Find research datasets worth reusing

opencc-by-4.0Sep 2024View details →

Human salivary microbiota diversity according to ethnicity, sex, TRPV1 variants and sensitivity to capsaicin

Open the record for dataset details and reuse information.

opencc-by-4.0Oct 2024View details →

Carriers of a single cystic fibrosis transmembrane conductance regulator pathogenic variant and COVID-19 in pregnancy: A retrospective longitudinal cohort study

Open the record for dataset details and reuse information.

opencc-zeroDec 2014View details →

Data from: Gene-wise association of variants in four lysosomal storage disorder genes in neuropathologically confirmed Lewy Body disease

Objective: Variants in GBA are associated with Lewy Body (LB) pathology. We investigated whether variants in other lysosomal storage disorder (LSD) genes also contribute to disease pathogenesis. Methods: We performed a genetic analysis of four LSD genes including GBA, HEXA, SMPD1, and MCOLN1 in 231 brain autopsies. Brain autopsies included neuropathologically defined LBD without Alzheimer Disease (AD) changes (n = 59), AD without significant LB pathology (n = 71), Alzheimer disease and lewy body variant (ADLBV) (n = 68), and control brains without LB or AD neuropathology (n = 33). Sequencing of HEXA, SMPD1, MCOLN1 and GBA followed by 'gene wise' genetic association analysis was performed. To determine the functional effect, a biochemical analysis of GBA in a subset of brains was also performed. GCase activity was measured in a subset of brain samples (n = 64) that included LBD brains, with or without GBA mutations, and control brains. A lipidomic analysis was also performed in brain autopsies (n = 67) which included LBD (n = 34), ADLBV (n = 3), AD (n = 4), PD (n = 9) and control brains (n = 17), comparing GBA mutation carriers to non-carriers. Results: In a 'gene-wise' analysis, variants in GBA, SMPD1 and MCOLN1 were significantly associated with LB pathology (p range: 0.03–4.14 x10-5). Overall, the mean levels of GCase activity were significantly lower in GBA mutation carriers compared to non-carriers (p<0.001). A significant increase and accumulation of several species for the lipid classes, ceramides and sphingolipids, was observed in LBD brains carrying GBA mutations compared to controls (p range: p<0.05-p<0.01). Interpretation: Our study indicates that variants in GBA, SMPD1 and MCOLN1 are associated with LB pathology. Biochemical data comparing GBA mutation carrier to non-carriers support these findings, which have important implications for biomarker development and therapeutic strategies.

opencc-zeroDec 2013View details →

Data from: Comparative genomics of Methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong

Background: The ST239 lineage is a globally disseminated, multiply drug-resistant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). We performed whole-genome sequencing of representative HA-MRSA isolates of the ST239 lineage from bacteremic patients in hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three published complete genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster strains were also undertaken. Results: Homology analysis, based on highest-percentage nucleotide identity, indicated that HK isolates were closely related to TW20, whereas BJ isolates were more closely related to T0131 from Tianjin. Phylogenetic analysis, incorporating a total of 30 isolates from different continents, revealed that strains from HK clustered with TW20 into the 'Asian clade', whereas BJ isolates and T0131 clustered closely with strains of the 'Turkish clade' from Eastern Europe. HK isolates contained the typical φSPβ-like prophage with the SasX gene similar to TW20. In contrast, BJ isolates contained a unique 15 kb PT1028-like prophage but lacked φSPβ-like and φSA1 prophages. Besides distinct mobile genetic elements (MGE) in the two clusters, OGG analyses and whole-genome alignment of these clusters highlighted differences in genes located in the core genome, including the identification of single nucleotide deletions in several genes, resulting in frameshift mutations and the subsequent predicted truncation of encoded proteins involved in metabolism and antimicrobial resistance. Conclusions: Comparative genomics, based on de novo assembly and deep sequencing of HK and BJ strains, revealed different origins of the ST239 lineage in northern and southern China and identified differences between the two clades at single nucleotide polymorphism (SNP), core gene and MGE levels. The results suggest that ST239 strains isolated in Hong Kong since the 1990s belong to the Asian clade, present mainly in southern Asia, whereas those that emerged in northern China were of a distinct origin, reflecting the complexity of dissemination and the dynamic evolution of this ST239 lineage.

