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Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of develo** Parkinson’s disease
Single-nucleotide variants (SNVs) associated with Parkinson’s disease (PD) have been investigated mainly through genome-wide association studies....
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Whole Genome Sequencing of African Swine Fever
Next-generation sequencing (NGS) technologies have been powerfully applied in both research and clinical settings for the understanding and control...
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Whole-Genome Sequencing-Based Confirmatory Methods on RT-qPCR Results for the Detection of Foodborne Viruses in Frozen Berries
Accurate detection, identification, and subsequent confirmation of pathogens causing foodborne illness are essential for the prevention and...
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Whole genome sequencing and genomic characterization of a DS-1-like G2P[4] group A rotavirus in Japan
After rotavirus was discovered in 1973, it became the leading pathogen in causing acute gastroenteritis in humans worldwide. In this study, we...
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Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models
BackgroundBreast cancer cell lines (BCCLs) and patient-derived xenografts (PDXs) are the most frequently used models in breast cancer research....
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CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the...
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Whole Genome Sequencing of Porcine Epidemic Diarrhea Virus and Porcine Deltacoronavirus
Swine enteric coronaviruses, such as porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV), are among the most important...
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Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies
Meta-analysis of whole genome sequencing/whole exome sequencing (WGS/WES) studies provides an attractive solution to the problem of collecting large...
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Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features
BackgroundExtension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite...
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Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data
Flaviviruses are a diverse group of RNA viruses, which include the etiological agents of Zika, dengue and yellow fever that are transmitted by...
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Best practices for the interpretation and reporting of clinical whole genome sequencing
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing...
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TMBur: a distributable tumor mutation burden approach for whole genome sequencing
BackgroundTumor mutation burden (TMB) is a key characteristic used in a tumor-type agnostic context to inform the use of immune checkpoint inhibitors...
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Whole genome sequencing and annotation of a lysogenic phage vB_EcoP_DE5 isolated from donkey-derived Escherichia coli
A lysogenic phage vB_EcoP_DE5 (hereafter designated DE5) was isolated from donkey-derived Escherichia coli . The bacteriophage was examined by...
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Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning
BackgroundRapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging task currently...
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Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data
BackgroundAbnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive...
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Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing
Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai...
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Molecular epidemiological characteristics of osteoarthritis-associated Brucella melitensis in China: evidence from whole-genome sequencing-based analysis
BackgroundBrucellosis, develo** complications including arthritis, spondylitis, sacroiliitis, and osteomyelitis, is one of the most common zoonotic...
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Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis
Whole genome sequencing (WGS) improves Mendelian disorder diagnosis over whole exome sequencing (WES); however, additional diagnostic yields and...
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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing
BackgroundKabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone...
