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To evaluate the performance of chromosomal microarray (CMA) as an independent method for prenatal cytogenetic diagnosis
Villus or amniotic fluid samples from women undergoing prenatal diagnosis at 31 centers were sent to a central karyotyping lab. The samples were split; standard karyotyping was performed on one portion and the other was de-identified and sent to one of four independent microarray labs for CMA. Microarrays consisted of 84 regions of known disease association, 43 centromeric and 41 telomeric regions and a backbone of oligoneucleotides spaced 75 -125 kb with regions >1Mb reported. After a preliminary study, uncultured samples were analyzed primarily, using culture only as a back-up. Karyotype and microarray results were reported to an independent data center. Microdeletions and duplications identified exclusively by CMA were classified as “of known clinical significance” or “benign” using predefined listings. All other copy number variants (CNVs) were designated as “of uncertain clinical significance”.
4401 women were enrolled with indications of AMA (46%), abnormal 1st or 2nd trimester screening (18%), abnormal ultrasound (26%), and other indications (9%). Successful results were obtained by CMA in 98.7% of cases; 88% were obtained using only uncultured material. Of the 4340 samples for which results were available for comparison, 316 (7.3%) autosomal and 57 (1.3%) sex chromosome non-mosaic aneuploidies were identified by karyotype. All of these were identified by CMA however, seven (all from CVS) were reported as mosaic. Notably, 5.8% of cases with a normal karyotype and structural fetal anomalies had either a microdeletion or duplication of potential or known clinical significance, as did 1.7% of those sampled for maternal age or positive screening.
For prenatal testing, karyotyping and CMA are equally effective in identifying aneuploidy. Microarray detects additional clinically relevant information both in cases with structural anomalies and in those sampled for routine indications.