Improve your Galaxy text life: The Query Tabular Tool

Johnson, James E.; Kumar, Praveen; Easterly, Caleb; Esler, Mark; Mehta, Subina; Eschenlauer, Arthur C.; Hegeman, Adrian D.; Jagtap, Pratik; Griffin, Timothy J.

doi:10.12688/f1000research.16450.1

Cited by 8 publications

(2 citation statements)

References 13 publications

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“…Variant calling was executed with SEQUENCE Pilot, module SeqNext v4.3.1 by JSI medical systems (Ettenheim, Germany). Data of individual patients and combined patient pool ( n = 279) was then queried for the data of the Genome Aggregation Database (gnomAD) and entries in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) (Landrum et al, 2018) using Query Tabular (Johnson et al, 2018) on the Galaxy Server (http://galaxy.bioinf.uni-leipzig.de/). Additionally, variant tables were annotated on the Combined Annotation Dependent Depletion (CADD) (Rentzsch, Witten, Cooper, Shendure, & Kircher, 2019) website.…”

Section: Methodsmentioning

confidence: 99%

Systematic assessment of monogenic etiology in adult‐onset kidney stone formers undergoing urological intervention–evidence for genetic pretest probability

Schönauer

Scherer

Nemitz‐Kliemchen

et al. 2022

American J of Med Genetics Pt C

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Kidney stone disease (KSD) is a prevalent condition associated with high morbidity, frequent recurrence, and progression to chronic kidney disease (CKD). The etiology is multifactorial, depending on environmental and genetic factors. Although monogenic KSD is frequent in children, unbiased prevalence data of heritable forms in adults is scarce. Within 2 years of recruitment, all patients hospitalized for urological kidney stone intervention at our center were consecutively enrolled for targeted next generation sequencing (tNGS). Additionally, clinical and metabolic assessments were performed for genotype-phenotype analyses. The cohort comprised 155 (66%) males and 81 (34%) females, with a mean age at first stone of 47 years (4-86). The diagnostic yield of tNGS was 6.8% (16/236), with cystinuria (SLC3A1, SLC7A9), distal renal tubular acidosis (SLC4A1), and renal phosphate wasting (SLC34A1, SLC9A3R1) as underlying hereditary disorders. While metabolic syndrome traits were associated with late-onset KSD, hereditary KSD was associated with increased disease severity in terms of early-onset, frequent recurrence, mildly impaired kidney function, and common bilateral affection. By employing systematic genetic analysis to a less biased cohort of common adult kidney stone formers, we demonstrate its diagnostic value for establishing the underlying disorder in a distinct proportion. Factors determining pretest probability include age at first stone (<40 years), frequent recurrence, mild CKD, and bilateral KSD.

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Section: Methodsmentioning

confidence: 99%

Systematic assessment of monogenic etiology in adult‐onset kidney stone formers undergoing urological intervention–evidence for genetic pretest probability

Schönauer

Scherer

Nemitz‐Kliemchen

et al. 2022

American J of Med Genetics Pt C

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“…To account for the biological relevance of these point mutations, polymorphisms were classified into genic or intergenic by mapping the SNPs to the reference genome. SNP-matrix tables were manipulated with Query Tabular Tool [112]. In addition, we developed a genotyper tool to provide SNP statistics reporting on the number of individual genotypes in the phylogeny.…”

Section: Core Genome Snp Phylogenymentioning

confidence: 99%

Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21

et al. 2022

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Infections with globally disseminated Shiga toxin-producing Escherichia coli (STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains’ featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.

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A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies

et al. 2022

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To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.

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Improve your Galaxy text life: The Query Tabular Tool

Cited by 8 publications

References 13 publications

Systematic assessment of monogenic etiology in adult‐onset kidney stone formers undergoing urological intervention–evidence for genetic pretest probability

Systematic assessment of monogenic etiology in adult‐onset kidney stone formers undergoing urological intervention–evidence for genetic pretest probability

Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21

A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies

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