18.05.06 Prenatal arrays Flashcards
What is the aim of implementing microarrays in the prenatal setting?
1) Provide greater resolution than karyotyping
2) Minimising the identification and reporting of CNVs of uncertain signifiance
When should microarray calls be reported?
Where there is clinical significance i.e. the finding explains the observed (ultrasound) abnormality or a clinically-actionable result has been otained.
What is the rationale behind the use of prenatal microarray in the prenatal context?
Major congenital abnormalities affect 1-1.5% of pregnancies
Chromosomal abnormalities account for 20-25% of major fetal anomalies
3% of pregnant women at high risk of having a fetus with a chromosomally anomaly after screening
Why should cultured/uncultured be kept?
Cultured cells or uncultured material (for future culture initiation) from these prenatal samples should be kept to safeguard follow up studies or the need for extra DNA i.e. if DNA extraction on uncultured material is too poor for a quality microarray result, cultured cells can be grown for repeat DNA extraction. This will impact on the overall turnaround time of the sample.
Compare higher density arrays to more targeted ones.
there is evolving evidence that the use of higher density arrays leads to no increase in the diagnostic utility but does lead to an increase in the discovery of benign and uncertain CNVs.
Conversely there is a risk that the use of targeted arrays and lower resolution arrays may fail to identify some abnormalities.
What are the advantages of using microarrays in prenatal diagnosis?
1) Culture is not required prior to reporting therefore there is a faster turnaround time and exclusion of cultural artefacts
2) Higher resolution and better detection of sub-microscopic abnormalities that may have clinical implications for the fetus = higher pick up rate. meta-analysis has shown a diagnostic yield of around 2.4% over karyotype for any referral reason and a diagnostic yield of 7% over karyotype for cases with abnormal ultrasound scan findings (Karampetsou et al 2014).
3) Where there is a known familial balanced translocation (or other balanced rearrangement), carriers are not identified. This removes the issue of testing for carrier status prior to consent obtained for testing in adulthood.
What are the disadvantages of using microarrays in prenatal diagnosis?
Microarrays require a high quantity of high quality DNA which may be difficult to obtain from prenatal samples.
Does not detect balanced rearrangements. This may be a disadvantage if the translocation has phenotypic consequences due to gene disruption. The future reproductive implications for the patient and other family members will also not be identified.
Lower level mosaicism may be missed. The detection of mosaicism is dependent on the overall quality of the DNA and the array platform. Some laboratories have validated mosaicism detection to 10%.
Triploidy will be missed or mis-classified.
Culturing may still be required for accurate follow-up by FISH which is important for positional information (for duplications) and accurate counselling of recurrence risk.
Difficulties faced in interpretation of genomic copy number variation within a clinically acceptable turn-around time, particularly if cultured cells required.
The costs of array CGH and eventual follow up (FISH parents) is higher than karyotype alone.
Variants of uncertain clinical significance (VOUS) may be detected. It is difficult to rule out a causative role and communicating the results may increase anxiety and lead to parents terminating a fetus potentially at a low risk of an adverse outcome. Appropriate counselling implies further training, revising guidelines and expand/perfect existing databases
Incidental findings may also be identified e.g. BRCA1/BRCA2, TP53 deletions which have an implication for the foetus and possible implications for the parents (if found to be inherited).
Possible problems of counselling the findings of a known microdeletion with a variable postnatal phenotype/penetrance.
Getting a balance between coverage and optimal resolution
What cautionary measures can be taken when implementing prenatal arrays?
Prreferable to use the same platform for both prenatal and postnatal settings
Experience is very important in the interpretation process, must be familiar with the platform used and know its strengths and weaknesses
High-resolution array guarantees a minimum of false-negative results
Interpretation is easier if the laboratory has an in-house control dataset, analysed with the same array platform
Why can you not fully exclude the pathogenicity of a cNV that has been inherited from an apparently normal parent?
- gene within the deletion region located on the homologous non-deleted chromosome can be mutated, thus leading to an autosomal recessive condition
- the CNV can contain an imprinted gene that has a pathogenic effect only when inherited from the mother and not from the father, or vice versa
- the CNV itself is a risk factor promoting a given disease in a specific but unknown genomic context, i.e., the CNV has its own pathogenic burden but exhibits incomplete penetrance.
What is the advantage of using FISH as a parental follow-up for a VUS detected on a prenatal array?
detecting incidental findings in the parents e.g. cancer susceptibility loci or late-onset neurodegenerative loci, partly reducing the ethical issues associated with genome-wide analysis.
Which factors will determine the method of follow-up?
Size of aberration and whether FISH probes are available.
What considerations should there be around mosaic findings?
Where a mosaic result is detected, it is important that the laboratory and clinician are aware of the possibility of pseudomosaicism or confined placental mosaicism. A confirmatory sample is needed, especially if ultrasound findings are expected and are either not present or are inconsistent with the result.
What is the follow-up for a suspected structural imbalance on array?
Conventional karyotyping or metaphase FISH may be helpful in unravelling the underlying mechanism of the aberration and thus reveal information that is important for recurrence risk. However, these analyses will seldom affect the management of the current pregnancy.
More importantly, parental analysis should be performed to rule out a balanced translocation or insertion for an accurate estimation of the recurrence risk.
Which study set the precedent for microarray testing of prenatal samples?
EACH
Ahead of prenatal microarray implementation, what clinical measures should be in place?
Good communication between the lab and clinicians is essential.
As many different results can be generated by prenatal array, it is important that the counsellor has a close collaboration with the genetics laboratory. There should be an agreement on:
What to report to the clinician prior to testing,
What to report to the patient: This may depend on the indication for which the array was performed. It is important that the laboratory informs the clinician when a pathogenic CNV is not consistent with the ultrasound findings or when the origin of the CNV may have a contributing effect.
The laboratory and clinicians should reach a consensus on whether to report unsolicited findings resulting in an increased risk for diseases of known or unpredictable severity
