What is the consistency of the Preimplantation Genetic Testing for Aneuploidy (PGT-A) between the two platforms?

The use of prenatal chromosome screening can increase pregnancy rates but are the results consistent across different PGT-A/PGS testing platforms...
Author: Karen
Translator: Phillip

Comprehensive Chromosome Screening (CCS) has flourished, progressing from early-stage Fluorescent In Situ Hybridization (FISH) to the current Array Comparative Genomic Hybridization (array CGH) technology for analyzing the entire genome. However, FISH has a poor resolution for chromosomes, while although array CGH can detect all 23 pairs of chromosomes, its ability to detect low-rate mosaicisms is limited in the context of pre-implantation genetic testing. With the advent of Next-Generation Sequencing (NGS), its advantages of speed, cost-effectiveness, and superior detection of mosaicisms have made it the mainstream technology in the market. Among the widely used sequencing methodologies are fluorescent markers and semiconductor sequencing technology.

Comparison of two platforms for PGT-A

This article focuses on the consistency of PGT-A results between the two platforms using automatic and manual identification. The following is a comparison of the throughput, hands-on time, turnaround time, and identification method between the two platforms.



Hands-on time

Turnaround time


Ion S5Ⓡ (Thermo)


5 hours

1.5 day


MiseqⓇ (Illumina)


8 hours

1.5 day



Experimental Design and Procedures

The experimental design is divided into two stages, the first stage uses cell lines simulating different ratios of mosaic for sensitivity and specificity assessment, and the second stage is the clinical assay. The experimental workflow is shown in the figure below:

  • After receipt of the sample, Lysis and Pre-Amplification will be performed first, and then the sample will be separated for follow-up experiments.

  • In the automated identification platform, the DNA was then amplified and barcoded, and put into the Chef instrument with robotic arm for automated templating, then sequenced, and the experimental results were analyzed by the software.The table in the figure shows the results of the analysis, indicating the CNV of all chromosomes and their abnormal regions.

  • In the manual identification platform, the library is prepared by hand, put into the instrument for sequencing, and then interpreted by human eyes.

The gray background is the common steps of both, the yellow background is the automatic identification platform, and the purple background is the manual identification platform. The thick box represents the automatic steps.

Result 1: Cell line sensitivity and specificity assessment

In the first stage, we simulated different ratios of mosaic DNA using cell lines and observed whether the Copy Number Variation (CNV) had the expected trend.

(figure 1-a) Automatic identification

(figure 1-b) Manual identification

Next, the sensitivity and specificity of the two platforms were evaluated using cell lines. Definition of sensitivity: ratio of abnormal detections to all abnormal detections (Figure 2-a); Definition of specificity: the ratio of detected normal detections to all normal detections (Figure 2-b).

The results showed that both platforms showed the expected trend. There is no statistical difference in sensitivity and specificity between the two platforms, whether automatic or manual.

Experimental result 2: Clinical examination consistency assessment

A total of 40 participants with a mean age of 37.2 ± 4.3 years were included in the second phase of the clinical trial. 589 eggs were retrieved, with 514 mature MII and 386 fertilized eggs (2PN). Finally, a total of 108 blastocysts were performed in PGT-A. One of them was not amplified successfully. First, we compared the chromosomal results of the blastocysts, and then analyzed the results of each chromosome pair in more detail, and the results are as follows:



Automatic identification

Manual identification

Number of embryos tested



Number of embryos with conclusive result



Number of embryos with inconclusive result



Ploidy conclusion





Low-rate mosaicism



High-rate mosaicism






Number of concordant embryos


Concordance per embryo




Automatic identification

Manual identification

Total chromosome pairs



Chromosomes with conclusive result



Chromosomes with inconclusive result



Chromosome category





Low-rate mosaic



High-rate mosaic






Overall concordant chromosome pairs


Concordance rate per chromosome pair



The results showed 99.0% concordance for the blastocyst results and 99.5% concordance for each chromosome pair analyzed.

The consistency evaluation of the two platforms is summarized as follows:

  1. Sensitivity and specificity assessments using cell lines are similar, with no statistical difference.

  2. Whether analyzing blastocyst or chromosome pair results, the concordance rate is high.

  3. In both PGT-A platforms, whether it is an automatic identification or manual identification, it has a high degree of accuracy and consistency.

The conclusion of this study is: no matter which PGT-A platform is used, the detection results with high consistency can be obtained. Advances in reproductive medicine allow us to use PGT-A plus correct implantation time, and exclude immune and thrombotic factors, the pregnancy rate can be as high as 80%!

*This article only reflects the treatment status at the time of writing, and the actual situation should be discussed with the doctor.


  1. PGT-A and PGS are both synonymous with preimplantation chromosome screening. The current mainstream protocol is to culture the embryos to the blastocyst stage and sample 3-5 cells from the trophectoderm cells that will later develop into the placenta for testing. By amplifying, librarying and sequencing the DNA in the cells, the number of chromosomes in the embryo is calculated and analyzed by comparing it with standard genomic sequences. The normal number of embryonic chromosomes has been shown in many studies to have a high positive correlation with pregnancy rates.

  2. The sequencing principles and data processing logic of each PGT-A platform are different, and different platforms have different strengths. The difference in analysis results between platforms for the same specimen is a major concern for physicians and laboratory personnel, and this is what this study aims to investigate. From the comparative data of standard cell lines and clinical samples, the two platforms have statistically credible accuracy and consistency rates, and there is no difference between them.

  3. After the introduction of the first sequencing analysis system in 2014, and after five years of use, we felt the need to provide more efficient testing services to our customers, so we purchased an automated sequencing platform to meet the expectations of most couples seeking a baby. To strive for excellence in the invisible places is the self-challenge that Stork Fertility Center has always insisted on.