Tag: GWAS

Professor of Medical Bioinformatics and Statistical Genetics job with Aarhus University (AU)

The Department of Biomedicine at Faculty of Health at Aarhus University invites applications for a position as Professor in the field of Medical Bioinformatics and Statistical Genetics as per 1 July 2024 or as soon as possible thereafter. The position is a time-limited full-time position for 5 years with extension…

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Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

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Causality-enriched epigenetic age uncouples damage and adaptation

Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article  PubMed  PubMed Central  Google Scholar  Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article  PubMed …

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ALS Agent PrimeC Moves to Phase 3, FDA Clears IND for AB126, APOE Carrier Status Impacts ARIA

WATCH TIME: 3 minutes Welcome to this special edition of Neurology News Network. I’m Marco Meglio. Shortly after positive topline data from the phase 2 PARADIGM study of PrimeC was released, NeuroSense Therapeutics has announced that the FDA has confirmed its development plans for a phase 3 pivotal trial with…

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Week10 F22.docx 1 .pdf – Project Ten: eQTL GWAS and SARS-CoV2 We’ll use this last project to learn a bit more about SARS-CoV-2 and about approaches

Project Ten: eQTL, GWAS, and SARS-CoV2 We’ll use this last project to learn a bit more about SARS-CoV-2, and about approaches used by population geneticists to investigate aspects of its pathogenicity and transmission among humans. You’ll be introduced to the concept of eQTLs (expression quantitative trait loci) and how they…

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Mapmygenome Jobs For Bioinformatics – Analyst Vacancy

–Must See– Mapmygenome Jobs For Bioinformatics – Analyst Vacancy Hot Job Opportunity: Bioinformatics Analyst at Mapmygenome™! Mapmygenome™ is a leading genomics company based in Hyderabad. We specialize in providing personalized healthcare solutions based on an individual’s genetic makeup. Our mission is to empower individuals to make informed choices about their…

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Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry

To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…

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TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Cao, C. et al. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet. 17(2), e1009405 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  De Camargo, G. M. F. et al. Prospecting major genes in dairy buffaloes. BMC Genomics 16, 1–14 (2015). Article  Google Scholar  El-Halawany, N….

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GWAS Catalog

Available data: Associations Studies Full summary statistics LocusZoom Download Associations Download files Include background traits data Associations Variant and risk allele P-value P-value annotation RAF OR Beta CI Mapped gene Reported trait Trait(s) Background trait(s) Study accession First Author PubMed ID Location Variant and risk allele P-value P-value annotation RAF…

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Relatedness and GWAS False Signals

Relatedness and GWAS False Signals 1 I have just realized that a GWAS that I ran sadly included related individuals (the flagged samples file that came with the dataset did not include relatedness). As relatedness is expected to increase false positives, is it reasonable to solely rerun the GWAS on…

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extracting instruments for mendelian randomization analysis

extracting instruments for mendelian randomization analysis 0 Cross-posted on bioinfo SE: bioinformatics.stackexchange.com/questions/21952/extracting-instruments-for-mendelian-randomization-analysis I am looking at extracting genetic variants associated with physical activity (to be used as exposure) from gwas id ebi-a-GCST006097. The gwas has nsnp = 11808007 library(TwoSampleMR) library(ieugwasr) gwasinfo (“ebi-a-GCST006097”) However, when I extract this, I end up…

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Zhana Kuncheva “The future of GWAS in drug discovery & biobank design”, Thu, Dec 28, 2023, 6:45 PM

Or the full title: ‘The future of GWAS in drug discovery and biobank design: are tools like isGWAS the solution to a pressing problem?’ Zhana (from Optima Partners) will be talking about their work on isGWAS: While genome-wide association studies (GWAS) have proven a powerful tool for human geneticists, there…

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MD Anderson Research Highlights for December

HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent developments at…

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Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution

Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…

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Single Cell Data Scientist at European Molecular Biology Laboratory (EMBL)

About the team/job We are looking for a Bioinformatician to join the Open Targets data team. We are seeking an enthusiastic team member to expand our informatics platforms through the integration of single cell omics data to enhance drug discovery. This role would suit someone with experience in data integration…

