent in situ hybridisation. Can only be used when the mutation is known. This can be used on chromosomes in metaphase of interphase, producing a green spot on the chromosome where the mutation lies. The target DNA is Denatured and the probe recognises the template and find specific sequences, this appears as a fluorescence.

FISH can be used to test for micro deletions in Willian Beuren Syndrome - a probe is used to find chromosome 7 to ensure it works. Another probe is used to find the gene where the deletion lies. If a signal is not detected, there is a micro deletion. It can also be used in the test fro Di George’s Syndrome.

Question 32

What is Karyotyping?

Answer 32

Karyotyping is the process of pairing and ordering all the chromosomes of an organism, thus providing a genome-wide snapshot of an individual’s chromosomes. This produces visible chromosomes which can then be identified - this helps to identify chromosomal number abnormalities. It also helps to identify deletions, translocations, duplications and inversions. Chromosome 1 is the largest - occupying 10% of the genome - and chromosome 21 is the smallest - occurring only 1.2% of the genome.

In order to do this test you need actively dividing tissue - bone marrow, tumour cells, tissue culture, lymphocytes etc.

Question 33

What is Chromosome branding?

Answer 33

The condensed chromosome is branded using G-branding (a stain known as Geisma). This produces regions of dark and light bands on the chromosome. Heterochromatic regions, which tend to be rich with adenine and thymine (AT-rich) DNA and relatively gene-poor, stain more darkly in G-banding. In contrast, less condensed chromatin (Euchromatin)—which tends to be rich with guanine and cytosine (GC-rich) and more transcriptionally active—incorporates less Giemsa stain, and these regions appear as light bands in G-banding. This numbering system allows any band on the chromosome to be identified and described precisely.

Question 34

What is PCR?

Answer 34

A method used to amplify a piece of DNA so that multiple tests can be done on it.

1. Use a Hot temperature to denature the DNA by breaking hydrogen bonds. This producing single strands.
2. In the PCR reaction there is an excess of dNTPs, synthetic single stranded DNA (oligonucleotide) at a lower temperature of around 30 degrees Celsius. They will bind through hydrogen bonding to the single strand.
3. The temperature is then raised again so Taq Polymerase can add the monomers to the strand, thereby amplifying the sequence as this cycle continues thousands of times.

Question 35

What is Sanger Sequencing?

Answer 35

A methods to sequence DNA - used when the mutation causing a genetic disorder is not known.

It uses ddNTPs to produce DNA of different lengths, the scan then be ordered using gel electrophoresis so that the DNA can be sequenced.

Question 36

What is PKU?

Answer 36

Phenylketonuria (PKU) is an inborn error of metabolism that results in decreased metabolism of the amino acid phenylalanine due to the deficiency in phenylalanine hydrogenase. It is a rare condition that is screened. It can cause: mousy blonde hair and pale skin due to the inability to produce melanin; high levels of phenylalanine; musty odour; delayed intellectual development; hyperpigmentation in the eye and epilepsy.

The intervention ins restricting phenylalanine form the diet and enzyme replacement.

Question 37

How is DNA separated in electrophoresis? How is it able to do so?

Answer 37

It is ordered by size - shorter strands travel further than the longer strands.
It is able to do so as DNA is negatively charged.

Question 38

Why do ddNTP’s enable the termination of Taq Polymerase?

Answer 38

They have no terminal 3’ hydroxyl group which is needed for the enzyme to polymerase.

Question 39

What is Amniocentesis?

Answer 39

Amniocentesis is a prenatal test in which a small amount of amniotic fluid is removed from the sac surrounding the fetus for testing. The sample of amniotic fluid (less than one ounce) is removed through a fine needle inserted into the uterus through the abdomen, under ultrasound guidance. These cells in the amniotic sac are the product of the renal system, and will contain genetic material which can then be testes. Extremely uncomfortable and carries a high risk of abortion as a result must be used after all other testing has been done.

Question 40

What is Chronic Villus Sampling?

Answer 40

During the test, a small sample of cells (called chorionic villi) is taken from the placenta where it attaches to the wall of the uterus.