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Updated: Aug 2, 2025

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
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A comprehensive performance analysis of sequence-based within-sample testing NIPT methods.

Tom Mokveld1, Zaid Al-Ars2, Erik A Sistermans3

  • 1Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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|April 14, 2023
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Summary
This summary is machine-generated.

The latest Wisecondor version offers superior Non-Invasive Prenatal Testing (NIPT) for fetal copy number variations. This within-sample method provides stable, robust results without costly reference panels.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Non-Invasive Prenatal Testing (NIPT) uses shallow whole genome sequencing for fetal copy number variation detection.
  • Current methods rely on binned genome representations compared to reference panels, which is costly.
  • Within-sample testing methods offer a bias-free alternative by comparing genomic bins within the same sample.

Purpose of the Study:

  • To comprehensively analyze the performance of the Wisecondor within-sample testing method and its variants.
  • To evaluate Wisecondor's effectiveness with both experimental and simulated data.
  • To assess Wisecondor's suitability for detecting fetal copy number variations using paired-end sequencing data.

Main Methods:

  • Performance analysis of Wisecondor and its variants using experimental and simulated datasets.
  • Modification of Wisecondor to leverage paired-end sequencing data.
  • Evaluation of results across various bin sizes and fetal fraction ranges.

Main Results:

  • Wisecondor demonstrated the most stable performance across different bin size scales.
  • The method produced more robust calls with higher Z-scores across all fetal fraction ranges.
  • Alterations to Wisecondor effectively addressed and exploited paired-end sequencing data.

Conclusions:

  • The most recent version of Wisecondor exhibits the best performance.
  • Within-sample testing with Wisecondor provides a cost-effective and accurate approach for NIPT.
  • Wisecondor is a promising tool for reliable fetal copy number variation detection.