Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Testing performance of microbial variant callers

The repository contains duplex consensus sequences used for testing three variant callers: <ol> <li>FreeBayes</li> <li>Mutect2</li> <li>loFreq</li> </ol> The data is derived from <a href="https://academic.oup.com/gbe/article/11/10/3022/5572121">Mei et al. 2019</a>.  Gzipped fastq files correspond to time points s0 (0 hours) and s5 (60 hours) as shown in <a href="https://academic.oup.com/view-large/figure/165998113/evz197f1.tif">Fig. 1</a> of the publication. s0 appears to have no variation, while s5 contains variants in the plasmid copy number control region.

opencc-by-nc-sa-4.0Mar 2019View details →

Genotypes, variants and pedigree from a human parent-offspring trio (NA12878)

This dataset includes whole genome sequencing data, produced at the French National Research Center for Human Genomics (CNRGH), with known pedigree information: - The VCF file contains genotypes and variants from a CEU parent-offspring trio comprising NA12878 (child), NA12891 (father) and NA12892 (mother). For each member, 150-bp paired-end whole genome sequencing data were generated on the Illumina HiSeq X system, from a PCR-free library (40x). - The TFAM file contains pedigree information of this CEU parent-offspring trio.

opencc-by-4.0Apr 2020View details →

EMERGENCE OF DRIFT VARIANTS THAT MAY AFFECT COVID-19 VACCINE DEVELOPMENT AND ANTIBODY TREATMENT

Supplemental File 1

opencc-by-4.0Dec 2019View details →

Raw diffraction data for [NiFeSe] hydrogenase G491A variant pressurized with O2 gas - dataset G491A-O2

Diffraction data measured at ESRF beamline ID30A-3 on September 27, 2017. N.B. Image files 1416-1419 are damaged and cannot be used for integration.

opencc-by-4.0Dec 2019View details →

Raw diffraction data for [NiFeSe] hydrogenase G491A variant pressurized with O2 gas - dataset G491A-O2-LD

Diffraction data measured at ESRF beamline ID30B on April 8, 2018. Image files are uploaded in blocks of gzip-compressed cbf files.

opencc-zeroJun 2021View details →

Data from: A homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy

Objective: Facioscapulohumeral muscular dystrophy (FSHD) is a heterogenetic disorder predominantly characterized by progressive facial and scapular muscle weakness. FSHD patients either have a contraction of the D4Z4 repeat on chromosome 4q35 or mutations in D4Z4 chromatin modifiers SMCHD1 and DNMT3B, both causing D4Z4 chromatin relaxation and inappropriate expression of the D4Z4-encoded DUX4 gene in skeletal muscle. In this study we tested the hypothesis if LRIF1, a known SMCHD1 protein interactor, is a disease gene for idiopathic FSHD2. Methods: Clinical examination of an idiopathic FSHD2 patient was combined with pathological muscle biopsy examination and with genetic, epigenetic and molecular studies. Results: A homozygous LRIF1 mutation was identified in a patient with a clinical phenotype consistent with FSHD. This mutation resulted in the absence of the long isoform of LRIF1 protein, D4Z4 chromatin relaxation, and DUX4 and DUX4 target gene expression in myonuclei, all molecular and epigenetic hallmarks of FSHD. In concordance, LRIF1 was shown to bind to the D4Z4 repeat and knock down of the LRIF1 long isoform in muscle cells results in DUX4 and DUX4 target gene expression. Conclusions: LRIF1 is a bona fide disease gene for FSHD2. This study further reinforces the unifying genetic mechanism which postulates that FSHD is caused by D4Z4 chromatin relaxation resulting in inappropriate DUX4 expression in skeletal muscle.

opencc-zeroAug 2020View details →

Data from: Variant files for genotypic and sex-reversed males

X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

opencc-by-4.0Sep 2020View details →

Supplementary Materials for Digenic Variants in the FGF21 Signaling Pathway Associated with Severe Insulin Resistance and Pseudoacromegaly

Supplementary Materials for Digenic Variants in the FGF21 Signaling Pathway Associated with Severe Insulin Resistance and Pseudoacromegaly. This includes additional photographs of the proband and family, bone age x-ray, smell identification testing, ERK phosphorylation in HeLa Cells, Candidate genes from research exome, and full plasmid sequences used in the study.

opencc-by-4.0Sep 2020View details →

DeepArk variant effect predictions for MPRA of ALDOB enhancer in mouse

The individual DeepArk predictions for every possible variant tested by the massively parallel in vivo reporter assay of the ALDOB enhancer in mouse livers from Patwardhan et al. 2012 (DOI:10.1038/nbt.2136). Predictions are provided for all regulatory features modeled in M. musculus. Accession numbers correspond to training data corresponding to an individual output probability from DeepArk.

opencc-by-4.0Oct 2020View details →

HeartENN variant effect predictions for Richter et al. (2020)

Variant effect predictions used in the publication: <a href="https://doi.org/10.1038/s41588-020-0652-z">Genomic analyses implicate noncoding de novo variants in congenital heart disease</a>  All variants are specified in hg19 coordinates

opencc-zeroSep 2020View details →

Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls

Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.

