Prenatal molecular karyotype (arrayCGH-aCGH)

Molecular karyotype (arrayCGH-aCGH) has brought about revolutionary changes in clinical cytogenetics and today is the undisputed reference method for the diagnosis of many genomic diseases (mental retardation, developmental delay, congenital malformations, etc.) associated with chromosomal imbalances, also known as Copy Number Variations – CNV’s, not only in postnatal investigations, but also in prenatal diagnosis.

Prenatal aCGH is able to detect all chromosomal aneuploidies and imbalances revealed by ‘classic’ prenatal karyotype analysis (amniotic fluid or CVS), such as trisomy 13, 18, 21, etc., while it additionally allows the investigation of other chromosomal imbalances (deletions and/or duplications), undetectable by classic karyotype, at an analytical level of about 10-100 times higher resolution than classic karyotype analysis.

Please note that molecular karyotype-aCGH is not in a position to detect balanced structural rearrangements (balanced translocations, inversions), triploidy, mosaicism at a level <15-20% and also gene mutations which are the main cause of several thousand genetic disorders, such as thalassemia, cystic fibrosis, etc..

To the extent that the test will detect syndromes and other birth defects that appear suddenly in an otherwise normal pregnancy and usually without any prior family history or ultrasound findings, it may be applied to all cases requiring prenatal chromosomal testing.

The anomalies revealed through prenatal molecular karyotype are associated with hundreds of known genetic diseases and syndromes, which occur with various congenital anomalies with or without mental/psychomotor retardation and which would have remained otherwise undiagnosed by conventional karyotype analysis.

For these reasons, it is now internationally recognized that this test may replace classical karyotype analysis, as it is able to diagnose all pathological chromosomal abnormalities and also chromosomal mosaicism. In selected cases and whenever deemed necessary, molecular karyotype may be complemented with classic karyotype.

Today, the percentage of affected embryos detected through test is about 3% (~ 1 in 30), which is more than twice that of the conventional karyotype. Moreover, the application of the test does not require the time-consuming culture of amniotic fluid or chorionic villus sample (CVS) cells, resulting in a reporting time of 7-8 days.

The analytical level of prenatal molecular karyotype-aCGH, as currently applied by InterGenetics, following extensive experience of many thousands of cases and taking into account international recommendations, is based on the proven 2x105K microarray platform and it evaluates:

1. Deletions/duplications ≥100Kb in size, in approximately 800 targeted genomic regions with known clinical significance (see below the indicative table)
2. Deletions/duplications ≥350-500Kb in size in the remaining parts of the genome (backbone). Specifically, deletions ≤350 Kb in size and duplications ≤500 Kb in the genome backbone are generally not evaluated and will not be reported.

Table of diseases.pdf

The final level of analysis achieved may vary (a relevant statement will be included in the final report), depending on technical parameters relating to sample quantity and/or quality.

Also note that the final report will only contain findings that are assessed as having clinical significance and every effort will be made not to report findings of unknown clinical significance, which often cause unnecessary anxiety during pregnancy. Moreover, a number of microdeletion/microduplication syndromes exhibit variable penetrance and expressivity, which means not all individuals with the microdeletion or microduplication will necessarily express the disease or the clinical signs may vary significantly.

In summary, the final report will include microdeletions/microduplications and other chromosomal imbalances of known clinical significance. The assessment and reporting of other deletions/duplications will be determined following internal expert clinical evaluation. In selected cases and depending on the nature of the finding, testing of the parents may be required before the final evaluation.

(see our recent scientific publication)

The test is highly sensitive and complex. Therefore, the analysis and the clinical evaluation of the results should be performed by a highly skilled group of clinical and molecular geneticists, ensuring the maximum diagnostic validity for the patient and the family.

Proper clinical genetic assessment and genetic counseling, both before and after testing, is essential in order to determine the optimum testing strategy and also to communicate properly the concepts of pathological and normal.

The method reveals only imbalances (quantitative changes) of genetic material. It is therefore not able to detect balanced rearrangements/translocations and also triploidy. Furthermore, aCGH analysis may not detect all types of chromosomal mosaicism occurring at <15% of cells, which in any case are usually non-pathogenic.

Finally, it is obvious that the method does not detect point mutations in DNA (gene mutations) which are the main cause of several thousand genetic disorders, such as thalassemia, cystic fibrosis, etc..

Since 2013, InterGenetics pioneered the application of a prenatal screening test for 2 common neurogenetic diseases, in all samples requesting prenatal chromosomal diagnosis by classic karyotype or prenatal molecular karyotype (in amniotic fluid cells or chorionic villi). This screening test aims at the diagnosis of affected fetuses for:

• Fragile X syndrome (FRAXA), applied only in male embryos,

and

• Spinal Muscular Atrophy (SMA), both in male and female fetuses.

With this option, it is possible to diagnose prenatally (and we have already diagnosed) a number of affected embryos, which would result in the expression of a particularly severe genetic disease in the newborn child.

Please note that today, the application of prenatal molecular karyotype replaces the Extended prenatal panel – EPP, as it offers multiple advantages.

The method reveals only imbalances (quantitative changes) of genetic material. It is therefore not able to detect balanced rearrangements / translocations or rearrangements / translocations with imbalances of size <0.5-1Mb. It is worth noting that classical prenatal karyotype analysis is NOT able to detect unbalanced rearrangements / translocations involving imbalances <5Mb.

Furthermore, as with classical prenatal karyotype, aCGH analysis may not detect all types of chromosomal mosaicism occurring at <10-15% of cells, which in any case are usually non-pathogenic. Finally, it is obvious that the method does not detect point mutations in DNA, associated with gene disorders such as thalassemia, cystic fibrosis, etc.