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The first major set of genetic associations found in long COVID

PrecisionLife’s Dr Sayoni Das, a computational biologist who leads the research and development of bioinformatics pipelines that generate biological insights from PrecisionLife’s core technology and support drug discovery programmes, details a new study. Using combinatorial analysis, genetic variants associated with long COVID have been identified and, furthermore, it has been…

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genetics – Trouble with Phenotype File in PLINK GWAS – 0 Individuals with Non-Missing Phenotypes

Problem Description: I am facing an issue while running a Genome-Wide Association Study (GWAS) using PLINK. Despite specifying the phenotype file and confirming the presence of the phenotype column (‘ChildPhenotype’), I consistently receive the error message: “0 individuals have non-missing phenotypes.” I have ensured that the values in the specified…

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Do you have to run separate pca or covariate file for different number of samples?

Hi. I have two different phenotypes to run GWAS quantitative analysis (–glm), which are bmi and hdl.  As for input, I have input phenotype file, genotype file and covariate file. The special circumstance here is that I have different number of participants for each different phenotype, meaning that some participants…

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The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

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Northumbria University Research Fellowship Health & Life Science

–Must See– Northumbria University Research Fellowship Research Fellow in Health and Life Sciences Northumbria University, Newcastle City Campus, United Kingdom ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science…

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Genetic architecture of cardiac dynamic flow volumes

Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article  PubMed  Google Scholar  Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article  CAS …

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ncRNA | Free Full-Text | Regulation of Macrophage Polarization in Allergy by Noncoding RNAs

1. Introduction Allergies affect millions of people worldwide and are characterized by an excessive type 2 immune response to normally harmless substances, generally known as antigens or allergens, specifically [1,2]. Consequently, this response leads to the development of various allergic symptoms, including asthma, allergic rhinitis, and atopic dermatitis. In the…

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Study Links Gene Network To Diabetes 2

In a collaborative effort co-led by teams from Vanderbilt University Medical Center (VUMC) and the University of Michigan, a comprehensive study that integrates multiple analytic approaches has linked a regulatory gene network and functional defects in insulin-producing pancreatic beta cells to Type 2 diabetes. The study, published in the journal…

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encounter fatal error when opening Rstudio IDE – RStudio IDE

hello~ I’ve been seeing fatal error warning whenever I try to open Rstudio.The warning are as follows: R Session Startup Failure Report RStudio Version RStudio 2023.06.1+524 “Mountain Hydrangea ” (547dcf86, 2023-07-06) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.06.1+524 Chrome/110.0.5481.208 Electron/23.3.0 Safari/537.36 Error message…

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Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts

Benjamin, E. J. et al. Heart disease and stroke statistics-2019 update: A report from the American Heart Association. Circulation 139, e56–e528 (2019). Article  PubMed  Google Scholar  Yusuf, S. et al. Effect of potentially modifiable risk factors associated with myocardial infarction in 52 countries (the INTERHEART study): Case-control study. Lancet 364,…

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Test for multiplicative effect in mendelian randomization?

Test for multiplicative effect in mendelian randomization? 0 A study reported that exposure A and B had multiplicative effect on the outcome C. Let’s say I want to prove in MR that A*B had multiplicative effect on outcome C. I already knew that MVMR (multivariate MR) could investigate the causal…

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Type 2 Diabetes Risk Correlates with Gene Signatures of Beta Cell Dysfunction

A joint effort involving research teams from Vanderbilt University Medical Center (VUMC) and the University of Michigan has linked the activities of a regulatory gene network and functional defects in insulin-producing pancreatic beta cells to type 2 diabetes. Details of the study are published in a Nature paper titled, “Genetic…

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Converting txt.gz to PLINK bim

Converting txt.gz to PLINK bim 0 Hello, I’m trying to do a stratified LDSC (or S-LDSC/partitioned LDSC) between locus of interest and diseases (diabetes, arthritis, etc.). For locus of interest, I have a bed file from previous research. For diseases, I have downloaded GWAS sumstats from the GWAS atlas. I…