opencc-by-4.0Nov 2020View details →

TGFBI case WES variants

Novel mutation in the TGFBI gene in a Moroccan family with atypical corneal dystrophy: a case report Data of VCF of three affected members who shared a phenotype of corneal dystrophy in different stages of severity

opencc-zeroDec 2020View details →

Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Sweet corn (Zea mays L.) is highly consumed in the United States, but does not make major contributions to the daily intake of carotenoids (provitamin A carotenoids, lutein and zeaxanthin) that would help in the prevention of health complications. A genome-wide association study of seven kernel carotenoids and twelve derivative traits was conducted in a sweet corn inbred line association panel ranging from light to dark yellow in endosperm color to elucidate the genetic basis of carotenoid levels in fresh kernels. In agreement with earlier studies of maize kernels at maturity, we detected an association of ß-carotene hydroxylase (crtRB1) with ß-carotene concentration and lycopene epsilon cyclase (lcyE) with the ratio of flux between the α- and ß-carotene branches in the carotenoid biosynthetic pathway. Additionally, we found that 5% or less of the evaluated inbred lines possessing the shrunken2 (sh2) endosperm mutation had the most favorable lycE allele or crtRB1 haplotype for elevating ß-branch carotenoids (ß-carotene and zeaxanthin) or ß-carotene, respectively. Genomic prediction models with genome-wide markers obtained moderately high predictive abilities for the carotenoid traits, especially lutein, and outperformed models with less markers that targeted candidate genes implicated in the synthesis, retention, and/or genetic control of kernel carotenoids. Taken together, our results constitute an important step toward increasing carotenoids in fresh sweet corn kernels.

opencc-zeroAug 2021View details →

Association of common genetic variants with brain microbleeds: A genome-wide association study

Objective: To identify common genetic variants associated with the presence of brain microbleeds (BMB). Methods: We performed genome-wide association studies in 11 population-based cohort studies and 3 case-control or case-only stroke cohorts. Genotypes were imputed to the Haplotype Reference Consortium or 1000 Genomes reference panel. BMB were rated on susceptibility-weighted or T2*-weighted gradient echo magnetic resonance imaging sequences, and further classified as lobar, or mixed (including strictly deep and infratentorial, possibly with lobar BMB). In a subset, we assessed the effects of APOE ε2 and ε4 alleles on BMB counts. We also related previously identified cerebral small vessel disease variants to BMB. Results: BMB were detected in 3,556 of the 25,862 participants, of which 2,179 were strictly lobar and 1,293 mixed. One locus in the APOE region reached genome-wide significance for its association with BMB (lead SNP rs769449; ORany BMB (95% CI)=1.33 (1.21-1.45); p=2.5x10-10). APOE ε4 alleles were associated with strictly lobar (OR (95% CI)=1.34 (1.19- 1.50); p=1.0x10-6) but not with mixed BMB counts (OR (95% CI)=1.04 (0.86-1.25); p=0.68). APOE ε2 alleles did not show associations with BMB counts. Variants previously related to deep intracerebral hemorrhage and lacunar stroke, and a risk score of cerebral white matter hyperintensity variants, were associated with BMB. Conclusions: Genetic variants in the APOE region are associated with the presence of BMB, most likely due to the APOE ε4 allele count related to a higher number of strictly lobar BMB. Genetic predisposition to small vessel disease confers risk of BMB, indicating genetic overlap with other cerebral small vessel disease markers.

Isoform specific activities of androgen receptor and its splice variants in prostate cancer cells

Androgen receptor (AR) signaling continues to drive castration resistant prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT). Constitutively active shorter variants of AR, lacking the ligand binding domain, are frequently expressed in CRPC and have emerged as a potential mechanism for prostate cancer to escape ADT. ARv7 and ARv567es are two of the most commonly detected variants of AR in clinical samples of advanced, metastatic prostate cancer. It is not clear if variants of AR merely act as weaker substitutes for AR or can mediate unique isoform specific activities different from AR. In this study, we employed LNCaP prostate cancer cell lines with inducible expression of ARv7 or ARv567es to delineate similarities and differences in transcriptomics, metabolomics and lipidomics resulting from the activation of AR, ARv7 or ARv567es. While the majority of target genes were similarly regulated by the action of all three isoforms, we found a clear difference in transcriptomic activities of AR versus the variants, and a few differences between ARv7 and ARv567es. Some of the target gene regulation by AR isoforms was similar in the VCaP background as well. Differences in downstream activities of AR isoforms were also evident from comparison of the metabolome and lipidome in an LNCaP model. Overall our study implies that shorter variants of AR are capable of mediating unique downstream activities different from AR and some of these are isoform specific.

Copy Number variants in Mallotus villosus

Taking advantage of recent developments allowing CNV analysis from RAD-seq data (<a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15565?_sg%5B0%5D=-uwA9TZisRRXnspI5ElYUaPv2ChLuHLDZPIJZABoML2rc-geS2mVnZVIt2u4FAB6_SPD-DeRxtzyN3RjHivkmfmvEg.JqPMUYewJwfNoZvoALtl54UTEL4BWYI0NA87y3HrK16wm8cRVOG0c0owiV4QoaSysHfAZCLPkLmn-UaqCdolJQ">10.1111/mec.15565</a>), we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. Raw sequencing data for GBS libraries have been published in a previous study (Cayuela et al. 2020, <a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15499?_sg%5B0%5D=OGdqMkvPArx5ICrgLrdT_ifFufXzoOZp0J7gLQEctL4EWpJv-h9FK8yFaom_h68N368lpxVYXRREN9BRpAi7lH0n8A.ylPnOWuObAEr1NJn9bzfYxNNAAwvYDvN0jDBR05xnfdW8Azf-PmnI7jDZFhecO1Kt1aTdFuxG0Yr3ff2e10XCg">10.1111/mec.15499</a>) and are available under accession no. PRJNA631144. Here, we provide the files of normalized read depth for the 6620 putative CNVs and environmental data used in our CNV analyses.

Supplementary material 3 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936

United Kingdom variant interactions

Supplementary material 1 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936

RBD-ACE2 complexes

Supplementary material 2 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936

RBD-ACE2 interface detail