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opencc-by-4.0Apr 2024View details →

Transposase-Assisted Tagmentation: An Economical and Scalable Strategy for Single-Worm Whole-Genome Sequencing (elegans)

AlphaMissense identifies 23 million human missense variants as likely pathogenic, but only 0.1% have been clinically classified. To experimentally validate these predictions, chemical mutagenesis presents a rapid, cost-effective method to produce billions of mutations in model organisms. However, the prohibitive costs and limitations in the throughput of whole-genome sequencing (WGS) technologies, crucial for variant identification, constrain its widespread application. Here, we introduce a Tn5 transposase-assisted tagmentation technique for conducting WGS in C. elegans, E. coli, S. cervisiae, and C. reinhardtii. This method, demands merely 20 minutes of hands-on time for a single worm or single-cell clones and incurs a cost below 10 US dollars. It effectively pinpoints causal mutations in mutants defective in cilia or neurotransmitter secretion and in mutants synthetically sterile with a variant analogous to the oncogenic BRAF(V600E) mutation. Integrated with chemical mutagenesis, our approach can generate and identify missense variants economically and efficiently, facilitating experimental investigations of missense variants in diverse species.

opencc-by-4.0Jun 2024View details →

CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING

Table S1. Metadata for the 21 Salmonella enterica genomes used to perform phylogenetic analysis. Table S2. Comprehensive overview of sequences of targeted serovars present in the genomic database by prescribed selection criteria.

opencc-by-4.0Jun 2024View details →

CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING

Table S1: Metadata for the 317 Salmonella Heidelberg genomes retrieved from the Enterobase database to perform genomic analysis in this study.

Fig 6 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 6. Venn diagram depicting orthologous groups of predicted proteins encoded in four sphingobacterial genomes. C1: Sphingobacterium spiritivorum ATCC 33300; C2: Sphingobacterium paucimobilis HER1398; C3: Sphingobacterium thalpophilum DSM11723; and C4: Sphingobacterium deserti ZWT. doi:10.1371/journal.pone.0122254.g006

Fig 4 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 4. Genome map of Sphingobacterium deserti sp. nov. ZWT. Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. doi:10.1371/journal. pone.0122254.g004

Fig 1 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 1. Electron micrograph of the cell morphology of strain ZWT. doi:10.1371/journal.pone.0122254.g001

Fig 5 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

Fig 5. Whole-genome optical mapping barcode of Sphingobacterium deserti sp. nov. ZWT. Vertical lines represent restriction sites; distances between lines represent fragment sizes.

opencc-by-4.0Sep 2024View details →

Whole genome RNA-sequencing reveals modulation of genes related to brain disorders by Withania somnifera in human neuroblastoma SK-N-SH cells

Table S1: Human reference genome based differential gene expression; Figure S1: Reactome Pathway (50 μg/mL_3h vs C_3h); Figure S2: Reactome Pathway (50 μg/mL_9h vs C_9h); Figure S3: Reactome pathway (100 μg/mL_3h vs C_3h); Figure S4: GO Dose comparison; Reactome pathway (100 μg/mL_3h vs 50 μg/mL_3h); Figure S5: GO Dose comparison; Reactome pathway (100 μg/mL_9h vs 50 μg/mL_9h); Figure S6: GO Time comparison; Reactome pathway (50 μg/mL_9h vs 50 μg/mL_3h); Figure S7: GO Time comparison; Reactome pathway (100 μg/mL_9h vs 100 μg/mL_3h); Table S2: Disease ontology analysis of 100 μg/mL_3h vs 50 μg/mL_3h WS-treated SK-N-SH cells; Table S3: Disease ontology analysis of 100 μg/mL_9h vs 50 μg/mL_9h WS-treated SK-N-SH cells; Table S4: Disease ontology analysis of 100 μg/mL_9h vs 100 μg/mL_3h WS-treated SK-N-SH cells.

opencc-zeroDec 2014View details →

Data from: Whole genome sequencing shows sleeping sickness relapse is due to parasite regrowth and not reinfection

