Journal Article

Cost-effective and flexible preimplantation genetic testing (PGT) by nanopore adaptive sampling

Li, Xiaolan, Lu, Sijia, Ren, Zi, Zhang, Shihui, Sun, Peng, Zeng, Haitao, Liang, Xiaoyan, Yang, Ji, Xu, Linan, Su, Wenlong, Ren, Jun, He, Shujing, Fang, Cong, Zhang, Zhiqiang, Ding, Taoli, Jia, Lei

2025

Overview

Genetic diseases encompass a spectrum of disorders resulting from DNA variations. Preimplantation genetic testing (PGT) is a critical strategy for preventing recurrent miscarriage, fetal malformations, and the birth of children affected by chromosomal abnormalities and monogenic disorders. Traditional PGT techniques necessitate comprehensive pedigree genetic data for haplotype linkage analysis. In contrast, PGT employing third-generation sequencing (TGS) has distinct advantages, particularly in cases of incomplete pedigree information, de novo mutations, and complex pathogenic variants. Nevertheless, the widespread application of TGS-based PGT in clinical practice encounters hurdles owing to its high costs. Targeted sequencing technologies present a promising solution by selectively enriching regions of interest while disregarding non-targeted regio n s, offering a more cost-effective and flexible alternative. In this proof-of-principle study, we employed low-coverage short-read next-generation sequencing (NGS), microarray analysis and nanopore adaptive sampling to analyze samples from five couples who carried balanced translocations and HBB gene pathogenic mutations, as well as three additional couples with monogenic diseases caused by mutations in PKD1 , ASNS , or ALPL . Nanopore adaptive sampling successfully identified various mutations and facilitated haplotype linkage analysis, confirming its accuracy and reliability. Successful embryo transfer and subsequent prenatal diagnosis in certain families underscore the potential of nanopore adaptive sampling in assisted reproduction. Compared with traditional PGT techniques based on low-coverage short-read NGS combined with microarray analysis, our work highlights that nanopore adaptive sampling is a promising tool for PGT, offering cost-effective solutions, especially for incomplete pedigrees and de novo mutations, and provides preliminary proof-of-principle evidence for its broader clinical application. Graphical Abstract Workflow summarizing embryonic CNV detection, haplotype analysis, targeted variant profiling, and verification by Sanger sequencing, leading to the transfer of euploid embryos with normal haplotypes

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abnormalities / Adaptive sampling / Analysis / Biotechnology / Birth defects / Blood diseases / Chemistry / Chemistry and Materials Science / Chromosomal disorders / Chromosome aberrations / Chromosome translocations / Cost effectiveness / Cost-Benefit Analysis / Costs / Disease prevention / Disorders / DNA microarrays / DNA sequencing / Economic aspects / Embryo transfer / Embryos / Female / Fetuses / Genes / Genetic disorders / Genetic diversity / Genetic screening / Genetic testing / Genetic Testing - economics / Genetic Testing - methods / Genomes / Haplotype linkage analysis / Haplotypes / HBB gene / High-Throughput Nucleotide Sequencing - economics / High-Throughput Nucleotide Sequencing - methods / Humans / Laboratories / Linkage analysis / Male / Molecular Medicine / Monogenic diseases / Mutation / Nanopores / Nanopores for Biotechnology – From Fabrication to Application / Nanotechnology / Next-generation sequencing / Nucleotide sequencing / Pedigree / Pregnancy / Pregnant women / Preimplantation Diagnosis - economics / Preimplantation Diagnosis - methods / Prenatal diagnosis / Regions of interest (ROIs) / Sampling / Software / Sperm / Third-generation sequencing (TGS)