Clinical Genetics In Practice

Question 1

What is a mitomycin C assay and what is it used for?

Answer 1

Mytomycin C can induce chromosome breakage if they are susceptible, so it is used to test the fragility. If they are fragile then it suggests Pancytopenia or Fanconi syndrome (causes severe anaemia).

Question 2

What is standard cytogenetic nomenclature?

Answer 2

29 is the chromosome 1 is the copy number (should be 2)
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arr 3q29(195,804,645-197,837,069)x1
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q is the arm In the brackets are the
of the coordinates of the
chromosome missing gene

Question 3

What condition does ‘arr 3q29(195,804,645-197,837,069)x1’ indicate?

Answer 3

The recurrent 3q29 microdeletion syndrome region is associated with a variable phenotype including; mild-moderate learning disability, speech delay, microcephaly and mildly dysmorphic facial features.

In the majority of cases deletions arise as new mutations with low parental recurrence risks. But in a minority of cases the deletion is inherited, either directly or as an unbalanced form of a balanced rearrangement, and the recurrence risk is high.
In order to investigate the mode of inheritance and risk of recurrence, parent’s blood is tested for FISH studies.

The patient is at 50% risk of transmitting this deletion to children.

Question 4

What is the gene associated with diamond black fin anaemia, and what are the symptoms of the condition?

Answer 4

The DE NOVO deletion occurs in the large ribosomal subunit protein Rp135a, responsible for RNA processing ribosomal biogenesis, selective cell proliferation and apoptosis.

Gene deletions described in Diamond-Blackfan anaemia (DBA) - dominant condition with many gene associations that typically presents in infancy.

Leads to an enhanced sensitivity of haematopoetic progenitors to apoptosis - affects RBC production.
- Occasional neutropenia and thrombocytopenia
- 40% congenital anomalies:
- craniofacial, cardiac, GU, upper limb/hand malformations
- Potential cancer predisposition - as gene involves maintenance
of chromosome efficiency
- haem malignancy
- osteogenic sarcoma

Question 5

What microdeletions cause the following conditions and what is the incidence?

• DiGeorge
• Williams
• Prader-Willi/Angelman
• 1p36 deletion
• Smith-Magenis
• WAGR
• Miller-Deiker
• Rubinstein-Taybi
• Rolf Hirschhorn
• Cri du chat
• Charcot-Marie-Tooth 1A

Answer 5

• DiGeorge - 22q11.2 - 1 in 3000
• Williams - 7q11.2 - 1 in 7-20,000
• Prader-Willi/Angelman - 15q11-13 - 1 in 12-20,000
• 1p36 deletion - 1p36 - 1 in 5-10,000
• Smith-Magenis - 17p11.2 - 1 in 25,000
• WAGR - 11p13 - 1 in 500,000
• Miller-Deiker - 17p13.3 - rare
• Rubinstein-Taybi - 16p13.3 - 1 in 100,000
• Rolf Hirschhorn - terminal 4p - 1 in 50,000
• Cri du chat - terminal 5p - 1 in 20-50,000
• Charcot-Marie-Tooth 1A - 17p11.2 - 1 in 3000

Question 6

Which sequencing technique is most appropriate for each mutation?

Answer 6

PCR/Sanger - Conditions caused by a single gene which can be diagnosed clinically with a high degree of certainty (and some of which can’t be testing with NGS)

NGS - Heterogeneity - Multiple genes or an unusual combinations of problems, e.g. Epilepsy, cardiac, eyes, immunology

Exome sequencing: (targeting the protein coding sequence)
Panel: Assess a selection of pre-determined genes

Question 7

What are the cautions of using NGS?

Answer 7

Coverage not 100% across exome, can still miss things that would be detected by Sanger sequencing, when looking at one particular gene.

Can’t detect large insertions and deletions

May pick up incidental finding
What to do with the information we did not ask for – BRCA gene mutation.

Reporting unclassified variants can cause more concern (VUS)

… some reduction in incidental findings and VUS by using targeted panel