Correction to:Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome (BMC Microbiology, (2022), 22, 1, (39), 10.1186/s12866-021-02364-2)

Following the publication of the original paper [1], there’s an error on the first name of one of the authors. Mureil Derrien should be Muriel Derrien. Correct name is shown in the author group section above. The original article has been corrected

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation:A Genome-Wide Analysis among 1,800 South Asians

A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these transeQTLs were also cis-eQTLs (enrichment P</p

1000IBD

The department of Gastroenterology and Hepatology of the University Medical Center Groningen initiated the 1000IBD project to prospectively follow more than a 1000 IBD patients from the Northern provinces of the Netherlands. We have collected a uniquely large number of phenotypes and generated multi-omics profiles for these patients. To date, 1,215 participants have been enrolled in the 1000IBD project, and enrolment is on-going. Patients that participate in the 1000IBD project are followed prospectively and the phenotype data includes information on dietary and environmental factors, and drug response. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array, and HumanExomeChip), and sequencing (whole exome sequencing, and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies, and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.,Data categories: Biological samples, Medical records, Physiological/Biochemical measurements, Survey data Material collected: Feaces Experimental data: Genomics, Transcriptomics, Other Number of donors: 1000 Sex: Female, Male Age: 18-85 Year Diseases studied: Noninfective enteritis and colitis

Supplementary tables from A practical view of fine-mapping and gene prioritization in the post-genome-wide association study era

Tables containing a description of current functional and computational fine-mapping tools and database

Deconvolution of bulk blood eQTL effects into immune cell subpopulations

BACKGROUND: Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type-context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, current methods to do this are labor-intensive and expensive. We introduce a new method, Decon2, as a framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) followed by deconvolution of cell type eQTLs (Decon-eQTL). RESULTS: The estimated cell proportions from Decon-cell agree with experimental measurements across cohorts (R ≥ 0.77). Using Decon-cell, we could predict the proportions of 34 circulating cell types for 3194 samples from a population-based cohort. Next, we identified 16,362 whole-blood eQTLs and deconvoluted cell type interaction (CTi) eQTLs using the predicted cell proportions from Decon-cell. CTi eQTLs show excellent allelic directional concordance with eQTL (≥ 96-100%) and chromatin mark QTL (≥87-92%) studies that used either purified cell subpopulations or single-cell RNA-seq, outperforming the conventional interaction effect. CONCLUSIONS: Decon2 provides a method to detect cell type interaction effects from bulk blood eQTLs that is useful for pinpointing the most relevant cell type for a given complex disease. Decon2 is available as an R package and Java application (https://github.com/molgenis/systemsgenetics/tree/master/Decon2) and as a web tool (www.molgenis.org/deconvolution)

MITIGATION OF MARMOSET MONKEY EAE THROUGH A DIETARY SUPPLEMENT

The goal was to compare Marmoset monkeys with different diets in the efficasy to show MS-like symtoms after induction. Next to immunology the gut microbiota of the monkey was studied by 16S rRNA sequencing 16S rRNA-gene sequences of BioProject Accession: PRJNA693190 ID: 69319

MITIGATION OF MARMOSET MONKEY EAE THROUGH A DIETARY SUPPLEMENT

The goal was to compare Marmoset monkeys with different diets in the efficasy to show MS-like symtoms after induction. Next to immunology the gut microbiota of the monkey was studied by 16S rRNA sequencing 16S rRNA-gene sequences of BioProject Accession: PRJNA693190 ID: 69319

MITIGATION OF MARMOSET MONKEY EAE THROUGH A DIETARY SUPPLEMENT

The goal was to compare Marmoset monkeys with different diets in the efficasy to show MS-like symtoms after induction. Next to immunology the gut microbiota of the monkey was studied by 16S rRNA sequencing 16S rRNA-gene sequences of BioProject Accession: PRJNA693190 ID: 69319

Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb

Additional file 1: of The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Imputed MHC classic alleles and amino acids for infectious diseases. (XLSX 40 kb