opencc-zeroAug 2019View details →

A Streamlined and High-Throughput Error-Corrected Next-Generation Sequencing Method for Low Variant Allele Frequency Quantitation

Quantifying mutant or variable allele frequencies (VAFs) of ≤10−3 using next-generation sequencing (NGS) has utility in both clinical and nonclinical settings. Two common approaches for quantifying VAFs using NGS are tagged single-strand sequencing and duplex sequencing. While duplex sequencing is reported to have sensitivity up to 10−8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥10−4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10−5 to 10−1, then applied and tested on native genomic DNA. For both sources of DNA, there is a proportional increase in the observed VAF to input VAF from 10−4 to 100% mutant samples. Variability of quantitation was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥10−4, and it was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with the potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal-appearing tissue.

opencc-zeroDec 2018View details →

Data from: A synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers

Mast cell tumours are the most common type of skin cancer in dogs, representing a significant concern in canine health. The molecular pathogenesis is largely unknown, but breed-predisposition for mast cell tumour development suggests the involvement of inherited genetic risk factors in some breeds. In this study, we aimed to identify germline risk factors associated with the development of mast cell tumours in Labrador Retrievers, a breed with an elevated risk of mast cell tumour development. Using a methodological approach that combined a genome-wide association study, targeted next generation sequencing, and TaqMan genotyping, we identified a synonymous variant in the DSCAM gene on canine chromosome 31 that is associated with mast cell tumours in Labrador Retrievers. DSCAM encodes a cell-adhesion molecule. We showed that the variant has no effect on the DSCAM mRNA level but is associated with a significant reduction in the level of the DSCAM protein, suggesting that the variant affects the dynamics of DSCAM mRNA translation. Furthermore, we showed that the variant is also associated with mast cell tumours in Golden Retrievers, a breed that is closely related to Labrador Retrievers and that also has a predilection for mast cell tumour development. The variant is common in both Labradors and Golden Retrievers and consequently is likely to be a significant genetic contributor to the increased susceptibility of both breeds to develop mast cell tumours. The results presented here not only represent an important contribution to the understanding of mast cell tumour development in dogs, as they highlight the role of cell adhesion in mast cell tumour tumourigenesis, but they also emphasise the potential importance of the effects of synonymous variants in complex diseases such as cancer.

opencc-zeroAug 2021View details →

Data from: Pathogenic effect of TP73 gene variants in people with amyotrophic lateral sclerosis

Objective: To identify novel disease associated loci for amyotrophic lateral sclerosis (ALS), we utilized sequencing data and performed in vitro and in vivo experiments to demonstrate pathogenicity of mutations identified in TP73. Methods: We analyzed exome sequences of 87 sporadic ALS patients and 324 controls, with confirmatory sequencing in independent ALS cohorts of >2,800 patients. For the top hit, TP73, a regulator of apoptosis, differentiation, and a binding partner as well as homolog of the tumor suppressor gene TP53, we assayed mutation effects using in vitro and in vivo experiments. C2C12 myoblast differentiation assays, characterization of myotube appearance, and immunoprecipitation of p53-p73 complexes were perform in vitro. In vivo, we used CRISPR/Cas9 targeting of zebrafish tp73 to assay motor neuron number and axon morphology. Results: Four heterozygous rare, nonsynonymous mutations in TP73 were identified in our sporadic ALS cohort. In independent ALS cohorts, we identified an additional 19 rare, deleterious variants in TP73. Patient TP73 mutations caused abnormal differentiation and increased apoptosis in the myoblast differentiation assay, with abnormal myotube appearance. Immunoprecipitation of mutant ΔN-p73 demonstrated that patient mutations hinder ΔN-p73's ability to bind p53. CRISPR/Cas9 knockout of tp73 in zebrafish led to impaired motor neuron development and abnormal axonal morphology, concordant with ALS pathology. Conclusion: Together, these results strongly suggest that variants in TP73 correlate with risk for ALS and indicate a novel role for apoptosis in ALS disease pathology.