The trypanosome Trypanosoma brucei gambiense (Tbg) is a cause of human African trypanosomiasis (HAT) endemic to many parts of sub-Saharan Africa. The disease is almost invariably fatal if untreated and there is no vaccine, which makes monitoring and managing drug resistance highly relevant. A recent study of HAT cases from the Democratic Republic of the Congo reported a high incidence of relapses in patients treated with melarsoprol. Of the 19 Tbg strains isolated from patients enrolled in this study, four pairs were obtained from the same patient before treatment and after relapse. We used whole genome sequencing to investigate whether these patients were infected with a new strain, or if the original strain had regrown to pathogenic levels. Clustering analysis of 5938 single nucleotide polymorphisms supports the hypothesis of regrowth of the original strain, as we found that strains isolated before and after treatment from the same patient were more similar to each other than to other isolates. We also identified 23 novel genes that could affect melarsoprol sensitivity, representing a promising new set of targets for future functional studies. This work exemplifies the utility of using evolutionary approaches to provide novel insights and tools for disease control.

opencc-zeroDec 2012View details →

Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.

opencc-zeroAug 2019View details →

Data from: Whole genome sequencing and rare variant analysis in essential tremor families

Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n=40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.

opencc-by-4.0Oct 2021View details →

Automated application to assist in detecting novel gene-disease associations following whole genome sequencing

Results files, analysis scripts and original software from TierUp reanalysis performed on June 2020. These data contribute to the publication titled "Automated reanalysis application to assist in detecting novel gene-disease associations following whole genome sequencing".  <ul> <li> tierup_v0-3-0.tar.gz - source code used in the reanalysis </li> <li> tierup_results_summary.tar.gz - raw data and python code for publication figures </li> </ul>

opencc-zeroMay 2023View details →

Supporting data for: Whole genome sequencing reveals fine-scale environment associated divergence near the range limits of a temperate reef fish

Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (Tautogolabrus adspersus), is a temperate reef fish with both pelagic early life history stages and strong site-associated homing as adults; the species is also of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. We aimed to characterize genomic and geographic differentiation of cunner in the Northwest Atlantic. To achieve this, a chromosome-level genome assembly for cunner was produced and used to characterize spatial population structure throughout Atlantic Canada using whole genome resequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes; whole genome resequencing of 803 individuals from 20 locations from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four regional Atlantic Canadian groups. Pairwise FST and selection scans revealed signals of differentiation and selection at discrete genomic regions, including adjacent peaks on chromosome 10 across multiple pairwise comparisons (i.e., FST 0.5–0.75). Redundancy analysis suggested association of environmental variables related to benthic temperature and oxygen range with genomic structure. Results suggest regional scale diversity in this temperate reef fish and can directly inform the collection and translocation of cunner for aquaculture applications and the conservation of wild populations throughout the Northwest Atlantic.

opencc-by-4.0Aug 2023View details →

Estimating the rates of adaptive evolution in fungal species using whole-genome sequences - v0.1

GitHub script version v0.1

Public Perception and Policy for SARS-CoV-2 Whole Genome Sequencing and Genomics for All

ClinicalTrials.gov study NCT06441981. IPD Sharing: NO. Countries: 1. Publications: 2.

Rapid Whole Genome Sequencing Study

ClinicalTrials.gov study NCT03385876. IPD Sharing: NO. Countries: 1. Publications: 13.

Precision Medicine for Liver Tumours With Quantitative Magnetic Resonance Imaging and Whole Genome Sequencing

ClinicalTrials.gov study NCT04597710. IPD Sharing: NO. Countries: 1. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

An Ancillary Pilot Trial Using Whole Genome Sequencing In Patients With Advance Refractory Cancer

ClinicalTrials.gov study NCT01443390. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Diagnostic Odyssey: Whole Genome Sequencing (WGS)

ClinicalTrials.gov study NCT03458962. IPD Sharing: NO. Countries: 1. Publications: 2.