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A comparative investigation of single nucleotide variant calling for a personal non-Caucasian sequencing sample
BackgroundDrop** cost and increasing clinical application of whole genome sequencing (WGS) lead a necessity of efficient (accurate and rapid)...
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
BackgroundGenomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on...
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Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
BackgroundAccurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders....
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UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example
BackgroundAt a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of...
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Performance evaluation of pipelines for map**, variant calling and interval padding, for the analysis of NGS germline panels
BackgroundNext-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical,...
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Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data
Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms....
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Genomic variant benchmark: if you cannot measure it, you cannot improve it
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of...
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Evaluation of variant calling tools for large plant genome re-sequencing
BackgroundDiscovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for develo**...
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Whole-genome sequencing and variant discovery of Citrus reticulata “Kinnow” from Pakistan
Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits,...
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Comparison of structural variant callers for massive whole-genome sequence data
BackgroundDetecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational...
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GBA1 in Parkinson’s disease: variant detection and pathogenicity scoring matters
BackgroundGBA1 variants are the strongest genetic risk factor for Parkinson’s disease (PD). However, the pathogenicity of GBA1 variants concerning...
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Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
BackgroundThe widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However,...
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Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing
Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid,...
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Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater
BackgroundCentral Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were...
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Identifying and predicting the pathogenic effects of a novel variant inducing severe early onset MMA: a bioinformatics approach
BackgroundMethylmalonic acidemia (MMA) is a rare metabolic disorder resulting from functional defects in methylmalonyl-CoA mutase. Mutations in the MMAB...
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Targeted sequencing of the Panicum miliaceum gene space and genoty** of variant sites from population genetics studies, combined in a single assay, as a tool for broomcorn millet assisted breeding
Broomcorn millet ( Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor crop with low yields but with a renewed interest for...
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SARS-CoV-2 Mu variant in dogs visiting veterinary clinics during the third pandemic peak in Eastern Colombia
The global presence of SARS-CoV-2 in household pets is acknowledged, yet documentation remains scarce, leaving many regions unexplored. Thus, our...
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A novel homozygous missense variant identified in the myosin VIIA motor domain of a Moroccan patient with usher syndrome
BackgroundUsher syndrome 1 (USH1) is the most severe subtype of Usher syndrome characterized by severe sensorineural hearing impairment, retinitis...
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Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
BackgroundAmino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues...
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Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
BackgroundThe cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation,...
