Week 4 Part 2 - Using Microarrays for Diagnosis of Human Genetic Diseases

Question 1

Trisomy 21

Answer 1

Down syndrome
Features: 
- poor immune function 
- developmental delay 
- intellectual disabilities 
- single palmar crease
Increased risk of:
- congenital heart disease
- leukaemia 
- thyroid disorders

Question 2

Microdeletion and Microduplication Syndromes

Answer 2

Hundreds of syndromes are known to be caused by small deletions or duplications that cannot be seen by conventional cytogenetics
Mostly detected by microarray, MLPA or FISH
Many are recurrent - occur in same location in the genome in many different patients
Low copy repeat (LCR) sequences can cause DNA to misalign at meiosis or mitosis and result in deletions or duplications
LCRs predispose the region to recurrent genomic rearrangements by non-allelic homologous recombination (NAHR)

Question 3

DiGeorge Syndrome (22q11.2 Deletion Syndrome)

Answer 3

Most frequent contiguous gene deletion syndrome
Includes the TBX1 gene
Features:
- cardiac defects ~64% individuals (VSD in 23%)
- developmental delay ~70-90% individuals
- immune deficiency ~77% individuals (thymic hypoplasia)
- craniofacial features (ear anomalies, bulbous nose, micrognathia)
- cleft Palate/ palatal anomalies (~ 67% individuals)
- hypocalcemia (low calcium), secondary to hypoparathyroidism

Question 4

22q11.2 Duplication Syndrome

Answer 4

This duplication is the reciprocal event to the 22q11.2 deletion
Highly variable phenotype - duplication is milder than deletion
Features include:
- mild to moderate intellectual disability
- delayed psychomotor development
- growth retardation
- hypotonia
- some abnormalities associated with 22q11.2 deletion including heart defects
This duplication is also found in unaffected individuals including parent
Variable expressivity and incomplete penetrance therefore LIKELY PATHOGENIC

Question 5

Paternal UPD14 / Kagami-Ogata Syndrome

Answer 5

Large gestational age
Hypotonia
Feeding difficulties
Small bell shaped thorax with “coat hanger ribs”
Dysmorphic features: hairy forehead, full cheeks, protruding philtrum, micrognathia
Abdominal wall defects

Question 6

Maternal and Paternal 15q11q13 Deletion

Answer 6

Maternal deletion = Angelman syndrome
- developmental delay
- don't speak much
- floppy arms
- wide mouth
- widely spaced teeth
- seizures
Paternal deletion = Prader Willi Syndrome
- developmental delay
- hypotonia
- feeding difficulties
- after 2 years develop an obsession for food

Question 7

15q11q13 Duplication Syndrome

Answer 7

Recurrent duplication to the deletion region seen in Angelman and Prader-Willi syndromes
Clinical features
- autism
- intellectual disability
- seizures
- developmental delays (including speech)
- hypotonia
- behavioural problems
Duplications are mostly maternally in origin and de novo (Pathogenic)
Paternally inherited duplication have a mild or no abnormal phenotype

Question 8

PMP22 Gene on 17p12

Answer 8

17p12 duplication including the PMP22 gene causes Charcot Marie Tooth Type 1A (CMT1A)
Adult-onset progressive peripheral neuropathy (presents within first two decades of life)
CMT1A is characterised by distal symmetrical muscle weakness
PMP22 protein is produced predominantly by Schwann cells
It is critical to myelination in the peripheral nervous system (PNS)
PMP-22 duplication gives an increase in the protein which causes CMT1A
PMP-22 deletion gives a decrease in the protein which causes a milder peripheral neuropathy called hereditary neuropathy with liability to pressure palsies (HNPP)

Question 9

Quality Control Checks

Answer 9

The quality control (QC) parameters required for sample acceptance:

• LogR standard deviation ≤ 0.16
• B allele standard deviation (BAF dev) ≤ 0.04
• call rates ≥ 0.99

Question 10

Advantages of Microarray Analysis

Answer 10

Higher resolution that karyotype therefore higher diagnostic yield
Whole genome analysis
Tissue culture not needed
Potentially quicker than karyotype - urgents reported in 6-14 days
Some automation

Question 11

Disadvantages/Limitations of Microarray Analysis

Answer 11

Unable to detect balanced rearrangements, heterodisomic UPD or small variants
Low level mosaicism can be missed (<10%)
No positional information for a duplication – do not know if tandem or transposed elsewhere in the genome
Can be time consuming to analyse and report
Many CNVs are novel with unknown clinical significance
Can detect incidental finding

Question 12

Angelman Syndrome - Genetic Variation

Answer 12

70% maternal 15q11.2q13 deletion
3-7% paternal UPD15
3% imprinting defects
11% UBE3A variant
10% unknown
Loss of maternally expressed genes

Question 13

5p15 Deletion

Answer 13

Cri du Chat Syndrome
Features:
- speech delay
- characteristic cry
- facial dysmorphism
- intellectual disability
Pathogenic

Question 14

11p15 Duplication

Answer 14

Paternally inherited 11p15 duplications are associated with Beckwith Wiedemann syndrome (BWS)
Clinically heterogeneous overgrowth syndrome
- increased risk of Wilms tumour
Pathogenic