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Software Targeting to Improve CNV Calling in Prenatal Samples

Prenatal Cytogenetics

Prenatal cytogenetic testing can be considered when pregnancies are associated with a risk of chromosomal defects. The decision to go ahead with such tests is based mainly on maternal age, anomalous maternal serum results, or fetal abnormalities detected by ultrasound. G-band karyotyping and fluorescence in situ hybridization (FISH) are currently the main techniques used in prenatal diagnosis of chromosomal abnormalities. However, G-banding has limited levels of resolution making abnormal calls somehow problematic while FISH is often inadequate as it relies on syndrome-specific FISH probes that are mainly designed for targeted screening and not whole genome analysis. Consequently, prenatal cytogenetic testing requires alternative means capable of detecting chromosomal deletions and duplications spread throughout the genome.

Array Comparative Genomic Hybridization (aCGH)

Recent advances in genomics have dramatically increased our capacity to analyze abnormal cells, revealing a multitude of changes in genomic DNA, such as mutations and copy number alterations. Array comparative genomic hybridization has become a valuable, genome-wide screening tool for the detection of chromosomal aberrations in the form of copy number variations (CNVs) in the field of cytogenetics. The major advantage of aCGH is that it offers improved resolution in a rapid and high-throughput fashion compared to traditional techniques. Research laboratories rely more and more on this method to identify genetic disorders on a minimal amount of DNA in a variety of samples. Indeed, prenatal samples can yield exceptionally low amounts of DNA. This is the case with amniotic fluid and chorionic villus samples. However, the use of whole genome DNA amplification tools prior to aCGH analysis such as Enzo’s BIOSCORE® Screening and amplification kit avoids this issue. There is, however, no international consensus and the implementation of aCGH for prenatal testing remains a controversial subject as CNVs of unclear prognosis can cause unnecessary parental anxiety.

Detection of CNVs of Clear Clinical Significance

To that effect, Joo Wook Ahn and colleagues from Guy’s and St Thomas’ NHS Foundation Trust designed and validated a clinically-relevant prenatal testing approach. Using Enzo’s CYTAG® CGH labeling kit, the authors of this study labeled 342 prenatal samples. These were paired and co-hybridized with other samples mismatched for phenotype and matched for sex on a single 60K array, a technique used to decrease costs and improve throughput. Fluorescence signals were then quantified and analyzed by a combination of the ADM2 algorithm from Agilent and a custom software developed to detect CNVs greater than 3Mb and of 24 specific and well-characterized deletion/duplication regions. CNVs were ratified by either karyotyping or in situ hybridization to confirm sample identity.

Conclusion

23 prenatal samples with abnormalities were reported after confirmation (6.7%). 249 of the remaining samples were anonymized and re-analyzed at full resolution using a standard postnatal analysis with three-probe cut-off for CNV calls. 46 CNVs were found in 44 samples but none of these CNVs were deemed to be of clinical relevance, thereby validating the software-based strategy. Altogether, these results demonstrated the ability of this prenatal testing approach to detect all CNVs of clear clinical significance. It also circumvented the need to interpret CNVs of unknown clinical significance and the parental anxiety associated with it. Further work will be, however, required to improve the selectivity of the software and refine its capacity to differentiate between reduced and augmented CNVs. Enzo Life Sciences offers geneticists a comprehensive portfolio for genomic analysis including our CYTAG® CGH labeling kit as well as a brand new Nick translation DNA labeling system with ready-to-use nick translation enzyme mix and shorter labeling time, some of which are described below:

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Reference:

  1. J.W. Ahn, et al. A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings. Peer J. (2014) 2: e354.

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