Reliable detection of subchromosomal deletions and duplications using cell‐based noninvasive prenatal testing

Abstract

Objective To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low‐coverage shotgun next‐generation sequencing for cell‐based noninvasive prenatal testing (NIPT). Method Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density‐based cell separation, immunofluorescence staining, and high‐resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome‐wide copy number analysis and genotyping to confirm the fetal origin of the cells. Results Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis. Conclusion We demonstrate that this cell‐based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size.

Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases

“…[ 30,31 ] Cell‐based testing has several advantages over cffDNA‐based test, in that fetal cells provide pure fetal DNA of high integrity. [ 32 ] A total of 11 pregnancies whose fetuses may carry thalassemia mutations were investigated: five were at risk for – SEA / thalassemia and six were at risk for β‐thalassemia. Thalassemia‐related mutations could be reliably detected by analyzing these rare fetal cells.…”

Application value of NIPT for uncommon fetal chromosomal abnormalities

“…More people are becoming aware that there are fetal chromosomal abnormalities other than trisomy 21, trisomy 18, and trisomy 13 [5,6] that lead to neonatal birth defects, and the prevalence rate of these other chromosomal abnormalities is rising [7]. Compared to traditional serological screening, noninvasive prenatal testing (NIPT) has been welcomed by pregnant women and clinicians for fetal chromosomal aneuploidy screening due to its high detection rate, low false positive rate, and noninvasiveness [8,9]. However, a large portion of the literature has focused on the study of common chromosomal aneuploidy and has rarely reported on other chromosomal abnormalities [10].…”

Recent trends in prenatal genetic screening and testing

“…Although the cell-based approach has limitations, it has been shown that individual fetal cells can be isolated from maternal circulation and that their pure fetal DNA can be used for the detection of copy number abnormalities of at least 1 Mb by low-coverage NGS. Analysis of the fetal genome at a higher resolution would allow increased accuracy and improved positive and negative predictive values compared with cfDNA-based NIPT in the detection of microdeletion syndromes 48 .…”