opennotspecifiedNov 2011View details →

FIGURE 1 in Sexual morphs and colour variants of Aphis (formerly Toxoptera) odinae (Hemiptera, Aphididae) in Japan

FIGURE 1. Slide-mounted specimens of A. odinae: a, fundatrix; b, oviparous female; c, male.

opencc-zeroSep 2021View details →

Supplementary material - measuring atrophy in the behavioral variant of frontotemporal dementia: a multicenter study

Objective: To test the hypothesis that accesible and reproducible measures of atrophy may have high clinical utility for the study of patients with the behavioral variant of frontotemporal dementia (bvFTD), we determined the diagnostic and prognostic value of six previously-validated visual atrophy scales (VAS) and the Magnetic Resonance Parkinsonism Index (MRPI). Methods: We gathered data from 235 patients with bvFTD and 225 age- and MRI-matched healthy controls from three centers. One hundred twenty-one bvFTD participants had underlying frontotemporal lobar degeneration (bvFTD-FTLD) and nineteen did not have FTLD (bvFTD-noFTLD). Blinded clinicians applied VAS and the MRPI was calculated with a fully-automated approach. Cortical thickness and subcortical gray matter volumes were also calculated for comparison. We used linear mixed and Cox regression models to evaluate the ability of atrophy measures to predict clinical deterioration and survival. Results: The bvFTD atrophy score (sum of atrophy scores in orbitofrontal, anterior cingulate, anterior temporal, medial temporal lobe and frontal insula regions) was usefull to discriminate bvFTD-FTLD from healthy controls (AUROC=.930; 95%CI, .903 to .957) and bvFTD-FTLD from bvFTD-noFTLD (AUROC=.880; 95%CI, .787 to .972) and had similar accuracy than cortical thickness and subcortical gray matter volumes. MRPI was increased in patients with bvFTD with underlying 4R tauopathies. The bvFTD atrophy score was an independent predictor of clinical deterioration and survival in bvFTD. Conclusions: In bvFTD, the bvFTD atrophy score can increase the diagnostic certainty of underlying FTLD and predict disease progression. Moreover, the MRPI can identify bvFTD participants with an increased risk of underlying 4R tauopathies.

opencc-by-4.0Sep 2021View details →

Supplementary data --The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner

Supplementary data for the Cell Systems manuscript 'The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner', by Hamelin et al. GISAID_Authors_Recognition_2021-01-19. Metadata concerning the SARS-CoV-2 viral sequences analysed, and generously provided by GISAID.  Table S1. SARS-CoV-2 mutations identified from 330,246 GISAID entries (December 31st 2020), Related to Figure 1 and Figure 2. SARS-CoV-2 mutations at the nucleic and amino acid level are indicated. Number of genomes carrying mutation show the frequency of individual mutations among all SARS-CoV-2 variants.  Table S2. SARS-CoV-2 prevalent mutations identified from 330,246 GISAID entries (December 31st 2020) and detected in at least 100 individuals, Related to Figure 2. Table S3. Previously validated SARS-CoV-2 CD8+ T cell epitopes and their matching mutated forms identified in this study, Related to Figure 1 and Figure 2. Table S4. List of previously validated SARS-CoV-2 CD8+ T cell epitopes. Epitopes were downloaded from https://www.mckayspcb.com/SARS2TcellEpitopes/ (as of January 2021). This database has effectively catalogued all SARS-CoV-2 CD8+ epitopes validated by 18 separate studies. See Quadeer et al. 2021 for details, Related to Figure 1 and Figure 2.

