Chip-Based Digital PCR Approach Provides A Sensitive and Cost-Effective Single-Day Screening Tool for Common Fetal Aneuploidies-A Proof of Concept Study.

Anna Nykel,Agnieszka Gach,Wojciech Fendler,Marcin Kaszkowiak

doi:10.3390/ijms20215486

Abstract

In the prenatal period, the copy number aberrations of chromosomes 13, 18, 21, X and Y account for over 80% of the clinically significant chromosome abnormalities. Classical cytogenetic analysis is the gold standard in invasive prenatal diagnostics but the long test waiting time affects its clinical utility. Several molecular rapid tests have been developed and employed in clinical practice, however all have substantial drawbacks. The aim of the study was to design and evaluate an optimized tool for rapid molecular detection of fetal aneuploidies. We established a novel single-day method using a chip-based platform, the QuantStudio 3D Digital PCR system. In order to assess the clinical usefulness of our screening test, we analyzed 133 prenatal samples. The difference in distributions of euploid and aneuploid samples identified the ploidy of each of the target chromosomes with high precision. The distribution of the chromosome ratio for euploid and aneuploid samples showed a statistically significant result (p = 0.003 for trisomy 13, p = 0.001 for trisomies 18 and 21, Mann–Whitney U test). Our results suggest that this novel chip-based approach provides a tool for rapid, technically simple, cost-effective screening for common fetal aneuploidies.

Highlights

3 to 5% of all clinically recognized pregnancies are complicated by birth defects or genetic disorders [1]
We developed a novel chip-based Digital PCR (dPCR) system for a rapid testing of the most common fetal aneuploidies
The method is based on the concept of digital PCR, which relies on the precise quantification of single template molecules without standards

Summary

Introduction

3 to 5% of all clinically recognized pregnancies are complicated by birth defects or genetic disorders [1]. Fetal nuchal translucency (NT) thickness and maternal serum free β-human chorionic gonadotropin (β-hCG) and pregnancy-associated plasma protein-A (PAPP-A) are the key indicators for aneuploidy risk calculation at 11 to 13 + 6 weeks of gestation [2]. For high risk pregnancies diagnostic prenatal testing can be performed by invasive sampling and karyotyping [3]. The incidence of aneuploidies in clinically diagnosed early miscarriages is greater than 50%. It is estimated that fetal aneuploidies account for 6–11% of all stillbirths and neonatal deaths [2]. 13, 18, 21, X, Y chromosome aneuploidies are the most common aberrations and account for more than 80% of the clinically significant prenatally diagnosed chromosomal abnormalities [4]. The incidence of trisomy depends on maternal age and shows geographical differences. Trisomy 13 and 18 have a much lower incidence, 1.77 (1.68–1.86) and 4.67 (4.52–4.82) respectively [5]

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