Integrated FISH, Karyotyping and aCGH Analyses for Effective Prenatal Diagnosis of Common Aneuploidies and Other Cytogenomic Abnormalities

Abstract

Current prenatal genetic evaluation showed a significantly increase in non-invasive screening and the reduction of invasive diagnostic procedures. To evaluate the diagnostic efficacy on detecting common aneuploidies, structural chromosomal rearrangements, and pathogenic copy number variants (pCNV), we performed a retrospective analysis on a case series initially analyzed by aneuvysion fluorescence in situ hybridization (FISH) and karyotyping then followed by array comparative genomic hybridization (aCGH). Of the 386 cases retrieved from the past decade, common aneuploidies were detected in 137 cases (35.5%), other chromosomal structural rearrangements were detected in four cases (1%), and pCNV were detected in five cases (1.3%). The relative frequencies for common aneuploidies suggested an under detection of sex chromosome aneuploidies. Approximately 9.5% of cases with common aneuploidies showed a mosaic pattern. Inconsistent results between FISH and karyotyping were noted in cases with pseudo-mosaicism introduced by culture artifact or variable cellular proliferation from cells with mosaic karyotypic complements under in vitro cell culture. Based on findings from this case series, cell-based FISH and karyotyping should be performed to detect common aneuploidies, structural chromosomal abnormalities, and mosaic pattern. DNA-based aCGH and reflex FISH should be performed to detect and confirm genomic imbalances and pCNV. Practice points to ensure the diagnostic accuracy and efficacy were summarized.

A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings

“…A recent study showed that the NIPT performed significantly better in predicting sex chromosome trisomies than monosomy X; which could potentially improve the under detection of sex chromosome aneuploidy in prenatal diagnosis (Xu et al, 2019). The integration of aCGH in prenatal diagnosis has extended its diagnostic scope to include pCNVs (Li et al, 2016; Chai et al, 2019). In this study, aCGH was performed in about one third of total prenatal cases with an ADR of 2.59% for pCNVs.…”

Clinical Selection of Prenatal Diagnostic Techniques Following Positive Noninvasive Prenatal Screening Results in Southwest China

“…Confined placental mosaicism is one of the main reasons for the inconsistency between NIPS results and prenatal diagnosis results (Grati, 2016). A reflex FISH test is recommended to confirm chromosome mosaicism when a mosaic pattern is highly suspected (Hultén et al, 2003;Cherry et al, 2017;Wang et al, 2018;Chai et al, 2019). Compared with the FISH results, we found a higher proportion of the 45,X counted by karyotyping.…”

“…Compared with karyotyping, CNV detection techniques can test uncultured amniotic fluid cells, thus reducing the influence of cell culture on the mosaic ratio and restrictions of the cell cycle on prenatal diagnosis. However, owing to fluctuations in the fluorescence signal intensity and background noise, CMA has a low sensitivity to a lower proportion of mosaic patterns than karyotype analysis and CNVseq (Chai et al, 2019;Hao et al, 2020). The CMA result of amniotic fluid cell testing for case 840 was inconsistent with that of karyotyping of neonatal peripheral blood; the false negative result of CMA may be caused by the above reasons or tissue-specific chimerism.…”

“…Besides the different number of cells analysed, better growth of the abnormal cell type is likely to be the major contributor. Culture and harvesting of amniotic fluid cells may lead to changes in the mosaic rate of different cell lines and even cause pseudo-mosaicism (Grati, 2014;Chai et al, 2019). Moreover, overgrowth by the X0 cell line might explain why the FISH results for cases 561 and 568 were inconsistent with those of karyotyping.…”

Fluorescent In Situ Hybridisation (FISH) as a Follow-up Test for Postnatal Microarray Results

“…Over the years, there has been signi cant development in laboratory protocols used to diagnose genetic conditions [1]. Each protocol has enabled new and enhanced ways of viewing the human genome [2,3]. Genetic testing is carried out based on the diagnosis and clinical indication which allows for the appropriate method to be selected.…”