Figure 2 from: Kilian N (2012) Two new mountainous species of Lactuca (Cichorieae, Asteraceae) from Iran, one presenting a new, possibly myrmecochorous achene variant. PhytoKeys 11: 61-77. https://doi.org/10.3897/phytokeys.11.2563

Figure 2 - Lactuca hazaranensis – A habit, left plant of holotype sheet B–G capitula, all to the same scale, before flowering (B–C), at fruiting (D–E), after fruiting (F–G); H plant in natural habitat A–G from the holotype H plant in the natural habitat at the type locality; photograph by M. Eskandari, 10 Aug 2010.

Figure 1 from: Kilian N (2012) Two new mountainous species of Lactuca (Cichorieae, Asteraceae) from Iran, one presenting a new, possibly myrmecochorous achene variant. PhytoKeys 11: 61-77. https://doi.org/10.3897/phytokeys.11.2563

Figure 1 - Lactuca denaensis – A habit, acaulescent form B–F capitula, all to the same scale, before flowering (B–D), with faded flowers (E), after flowering (F); G details of synflorescence, one capitulum at fruiting. – All from Remaudière, 5252E (IRAN 10625)

Figure 4 from: Kilian N (2012) Two new mountainous species of Lactuca (Cichorieae, Asteraceae) from Iran, one presenting a new, possibly myrmecochorous achene variant. PhytoKeys 11: 61-77. https://doi.org/10.3897/phytokeys.11.2563

Figure 4 - Distribution of Lactuca hazaranensis (circles) and the related species Lactuca rosularis (squares) and Lactuca denaensis (rhomb, actucal position as indicated by arrow), as well as of Cicerbita polyclada (triangles). – Georeferenced map based on the known collections (see Appendix and supplemented by collection cited in Kirpicznikov 1964 and Tuisl 1977) and generated with DIVA-GIS (Hijmans 2011) using an adaptation of the SRTM 90 m digital elevation data (CGIAR-CSI 2004).

Figure 3 from: Kilian N (2012) Two new mountainous species of Lactuca (Cichorieae, Asteraceae) from Iran, one presenting a new, possibly myrmecochorous achene variant. PhytoKeys 11: 61-77. https://doi.org/10.3897/phytokeys.11.2563

Figure 3 - Achenes of the Lactuca rosularis group and Cicerbita polyclada – A, F–I Lactuca hazaranensis; complete achene (A); achene after loss of easily detachable beak, dorsal view (F); ventral view (G); longitudinal section of achene showing two segments, proximal large segment with embry, distal small segment solid with yellow tissue (H); embryo (I); B Lactuca rosularis C Lactuca denaensis D–E Cicerbita polyclada, complete achene (D) and longitudinal section of distal portion showing apical cavity (E). – A–D and F–H each to the same scale A, F–I from the holotype at IRAN B from Rechinger 55980 B, C from Kotschy 662 (B 100426936) D–E from Strauss 14091 (B 100312952)

Pan-cancer study on variants of canonical miRNA biogenesis pathway components: A pooled analysis

Updated version of 10.5281/zenodo.7248080

Pan-cancer study on variants of canonical miRNA biogenesis pathway components: A pooled analysis

Supplementary Tables S30-S36

Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16

The data set contains: (1) topology (prmtop), (2) coordinate files to the run the simulation (3) A plumed.dat file (4) COLVAR and (5) HILLS files; (6) Trajectory (xtc) file and (7) corresponding pdb file.  The simulations were run as replicates.

Human genetic variants with dbSNP and pseudoDB

Human genetic variants with dbSNP and pseudoDB

Sheep genetic variants with dbSNP and pseudoDB

Sheep genetic variants with dbSNP and pseudoDB