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Research Fellow in Health and Life Sciences job with NORTHUMBRIA UNIVERSITY

ABOUT THE ROLE We are seeking to appoint a highly committed, motivated, and creative scientist to join the Northumbria University bioinformatics research group. The research will develop new data science methods that leverage the large amounts of public data from UKBiobank, dbGAP, and internal Whole Sequence data and use state-of-the-art…

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GWAS and eQTL disparity | Nature Methods

Genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) mapping use conceptually similar ideas to identify genetic variants contributing to complex trait and gene expression variation, respectively. Despite the proven role of gene expression in mediating biological functions, the observed level of colocalization between GWAS hits and eQTLs shows…

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Senior Bioinformatics Scientist – 127022

UCSD Layoff from Career Appointment: Apply by 12/08/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/20/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will work a hybrid schedule which includes a combination…

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Exploring Key Statistical Methods in Genetics Research: From T-Tests to ANOVA

Introduction to the T-test in Bioinformatics: The t-test is a statistical method used to determine if there is a significant difference between the means of two groups. This is particularly crucial in bioinformatics for analyzing gene expression data. Types of T-tests: – One-Sample T-test: Compares the mean of a single…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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New genetic links to coronary artery calcification uncovered

A recent research letter published in the journal Nature Cardiovascular Research describes two new genetic loci associated with coronary artery calcification (CAC). CAC is a measure of atherosclerosis and predicts coronary artery disease (CAD) events. Coronary calcification is a manifestation of atherosclerotic plaque. It is suggested to contribute to plaque…

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GAPIT p-value significance threshold

GAPIT p-value significance threshold 0 Hi all, I have GWAS results for several traits in barley. However, I have been told that 0.05 significance threshold may be too stringent for plants. Does anyone know how to adjust the significance threshold in GAPIT? Specifically, is the default setting 0.05 divided by…

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Noisy manhattan plot

Hi! I’m running GWAS on plink 2.00a4LM. My case cohort has roughly 600 individuals and control cohort has ~4000. Individuals. After running the GWAS, I plot the results using R. After some data exploration I decided to exclude some samples in order to avoid having samples with close family relationships…

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Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

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A Modular Parallel Pipeline Architecture for GWAS Applications in a Cluster Environment

Abstract A Genome Wide Association Study (GWAS) is an important bioinformatics method to associate variants with traits, identify causes of diseases and increase plant and crop production. There are several optimizations for improving GWAS performance, including running applications in parallel. However, it can be difficult for researchers to utilize different…

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Should I perform eQTL colocalization for just one of eGenes at a time?

Should I perform eQTL colocalization for just one of eGenes at a time? 0 Thank you for reading and answering in advance. Hello, now I want to do GWAS-eQTL colocalization analysis and I’m totally new to colocalization. I’m planning to use coloc or eCaviar. But, according to the manual, It…

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Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS  Google Scholar  Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….

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Postdoctoral Fellowship in bioinformatics and genetic epidemiology – University of Copenhagen – job portal

Job Portal                                                                                         Postdoctoral Fellowship in bioinformatics and genetic epidemiology   A two-year postdoctoral fellowship is available at the Section for Computational and RNA Biology, Department of Biology, University of Copenhagen. The position will be available from April 1st, 2024 or thereafter. The specific projects involve analyzing…

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Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios

Epigenetic changes are typically thought to be markers of cell differentiation or somatic changes caused by interactions with the environment16. However, recent studies have shown that some of these environmentally induced changes can be passed down from one generation to the next, demonstrating their heritability19,21,42,43. Though this mechanism has long…

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Identification of constrained sequence elements across 239 primate genomes

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

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Solved The following questions are based on the following

The following questions are based on the following paper: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. Nat Commun. 2018; 9:1512. (PMID: 29666371) (i) How is a cis-expression quantitative trait locus (cis-eQTL) defined? (ii) What experimental technique for detecting chromosomal interactions was applied…

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Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability

Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article  CAS  PubMed  Google Scholar  Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article  PubMed  PubMed Central  Google Scholar  Wang,…

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East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…

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result difference between FUMA GWAS and the eQTL catalog

