ArticleFrontiers in genetics2021
Allelic Dropout Is a Common Phenomenon That Reduces the Diagnostic Yield of PCR-Based Sequencing of Targeted Gene Panels.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels.Animal genetics · 2026Article
- Missing or Mis-Telling the Story? Trade-Offs for Restriction-Site Associated Compared to Whole Genome Sequencing.Molecular ecology · 2026Article
- Methodological Assessment of High-Throughput Sequencing Platforms: Illumina vs. MGI in Clinical-GradeInternational journal of molecular sciences · 2025Article
- Review
- Amplicon-based targeted next-generation sequencing using dried blood spots for 46,XY differences/disorders of sex development: Aiming for diagnosis by minimally invasive testing.Clinical pediatric endocrinology : case reports and clinical investigations : official journal of the Japanese Society for Pediatric Endocrinology · 2025Article
- Benchmarking Nanopore Sequencing for CLN2 (TPP1) Mutation Detection: Integrating Rapid Genomics and Orthogonal Validation for Precision Diagnostics.International journal of molecular sciences · 2025Article
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- Genetic Conservation and Population Management of Non-Human Primates: Parentage Determination Using Seven Microsatellite-Based Multiplexes.Ecology and evolution · 2025Article
- Application of Digital Polymerase Chain Reaction (dPCR) in Non-Invasive Prenatal Testing (NIPT).Biomolecules · 2025Review
- Allelic dropout in the endoglin (Frontiers in genetics · 2025Article
- High-resolution genetic map and SNP chip for molecular breeding inHorticulture research · 2024Article
- Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.Scientific reports · 2024Article
- Human complex mixture analysis by "FD Multi-SNP Mixture Kit".Frontiers in genetics · 2024Article
- A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii.Parasites & vectors · 2023Article
- Long-Read Sequencing in Blood Group Genetics.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2023Review
- Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat.Genes · 2023Article
- A pilot study of on-site evaluation as external quality assessment for ISO 15189 accreditation of laboratories performing next-generation sequencing oncology tests.Journal of clinical laboratory analysis · 2023Article
- Application of Long-Read Nanopore Sequencing to the Search for Mutations in Hypertrophic Cardiomyopathy.International journal of molecular sciences · 2022Article
- Genotype Complements the Phenotype: Identification of the Pathogenicity of an LMNA Splice Variant by Nanopore Long-Read Sequencing in a Large DCM Family.International journal of molecular sciences · 2022Article
- Hereditary Transthyretin-Related Amyloidosis: Genetic Heterogeneity and Early Personalized Gene Therapy.Biomedicines · 2022Review
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Authors and funding
4 authors.
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Abstract
Primary cardiomyopathies (CMPs) are monogenic but multi-allelic disorders with dozens of genes involved in pathogenesis. The implementation of next-generation sequencing (NGS) approaches has resulted in more time- and cost-efficient DNA diagnostics of cardiomyopathies. However, the diagnostic yield of genetic testing for each subtype of CMP fails to exceed 60%. The aim of this study was to demonstrate that allelic dropout (ADO) is a common phenomenon that reduces the diagnostic yield in primary cardiomyopathy genetic testing based on targeted gene panels assayed on the Ion Torrent platform. We performed mutational screening with three custom targeted gene panels based on sets of oligoprimers designed automatically using AmpliSeq Designer® containing 1049 primer pairs for 37 genes with a total length of 153 kb. DNA samples from 232 patients were screened with at least one of these targeted gene panels. We detected six ADO events in both IonTorrent PGM (three cases) and capillary Sanger sequencing (three cases) data, identifying ADO-causing variants in all cases. All ADO events occurred due to common or rare single nucleotide variants (SNVs) in the oligoprimer binding sites and were detected because of the presence of "marker" SNVs in the target DNA fragment. We ultimately identified that PCR-based NGS involves a risk of ADO that necessitates the use of Sanger sequencing to validate NGS results. We assume that oligoprimer design without ADO data affects the amplification efficiency of up to 0.77% of amplicons.
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