For the last 30 years, karyotyping has been widely used to detect chromosome abnormalities. Karyotyping can only detect relatively large chromosome abnormalities and is a lengthy process. A karyotype done on blood cells can take 3 to 7 days; a karyotype on amniocytes or from chorionic villi can take 10 to 14 days, depending on how fast the cells grow. 1
Since June 2010, patients with moderate to severe developmental delay, with or without autism spectrum disorder, moderate to severe learning disabilities, dysmorphic features or various congenital abnormalities have had aCGH replacing karyotyping to establish the underlying diagnosis of their clinical problems which was not possible before.2
Traditionally, blood samples are put into solutions which contain all of the chemicals they need to survive and are kept in an incubator at 37 degrees. 3 This provides the cells with the ideal conditions to grow. Once enough cells have been cultured to enable scientists to study them, cells are extracted from the solutions in which they have been grown. 3
Chromosomes are stained, commonly with Giemsa’s reagent and magnified under a light microscope so that it is possible to see each one’s distinctive pattern of light and dark bands that appear as horizontal stripes. 3 Scientists use the banding pattern to examine the number, arrangement, size and structure of chromosomes in approximately 10 cells. 3
If the change is large enough, it is possible to see whether there is a chromosome imbalance (loss or gain of chromosomal material) or if the chromosome is rearranged in any way. 3
What is aCGH?
The recent advanced technique used in place of karyotyping is called array comparative genomic hybridisation (aCGH) which accurately identifies both the location and gene content of pathogenic chromosome imbalances. 2
Array CGH compares DNA with a control DNA sample and identifies differences between the two sets of DNA. It allows us to use the whole human genome to rapidly detect submicroscopic pathogenic chromosome alterations (microdeletions and microduplications) which cannot be seen by conventional karyotyping. 2
Process of aCGH
A microarray works by exploiting the ability of a DNA strand to bind specifically (hybridise) to another DNA strand. 4 The DNA in our cells is arranged as a double helix in which the two strands of DNA are bound together by bonds between the base pairs. A single-stranded DNA fragment is made up of four nucleotides. Adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C). When two complementary sequences find each other they will hybridise.
Importance of aCGH
The Wessex Regional Genetics Laboratory has now reported 3,000 clinical aCGH tests and has found that 15% of those patients with pathogenic imbalances had gone undetected by conventional karyotyping. 7 Array CGH can detect genomic deletions or duplications with far greater sensitivity (>100 times) than can be achieved by chromosome analysis using light microscopy. Multiple studies have shown that aCGH, will detect up to three times more pathogenic chromosome imbalances than karyotyping. 7
Results from the test are typically available within 24-48 hours. 1
Array CGH is a cost effective diagnostic technological method which can be widely available, making it accessible to a large proportion of patients. 1
Additionally, when a specific chromosome imbalance is diagnosed, the parents (and other family members) can be tested to see if they are carriers of changes in their DNA that put them at risk of having more children with a chromosome change (genetic counselling), thus making aCGH an important tool for prevention in terms of public health. 4
Embryologists have up to 85% chance of eliminating the chromosomally abnormal embryos before transfer with only a 0.2% risk of accidentally damaging the egg. 1
Array CGH also comes with few ethical implications which allows it to be used by all members of society, ensuring that everyone has equal access to such medical technological techniques.
Therefore, the discovery of aCGH is vitally important in the early diagnosis of physical health and neurodevelopmental problems, helping to guide management in all aspects of a patient’s life and assisting with prognosis and the implementation of an optimum treatment plan for each patient, including the provision of appropriate education, social and respite care. 7
Further Applications of aCGH
Oncology – Genetic alterations and rearrangements occur frequently in cancer and contribute to its pathogenesis. These aberrations by aCGH provides information on the locations of important cancer genes and have clinical use in diagnosis, cancer classification and prognosis. It can therefore reduce the annual 7.6million deaths caused by cancer and help with the production of new treatment. It is a powerful tool to elucidate previously unknown genetic changes in neuroblastomas. 8
Neonatal/foetal use - to detect the chromosomal aberrations in foetal and neonatal genomes. 4
Limitations of aCGH
aCGH does not detect balanced chromosome translocations. This is because balanced chromosome translocations do not result in any loss or gain of chromosomal material and so the technique cannot detect tiny changes such as single base pair deletions. 6
The Future of aCGH
Prenatal Genetic Diagnosis can be used as a tool for pre-implantation genetic screenings. It has the potential to detect Copy Number Variants and aneuploidy eggs, sperm which may contribute to failure of the embryo to successfully implant, miscarriage or conditions such as Down Syndrome (trisomy 21). This makes array CGH a promising tool to reduce the incidence of life altering conditions and improve success rates of IVF. 1
It may also be used in couples carrying chromosomal translocations as balanced reciprocal translocations or Robertsonian translocations, which have the potential to cause chromosomal imbalances in their offspring. The use of aCGH in pre-implantation screening to discard affected eggs or sperm, reduces the ethical implications which may arise from the termination of an IVF embryo following the discovery of a chromosomal abnormality post implantation. 1
- Anderson RA & Pickering S. The current status of pre-implantation genetic screening: British Fertility Society Policy and Practice Guidelines, 2008; 11: 71-75.
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS. Genomic Diagnostics. Laboratory.Microarray (aCGH) Testing.
- NHS National Genetics and Genomics Education Centre.
- Hilary Burton, Evaluation of the use of array comparative genomic hybridisation in the diagnosis of learning disability, August 2006.
- NIM Genetics, New Integrated Medical Genetics.
- Centre for Assisted Reproduction and Endocrinology. Array CGH.
- Wessex National Regional Genetics Laboratory, Replacing Karyotyping With Array Comparative Genomic Hybridization (Acgh)
- Daniel Pinkel & Donna G Albertson, Nature Genetics 37, S11 – S17 (2005), Array comparative genomic hybridization and its applications in cancer, doi:10.1038/ng1569