Hi team, I am using FUMA GWAS to annotate my hit from GWAS. However I find some discrepency between the result from fuma and the original site. Based on the result from FUMA, G is the testing allele which will decrease the gene expression (Figure below). And the P value…

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threads in plink GWAS

hello, i am using plink with dosage file to do GWAS as below. when i set threads=10, however, i check the real cpu consuming, plink only use 1 cpu instead of 10. does plink make no difference with different threads option? module load plink/1.90b4.1 plink –dosage ${geno_dir}/${dosage_filename} noheader skip1=2 skip2=2…

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DNA methylation change in blood cells of FB and CFS patients

Introduction Fibromyalgia (FM) and Chronic Fatigue Syndrome (CFS) are characterized by chronic pain, fatigue, and weakness. Patients with these symptoms also suffer from sleep abnormalities and report affected cognitive processes such as memory. The diagnosis of these two syndromes is challenging and is based on questionnaires that make the diagnosis…

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DS Group hiring Bioinformatician in London, England, United Kingdom

Bioinformatician – Deep Learning, Python, PyTorch, GWAS, RNA At the company, a leading agbiotech start-up, safeguarding the future of food is at the heart of what drives and inspires every member of the team. With a mission to accelerate the development of more productive, sustainable, nutritious, and climate-resilient food sources,…

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Postdoctoral Researcher in Alzheimer’s disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA

Location: Department of Neurology, NeuroGenomics and Informatics Center, Washington University in St. Louis Description The Washington University School of Medicine, Department of Neurology, has an opening for a post- doctoral research associate to join the Belloy lab in the NeuroGenomics and Informatics Center (NGI). The successful candidate will be involved…

Continue Reading Postdoctoral Researcher in Alzheimer’s disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA

Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…

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–glm no-firth: Segmentation fault

I am running GWAS with binary phenotypes. PLINK v2.00a6LM AVX2 AMD (21 Nov 2023) First option: –glm hide-covar single-prec-cc cc-residualize => Error: Cannot proceed with –glm regression on phenotype ‘pheno1’,since covariate-only Firth regression failed to converge. Second option –glm hide-covar single-prec-cc cc-residualize no-firth => Segmentation fault Third option –glm hide-covar…

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Genome study unveils genetic ties between cannabis use disorder and lung cancer risk

In a recent study published in Nature Genetics, researchers conducted a genome-wide association study (GWAS) to gain novel insights into the pathophysiology of cannabis use disorder and public health concerns associated with the disorder. Study: Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health…

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Post-Doctoral Associate – Bioinformatics & Computational Biology Job in Minnesota

Required Qualifications: • A PhD degree in related field (Bioinformatics, Computer Science, Statistics, etc.) obtained in the last 1~2 years.• Strong quantitative data analysis background (machine learning, biostatistics, etc.) and/or computational genomics/genetics experiences (spatial transcriptomics, single-cell sequencing, high-throughput omics sequencing data analysis, TWAS/GWAS, etc.) or other relevant areas.• Strong…

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Merging several vcf files for GWAS?

Merging several vcf files for GWAS? 0 Hello! I am a Medical Student without much background in Bioinformatics trying to perform analysis for my first GWAS study, tremendously overwhelmed. It’s a Case Control Association Study with samples from 50 subjects, that we sampled using Novogene NGS platform. The problem is,…

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Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

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snp database using annotation

snp database using annotation 1 hello For 550,000 SNPs, we only have the chromosomal location or rs number. I would like to annotate ref/alt allele, strand, and frequency information for 550,000 SNPs. I downloaded the GCF_000001405.40.gz file, but there is no strand information. I am curious about a database that…

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How to identify the nearest gene associated with a specific SNPs?

How to identify the nearest gene associated with a specific SNPs? 0 Hi, I have a (what I think is) a very naive question but I am not an geneticist. I need to compile a list of gene to screen later in my in vitro model. I decided to define…

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ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry

Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article  Google Scholar  American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…

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Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications

Inclusion and ethics statement We included researchers from the iPSYCH biobank and the PGC, who played a role in study design. This research was not restricted or prohibited in the setting of any of the included researchers. All studies were approved by local instituational research boards and ethics review committees….

