MOLECULAR CYTOGENETICS: aCGH
Microarray-based comparative genomic hybridization (aCGH) provides comprehensive genetic testing which enables higher-resolution genome analysis. Microarray-based comparative genome hybridization is a single test that detects common genetic syndromes as well as submicroscopic copy number variants (CNVs) including DNA losses (deletions) or gains (duplications, triplications, etc.) across the entire genome. Microarray-based comparative genome hybridization allows for detection of CNVs up to 100 times smaller than what conventional cytogenetics can detect, therefore dramatically increasing the detection rate of genetic abnormalities.
While the test is very accurate, it cannot detect all genetic alterations. A typical aCGH result does not diminish the risk of other genetic conditions or birth defects. The types of genetic changes that escape detection by aCGH primarily include:
- The inability to detect genetic events that do not affect the relative copy number of DNA sequences, e.g. molecularly balanced chromosomal rearrangements.
- Low-level mosaicism for unbalanced rearrangements and aneuploidy.
- The chromosomal mechanism may not be elucidated.
- Tetraploidy or other ploidy levels will not be detected.
- Uniparental disomy cannot be detected with this platform.
- Copy number variations of genomic regions not represented on the platform will not be detected.
- The aCGH assay is not designed to detect duplications and deletions below the level of detection according to probe coverage and performance, point mutations, gene expression, and methylation anomalies that may contribute to the phenotype.
- The platform does not detect all mutations associated with a given syndrome, failure to detect a copy number alteration at any locus does not exclude the diagnosis of a disorder associated with that locus.
Prenatal and product of conception aCGH
aCGH is in the process of replacing conventional cytogenetics for invasive prenatal testing after excluding common aneuploidies and triploidy by quantitative fluorescent polymerase chain reaction (qf-PCR). aCGH testing can also be performed on products of conception to determine if there is a chromosomal aberration that might have caused the miscarriage, recurrent miscarriage or have implications for future pregnancies.
Reasons for referral:
- One or more structural anomalies identified on an ultrasound scan
- An isolated nuchal translucency NT≥3.5mm.
- Products of conception (POC) whereby there is a likelihood of finding too much or too little chromosomal material which might be of value in planning future pregnancies.
For prenatal arrays, the optimal samples are amniotic fluid or cord blood. For amniotic fluid, two 10ml sterile tubes of amniotic fluid, taken preferably between 16 and 19 weeks of gestation, will be required. For cord blood, the requirement is 4ml of blood in an EDTA vacutainer.
For product of conception arrays, most tissue samples derived from miscarriage products are acceptable. Acceptable samples include whole fetuses, fetal skin or muscle biopsies, umbilical cord, and cord blood in EDTA or placental tissue. Whole fetuses are preferred as it allows the selection of optimal tissue. Most tissues will work, with the limitation of the sample being very bloody. This poses the risk of maternal cells interfering with the fetal component/complement and thus, is called maternal cell contamination (MCC). Product of conception samples must be collected in saline or culture medium. Samples in formalin will not be accepted.
For prenatal and products of conception testing, the parental samples are recommended. Maternal samples are needed to exclude MCC in prenatal and POC samples. Maternal and paternal samples are also very useful in the interpretation of some CNVs, which will allow us to report if the CNV is inherited and could affect subsequent pregnancies. Four millilitres of blood collected in an EDTA vacutainer is required for each parent – If paternity is uncertain, please refrain from sending in a paternal sample.
Chromosomal microarray has been widely adopted as the first-tier clinical test for individuals with multiple congenital anomalies, developmental delay, intellectual disability and autism spectrum disorders.
Reasons for referral:
- Intellectual disability
- Developmental delay
- Autism spectrum disorder
- Multiple congenital anomalies
- Diagnosed genetic abnormalities to confirm breakpoints and gene dosage
- Suspected genetic disorder
For postnatal arrays, 4ml of blood in an EDTA vacutainer (Purple top) is required.
Parental blood samples are highly recommended as they are also very useful in the interpretation of certain CNVs, which will allow us to report if the CNV is inherited and could affect subsequent pregnancies. Four millilitres of blood collected in an EDTA vacutainer is required for each parent – If paternity is uncertain, please refrain from sending in a paternal sample.