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Chromosome Micro Analysis in Prenatal Testing
Prenatal tests are gaining more and more importance day by day, as parents are being highly concerned about their unborn baby. This is in turn to drop down any chances of still births or babies with congenital diseases. Until recent, karyotyping was the major method of analyzing for all the defects that could be figured out from the chromosomes.

Karyotyping is mostly used to find out those conditions like change in numbers of the chromosomes. It can be done by collection of amniotic fluid (by amniocentesis), bone marrow, blood, or from a tissue obtained from placenta. Karyotyping reveals data about number of chromosomes and changes in the structure of chromosome only. It can be used for finding out congenital conditions like Down’s syndrome, Turner’s syndrome, Klinefelter’s syndrome etc. These are only conditions that involve a change in the number of chromosomes that the karyotyping can reveal. Chromosomal Micro Analysis (CMA) gained popularity here, because it can detect a wide variety of serious genetic disorders that could not be revealed by the conventional chromosome analysis including those like autism.

Chromosome micro analysis makes use of the characteristic of DNA to specifically bind, which are said as the base pairs, adenine-thymine and guanine-cytosine pairs. In order to do the chromosomal micro analysis, a reference DNA is taken from known genes. This reference gene is one without any defects. Single strand of this DNA is obtained and labeled with fluorescent color. Then the DNA of the fetus is taken from the chorionic villus sampling (CVS) or from amniotic fluid, which leaves prenatal testing to still use invasive methods for sample collection, and labeled with another fluorescent color. It is also made into single strands of DNA and labeled with a fluorescent color. It should be noted that the reference DNA strand and subject’s DNA sample are labeled with different fluorescent colors. Commonly used fluorescent dyes are red and green. Both the strands are allowed to mix together in a chip where both of them bind together. Regions with any defects in the genetic material can be understood from the variations in the fluorescent color at that particular region of the strands. A micro array scanner is used for detecting the color variations. The color depends on the amount of mutual binding between both the strands. In case of duplication, the color of strand of fetus will be stronger and if it is a case of deletion, then the reference strand will be showing stronger fluorescent color. Deletion and duplication thus results in less and more combination respectively, between the reference DNA and the DNA of the fetus. The data obtained from the scanner is fed into specific computer software that can interpret the color variations and to obtain a detailed report. From identifying the locations of defects on the genes, the possible problems that the fetus will be facing when it is born, can be predicted.

Basically there are two types of chromosome micro analysis. This is depended on the type of the probe used. They are the bacterial artificial chromosome (BAC) and the oligo nucleotide probes. Both of these probes are used to find its applications in two different situations. Bacterial artificial chromosome probes are longer in length than the oligo probes. So they will detect the larger changes, while the oligo probes are able to detect smaller alterations.

Chromosomal micro analysis takes a deeper look at the chromosomes for possible abnormalities. One of the most important advantages of CMA is that the samples do not require any culturing preventing chances of introduction of artifacts or of degradation. CMA will give a better analysis of the measure and content of the chromosomal imbalance. It can detect micro deletion/duplication and subtelomeric deletion/duplication, that karyotyping cannot find out. CMA will provide accurate genotype-phenotype correlation. It is one among the prenatal tests which can be relied completely with the test results. The list of the diseases that CMA is capable of finding out includes Angelman syndrome, Wolf-Hirschhorn syndrome, Williams’s syndrome, Prader-Willi syndrome, autism, congenital cardiac disorders etc. In figures, chromosomal micro Analysis can detect around 150 diseases caused by defects in the genes. Because of prediction of possible diseases that may affect a fetus, at the time of birth or during its lifetime, precautions can be taken. This will help in order to prevent the diseases more effectively rather than diagnosing and treating it at the time of its occurrence at a later stage. Bh.

Chromosome micro analysis gives about 100 times better resolution than normal karyotyping methods for prenatal test. But, being a comparatively new test it is only considered as a secondary option in prenatal testing. Around 8% of newborns have got some kind of disease that is genetically related. And hence can be found out using chromosome micro analysis. So by extensive use of chromosome micro analysis as a primary option in pre natal testing almost all of these can be found earlier and proper treatments and precautions for prevention or management of the diseases can be done. Specific causes for these diseases can be analyzed, which will enable us to classify the genetic disorders based on whether the cause is a deletion or duplication. This will help in specifically giving treatment to each set of diseases.

One of the major disadvantages of chromosome micro analysis is that we still cannot avoid using the regular karyotyping methods. This is because it is unable to give any information about conditions of polyploidy. Still, karyotyping is needed for detecting polyploidy conditions. Another limitation is that it will not identify any reversed sections in the DNA. It will recognize only the unpaired part that will be seen as irregular pairing on the strands. So those symptoms associated with a balanced and reversed base pairing cannot be identified using the chromosome micro analysis method. It will not find out the single base pair reversing too, as it is very minute to produce any fluorescent color changes.

The use of chromosomal micro analysis that uses techniques of DNA micro arrays will help to detect a good number of diseases associated genetically, and to take precautions or preventive methods for preventing or managing the condition. It should be done as one of the primary tests during pregnancy period.
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Array comparative genomic hybridisation

The type of chromosomal microanalysis using arrays referred to in the previous article in the thread is developing. A method known as array comparative genomic hybridization has potential uses in both pre-natal diagnosis and in evaluation in adults and children. For example, in a Danish study, a high-resolution whole genome array comparative genomic hybridization method was used on foetuses with abnormal ultrasound. An 80-kb resolution oligonucleotide array-based comparative genomic hybridization (aCGH) was used. The discovery of clinically significant copy number variations in 11 foetuses with structural malformations and three foetuses with uncertain clinical significant variations led the authors to propose that array comparative genomic hybridization is a valuable diagnostic tool in the context of detection of foetal abnormalities.

The method has potential in a number of disorders, including autism as mentioned in the original article in this thread. A study from the University of Washington used retrospective array comparative genomic hybridization on patients who had been referred for genetic testing for autism spectrum disorders. Among the patients in whom a diagnosis of autism spectrum disorder was confirmed and in whom array comparative genomic hybridization was performed , 8.7% had ‘pathogenic or presumed pathogenic abnormalities’ while another 8.7% had’ likely pathogenic copy-number variants’ and another 22% had variants which are not yet sub-classified and whose significance is not yet understood. In another study from the University of Colorado, adults with an unexplained intellectual disability were considered. Out of 45 patients, three had abnormal high-resolution chromosome studies, which were confirmed by array comparative genomic hybridization while another 7 had ‘novel genomic losses identified only by array comparative genomic hybridization’. This is a method with a lot of potential.


STOBBE, G. et al., 2013. Diagnostic yield of array comparative genomic hybridization in adults with autism spectrum disorders. Genetics In Medicine: Official Journal Of The American College Of Medical Genetics

TAYLOR, M.R.G. et al., 2010. High prevalence of array comparative genomic hybridization abnormalities in adults with unexplained intellectual disability. Genetics In Medicine: Official Journal Of The American College Of Medical Genetics, 12(1), pp. 32-38

VESTERGAARD, E.M. et al., 2013. Prenatal diagnosis: array comparative genomic hybridization in fetuses with abnormal sonographic findings. Acta Obstetricia et Gynecologica Scandinavica, 92(7), pp. 762-768
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