Download Single Nucleotide Polymorphism Microarray testing

Single Nucleotide Polymorphism
Microarray testing
INTRODUCTION
For patients with intellectual disability, developmental delay, autism spectrum disorder or multiple congenital
anomalies, conventional cytogenetic testing (karyotyping) has previously been the diagnostic investigation of choice
for the detection of chromosomal imbalance. However, excluding trisomy 21 (Down syndrome), the detection rate of
karyotyping in these patients is only 3–5%.
Studies have shown that genome-wide microarrays detect a clinically significant genomic imbalance in up to 10% of
patients with normal karyotype results. In unselected patients with developmental delay, microarrays have a detection
rate of 15–20%, more than double the detection rate of conventional karyotyping.
Microarray testing is now recommended internationally as the first-tier test in patients with intellectual disability/
developmental delay. This has been recognised in Australia, with the introduction of a Medicare Benefits Schedule
item specifically for microarray testing.
Genome-wide Single Nucleotide Polymorphism Microarray (SNP microarray) testing is available through Sonic
Genetics, using the Illumina Cyto SNP 850K array platform.
WHAT IS MICROARRAY TESTING?
LIMITATIONS OF MICROARRAY TESTING
DNA is extracted from a patient’s blood sample, processed, and
applied to glass slide that is covered with millions of small beads.
Each bead has thousands of ‘oligonucleotide’ probes attached,
corresponding to a specific region of each chromosome.Reactions
then take place on this slide, involving fluorescently labelled
reagents. Regions where the genomic copy number differs between
the patient’s DNA and a reference sample set can be detected as a
difference in signal intensity.
Microarray testing cannot detect balanced genomic rearrangements,
such as translocations. However, it is estimated that these changes
account for < 1% of clinically significant abnormalities in patients
with intellectual disability. In addition, low level mosaic copy number
changes may not be detected by array technology.
In this way, deletions and duplications of genetic material can be
detected, at a resolution that is an order of magnitude higher than
conventional karyotype. Thus, a wide range of such ‘copy number
changes’ can be detected by microarray – from whole chromosome
aneuploidies such as trisomy 21 to small deletions affecting only a
few genes, which could not be detected by karyotype.
Each copy number change is analysed for possible clinical
significance in the laboratory, and results are reported to the
requesting clinician. In some cases parental studies may be required
to determine whether a change is familial.
In addition to detecting copy number changes, Single Nucleotide
Polymorphism microarrays can also detect large regions of
homozygosity in a chromosome, also known as ‘long contiguous
stretches of homozygosity’ (LCSH). CGH microarrays cannot detect
LCSH.
Presence of LCSH on a single chromosome can be an indicator of
UniparentalDisomy (UPD) for that chromosome.UPD is associated
with a clinical phenotype for certain chromosomes. In addition,
presence of LCSH across multiple chromosomes can indicate
inheritance from a common ancestor (‘identity by descent’), which
may be associated with an increased risk of a recessive single gene
disorder.
Finally, genetic changes affecting single genes cannot be detected
by either microarray or karyotype. These include point mutations and
triplet repeat expansions (such as the repeat expansion that causes
Fragile X syndrome).
COMPLEXITIES OF MICROARRAY TESTING
In some patients, novel copy number changes are detected, where
there is insufficient current evidence to classify them as either
clinically significant or benign variants. These are known as ‘variants
of unknown clinical significance’ (VUCS).
In addition, emerging data suggests that certain recurrent copy
number changes, although not having a known direct clinical
consequence, might be regarded as ‘susceptibility alleles’ for
neurodevelopmental disorders. For these copy number changes,
clinical outcome may be determined by a combination of as yet
unknown additional genetic and environmental factors.
Finally, ‘incidental findings’ may be detected. These are genomic
imbalances which affect genes unrelated to the clinical presentation
of the patient, but which may have significant clinical consequences
(e.g. deletion of a tumour suppressor gene may indicate that the
patient has an increased risk of developing cancer in later life).
In patients with ‘variants of unknown significance’, ‘susceptibility
alleles’ or ‘incidental findings’, referral of the patient and their families
to clinical genetics services for further assessment and counselling is
recommended.
SPECIMEN COLLECTION
How to request microarray testing
Please request ‘Microarray testing’ on the request form, and provide
full clinical information. Clinical information is needed for analysis
of the microarray results, and to determine whether the patient is
eligible for a Medicare Benefits Schedule (MBS) rebate. When testing
the parent of a child with an abnormality detected by microarray
analysis, please note the child’s name and date of birth for crossreferencing.
Peripheral blood samples (preferably 5 ml in EDTA + 5 ml in lithium
heparin; minimum 1 ml in each) should be collected for microarray
testing.
COST
An MBS rebate is available for microarray testing (Item 73292). The
item descriptor limits microarray testing to patients with intellectual
disability, developmental delay, autism spectrum disorder or multiple
congenital anomalies. Additional samples from parents and siblings
may be required in some cases to clarify preliminary microarray
results; an MBS rebate will also apply for these samples.
TURN-AROUND TIMES
Expected turn-around time of this test is 8 weeks.
NOTE
The MBS specifically excludes a rebate for karyotype analysis
when performed on the same sample as a microarray test. If both
karyotype and microarray are required, please send two separate
sets of samples. These will need to be taken on different days,
according to Medicare regulations.
References
Kimonis (2014) Clinical utility and dilemmas of SNP microarray testing. Molecular
Cytogenetics 7)Suppl 1):I34
Manning and Hudgins (2010) Array-based technology and recommendations for
utilization in medical genetics practice for detection of chromosomal abnormalities.
Genetics in Medicine, 12(11):742-745.
Miller et al. (2010) Consensus Statement: Chromosomal Microarray Is a First-Tier
Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital
Anomalies. American Journal of Human Genetics, 86(5): 749–764.
Sagoo et al. (2009) Array CGH in patients with learning disability (mental retardation)
and congenital anomalies: updated systematic review and meta-analysis of 19 studies
and 13,926 subjects. Genetics in Medicine, 11(3):139–146.
Vermeesch et al. (2007) Guidelines for molecular karyotyping in constitutional genetic
diagnosis. European Journal of Human Genetics, 15:1105–1114.
Dr James Harraway FRCPA DPhil
Special Interests: Somatic mutation testing, microarray testing, translation of next generation sequencing into clinical practice.
Dr James Harraway is a genetic pathologist who supervises genetic testing at Sullivan Nicolaides Pathology. As well as overseeing all clinical testing he consults widely with
referring doctors and pathologists from other disciplines on this new area of diagnostics. He is also active in the development and validation of new genetic tests.
Dr Harraway joined Sullivan Nicolaides Pathology in 2009. He completed his medical training at Otago University, New Zealand and went on to undergo training in genetic
pathology at Canterbury Health Laboratories, Christchurch, New Zealand. He was awarded a Nuffield Medical Fellowship and undertook a DPhil at Oxford University,
examining the molecular pathogenesis of Cockayne Syndrome. He was the first New Zealand pathologist to be awarded an FRCPA in genetic pathology.
Dr Harraway is available for consultation.
T: (07) 3377 8666
E: [email protected]
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ITEM 09213 May 2015
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