Cytogenetic microarray in structurally normal and abnormal foetuses: a five years experience elucidating increasing acceptance and clinical utility

Fetal mosaicism, should conventional karyotype always be performed?

BACKGROUND AND PURPOSE

The application of classical cytogenetic and DNA-based molecular techniques to detect cell lineages of mosaicism derived from cultured or noncultured fetal cells may result in discordant results. This retrospective study aimed to assess the inconsistent diagnostic outcomes, technical availability, and limitations of chromosomal microarray analysis (CMA) and karyotyping for mosaicism.

METHODOLOGY

A total of 75 fetuses diagnosed with mosaicism by karyotype analysis or CMA were selected, and the results from both the methods were compared and further analyzed.

RESULTS

A total of 42 (56%, 42/75) CMA results were consistent with karyotypes, consisting of 22 cases of mosaic sex chromosomal abnormalities, 8 routine autosomal aneuploidy cases, 8 other autosome aneuploidy cases, 3 large cryptic genomic rearrangements, and 1 small supernumerary marker chromosome. Discrepancy between karyotype analysis and CMA was observed in 33 (44%, 33/75) mosaicisms involving 15 sex chromosomal abnormalities, 1 routine autosomal aneuploidies, 5 other autosome aneuploidy cases, 8 large cryptic genomic rearrangements, and 4 small supernumerary marker chromosomes.

CONCLUSION

Considering the disparities between methods as well as the cell populations analyzed, both CMA and karyotype analysis have their own advantages and disadvantages. Therefore, CMA should ideally be used in combination with karyotyping to detect more cases of mosaicism than using either test alone.

Abnormal chromosomes identification using chromosomal microarray

In this study, we presented a case series to highlight the chromosomal microarray (CMA) in identifying chromosomal abnormalities which is undetectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis. Extensive studies showed that CMA was gradually accepted as a prenatal invasive testing during pregnancy. The aim of this study was to evaluate the diagnostic effect of CMA for foetuses with abnormal chromosomes unrecognised by conventional karyotyping. Pregnant women who need prenatal diagnosis with all indications were enrolled in this study. For aberrant cytogenetic findings that cannot be defined by routine karyotyping, single nucleotide polymorphism array (SNP-array) was used. Six cases with abnormal karyotype were included in the study. With higher resolution of translocation breakpoints, CMA could detect smaller chromosomal imbalances that were undetectable by karyotyping. This study highlights the value of CMA for the detection of submicroscopic abnormalities in foetuses that cannot be detected by conventional karyotyping. Impact StatementWhat is already known on this subject? Chromosomal microarray (CMA) offers additional diagnostic benefits by revealing submicroscopic imbalances or copy number variations (CNVs) that are too small to be identified on a standard G-banded chromosome preparation.What do the results of this study add? We added a case series to highlight the CMA in identifying chromosomal abnormalities not detectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis.What are the implications of these findings for clinical practice and/or further research? This study highlights the value of CMA in the case of associated foetuses with submicroscopic abnormalities that cannot detect by conventional karyotyping.

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis

Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

The difference between karyotype analysis and chromosome microarray for mosaicism of aneuploid chromosomes in prenatal diagnosis

OBJECTIVE

To compare karyotype and chromosomal microarray (CMA) analysis of aneuploid chromosome mosaicism in amniocentesis samples.

MATERIALS AND METHODS

A total of 2091 amniocentesis samples from pregnant women were collected from March 1, 2019, to January 31, 2020. Karyotype analysis was performed using G-banding and CMA analysis used the Affymetrix CytoScan 750K SNP microarray.

RESULT

Thirteen cases with aneuploid chromosome mosaicism were detected and compared between the karyotype and CMA methods. Seven of these cases were trisomic mosaicism, and the levels of mosaicism calculated from CMA were higher than those detected from karyotype analysis; noting three cases of trisomy mosaicism were not detected by karyotype analysis. Four cases exhibited monomeric mosaicism, and the levels of mosaicism detected in three of these cases were higher in karyotype compared with CMA analysis; one case had equivalent levels of monomeric mosaicism from both karyotype and CMA analysis. Two other cases from karyotype analysis were a mix of monosomic and trisomic mosaicism, whereas the CMA result was restricted to monosomic mosaicism for these cases.

CONCLUSION

Both karyotype and CMA analysis can be used to detect aneuploid chromosome mosaicism. However, the two methods produced different results. CMA and karyotype analysis have their own advantages in detecting aneuploid mosaicism, and the combination of these methods provides a more rigorous diagnosis.