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opencc-by-4.0Aug 2022View details →

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies

Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.   Link to article: https://www.science.org/doi/10.1126/science.abo1984 To match Clinical information (supplementary information) with Sample IDs on Zenodo, please access the Excel table "Additional_note_samples.xlsx" on the github repository: https://github.com/heiniglab/DCM_heart_cell_atlas

opencc-by-4.0May 2022View details →

The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.

Raw data corresponding to graphs in publication: The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines. Files are titled with the figure number. Each graph is on a different tab within the excel spreadsheet.

opencc-zeroAug 2022View details →

Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa

A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as Cannabis sativa (C. sativa), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of C. sativa. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high 𝐹̅ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene SMALLER TRICHOMES WITH VARIABLE BRANCHES 2 to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in C. sativa.

opencc-by-4.0Sep 2022View details →

The impact of genetic variants in the CYP2C8 gene on bladder cancer susceptibility 1 Short Title:Genetic variants on bladder cancer

Four SNPs including rs1934953, rs1934951, rs2275620, and rs17110453 in the CYP2C8 gene were selected and determined in 550 healthy subjects and 217 bladder cancer patients. SNPs genotyping was determined using Agena MassARRAY iPLEX platform.

opencc-by-4.0Sep 2022View details →

SNiffles structural variant vcf SHRSP genome

Variant cell format file generated by Sniffles2/SURVIVOR analysis

opencc-by-4.0Sep 2022View details →

ProgressiveMauve alignment of Xanthomonas oryzae pv. oryzae PXO35 assembly variants

Archive containing the alignment of eight assembly variants using different assembly programs and sequencing technologies. This alignment has been produced by the progressiveMauve algorithm (<a href="https://doi.org/10.1371/journal.pone.0011147">https://doi.org/10.1371/journal.pone.0011147</a>). The main alignment file is "PXO35_assembly_comparison", which can be opened and viewed interactively using the mauve program (<a href="https://darlinglab.org/mauve/download.html">https://darlinglab.org/mauve/download.html</a>).

Convergence in Determining Enzyme Functional Descriptors across Kemp Eliminase Variants

SI data for the paper with the same title: Initial topology and coordinate files for 18 KE07-R7-2.

Supplement table for Sparano et al.: Classic and follicular variant of papillary thyroid microcarcinoma: two different phenotypes beyond tumour size. Journal of the Endocrine Society, 2022.

Sparano et al. Supplement to: Classic and follicular variant of papillary thyroid microcarcinoma: two different phenotypes beyond tumour size. Journal of the Endocrine Society, 2022.

Methods for structural variant detection with long-read sequencing data

SV calls from different long-read based SV callers on sequencing data. SV results evaluated in Methods for structural variant detection with long-read sequencing data. NA24385_Pacbio_HiFi -> HiFi_L1 in paper NA24385_Pacbio_MtSinai -> CLR_L1 in paper NA24385_Pacbio_CLR_SRX7668835 -> CLR_L2 in paper NA24385_Pacbio_CLR_SRX6719924 -> CLR_L3 in paper NA24385_ONT_Promethion -> Nano_L1 in paper

opencc-zeroOct 2022View details →

Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main ABO allele groups: ABO*A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire ABO gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per ABO group were re-sequenced using Illumina and PacBio technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered four genetic variants putatively specific for ABO*A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

Archaic variants from Altai, Vindija, Chagyrskaya and Denisova (hg19)

This is the variants for Altai, Vindija, Chagyrskaya and Denisova mapped to hg19.

SARS-CoV2-Variants

Ionic current-time data of SARS-CoV-2 variants

opencc-by-4.0Dec 2017View details →

Chromatin accessibility QTL lead variants in macrophages stimulated with IFNg and Salmonella

Lead caQTL variants from RASQUAL and FastQTL analyses.

opencc-by-4.0Apr 2024View details →

On a Microservice System Benchmark with Multiple Architected Variants for Software Engineering Research

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opencc-by-4.0May 2024View details →

A mathematical model of COVID-19 with multiple variants of the virus under optimal control in Ghana

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opencc-by-4.0May 2024View details →

Data underlying the article: Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico

This repository contains the scripts and data for the project published in Frontiers in Molecular Biosciences under the title: Molecular insights into disease-associated glutamate transporter (EAAT1 / SLC1A3) variants using in silico and in vitro approaches (DOI <a href="https://www.frontiersin.org/articles/10.3389/fmolb.2023.1286673/full">10.3389/fmolb.2023.1286673</a>).

opencc-by-4.0May 2024View details →

Performance data for 10 DE variants on BBOB benchmark suite in 10 dimensions (13-24 problems)

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opencc-zeroMay 2024View details →

Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations

The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.

opencc-zeroJun 2024View details →

Data from: HLA-G 14 bp variant is associated with exercise-induced oxygen desaturation in the post-COVID-19 condition

The HLA-G molecule has been related to the lung inflammatory process in respiratory diseases. A 14 pb insertion/deletion in the gene encoding HLA-G has been associated with differential levels of the HLA-G molecule in plasma and with the severity of infectious diseases. Therefore, this study evaluates the association of the HLA-G variant 14 pb insertion/deletion (rs371194629) with COVID-19 susceptibility, severity, and oxygen desaturation in the post-COVID condition. We included 621 patients with severe COVID-19 hospitalized in a third-level hospital; 520 subjects Non-COVID (recruited previous to the COVID-19 pandemic); and 101 patients that were followed after discharge of COVID-19 (46.4% presenting exercise-induced oxygen desaturation). The severity of COVID-19 was evaluated through the invasive mechanical ventilation (IMV) requirement. We found that the DD genotype was more frequent among patients requiring IMV than non-IMV (0.372 vs 0.290, p= 0.046, OR =1.45, 95%CI = 1.01-2.08, dominant model). This genotype was also associated with exercise-induced oxygen desaturation in post-COVID patients (0.435 vs 0.196, p=0.011, OR=3.15, CI 95%=1.28-7.79, dominant model). The allele and genotype frequencies were similar when COVID-19 and non-COVID subjects were compared. Thus, the DD genotype of rs371194629 HLA-G was associated with COVID-19 severity and post-COVID condition.