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Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

Improved noninvasive fetal variant calling using standardized benchmarking approaches.

Tom Rabinowitz¹, Shira Deri-Rozov¹, Noam Shomron¹

¹Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

Computational and Structural Biotechnology Journal

|January 29, 2021

Summary

Noninvasive prenatal testing (NIPT) now offers comprehensive fetal genotyping for genetic variants using cell-free DNA (cfDNA). Benchmarking improved performance, especially for indels and biparental loci, advancing genome-wide NIPT for clinical use.

Keywords:

NIPD NIPT Noninvasive prenatal diagnosis Variant calling cell-free DNA cfDNA

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Last Updated: Nov 19, 2025

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Area of Science:

Genetics
Molecular Biology
Bioinformatics

Background:

Noninvasive prenatal testing (NIPT) analyzes cell-free DNA (cfDNA) in maternal blood for fetal genetic conditions.
Current NIPT primarily screens for chromosomal abnormalities, often replacing invasive diagnostic tests.
Recent advancements aim for genome-wide fetal genotyping, identifying all genetic variants and mutations.

Purpose of the Study:

To benchmark variant calling pipelines for genome-wide noninvasive prenatal diagnosis (NIPD).
To improve the performance of NIPT for identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), especially in biparental loci.
To establish standardized methods for evaluating genome-wide NIPT accuracy.

Main Methods:

Utilized standardized benchmarking methods for variant calling pipelines.
Applied these methods to noninvasive fetal variant calling using cfDNA.
Focused analysis on coding regions to enhance genotyping performance.

Main Results:

The best-performing pipeline significantly improved noninvasive fetal genotyping accuracy.
Performance gains were particularly notable for indels and biparental loci.
Demonstrated the effectiveness of standardized benchmarking in this field.

Conclusions:

Genome-wide NIPT for point mutations requires standardized evaluation concepts.
Benchmarking is crucial for advancing noninvasive prenatal diagnosis.
This study brings comprehensive NIPD closer to clinical application, potentially reducing pregnancy-related anxiety.