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Functional convergence of genomic and transcriptomic architecture underlies schooling behaviour in a live-bearing fish

Krause, J. & Ruxton, G. D. Living in Groups (Oxford Univ. Press, 2002). Réale, D., Reader, S. M., Sol, D., McDougall, P. T. & Dingemanse, N. J. Integrating animal temperament within ecology and evolution. Biol. Rev. 82, 291–318 (2007). Article  PubMed  Google Scholar  Gartland, L. A., Firth, J. A., Laskowski,…

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Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder

Phenotype imputation increases effective sample size We focused on the deepest available measure of MDD in UK Biobank11, LifetimeMDD, which we derived by applying clinical diagnostic criteria in silico to MDD symptom data from the Patient Health Questionnaire 9 (PHQ9) and the Composite International Diagnostic Interview Short Form (CIDI-SF) in…

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Navigating the Road Ahead with Genomics and Polygenic Risk Scores, ET HealthWorld

by Dr Firoz Ahmad Cardiovascular diseases (CVD) as a result of coronary artery diseases (CAD) are a group of health issues that affect the heart and the blood vessels which are essential for optimal heart functioning. It is a leading cause of death worldwide, particularly in India, where it accounts…

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CRISPR-Cas13d screens identify KILR a breast cancer risk-associated lncRNA that regulates DNA replication and repair.

Abstract Long noncoding RNAs (lncRNAs) have surpassed the number of protein-coding genes, yet the majority have no known function. We previously discovered >800 lncRNAs at regions identified by breast cancer genome-wide association studies (GWAS). Here, we performed a pooled CRISPR-Cas13d RNA knockdown screen to identify which of these lncRNAs altered…

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MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

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ncRNA | Free Full-Text | Ethanol

Received: 14 July 2023 / Revised: 23 October 2023 / Accepted: 3 November 2023 / Published: 17 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors Rizavi and colleagues present a study describing the effects of alcohol and PARP inhibitor on the lncRNA ribosomal binding. The study…

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How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: library(tidyverse) library(magrittr) library(data.table) library(rtracklayer) library(GenomicRanges) rm(list=ls()) gwas_data <- fread(“/gwas_sumstats_allchr.txt”) chain_file <- “/chain_files/hg38ToHg19.over.chain” chain <- import.chain(chain_file) # Convert to GRanges object (assuming GENPOS is 1-based) gwas_ranges…

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Where to Get Genotyping Data/GWAS Data

Tutorial:Where to Get Genotyping Data/GWAS Data 0 First of all, it is important to understand that genotyping data and GWAS data are central to eQTL studies. These two types of data provide the foundational genetic information needed to understand how variations in gene expression contribute to complex traits and diseases….

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Cis- and trans-eQTL TWAS of breast and ovarian cancer identify more than 100 risk associated genes in the BCAC and OCAC consortia

Abstract Transcriptome-wide association studies (TWAS) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have only considered regulatory effects of risk associated SNPs thought to act in cis on a nearby target gene. With growing evidence for…

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Bioinformatics Scientist, multi-omics of Immune-Mediated Inflammatory Diseases

We are looking for a highly motivated postdoctoral researcher to work in the multi-omic analysis of Immune-Medated Inflammatory Diseases (IMIDs). The successful applicant will work in IMIDomics, a rapidly growing company focused on bringing the power of precision medicine to IMID patients. A fundamental strategy at IMIDomics is to integrate…

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Hussman Institute Celebrates Banner Year at Global Human Genetics Conference

By: Lisette Hilton | November 14, 2023 | 9 min. read |  Share Miller School-led studies on neurodegenerative disease chosen for platform presentations, poster awards and abstracts at American Society of Human Genetics’ annual meeting. Many of the more than 8,000 international scientists attending the American Society of Human Genetics (ASHG)…

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Senior Bioinformatics Scientist @ Storm3

⚡ Senior Bioinformatics Scientist (HUMAN GENETICS) 🧪 Healthtech Start-Up 📌 Remote (US) 💰 $150K Base + Bonus + Impressive equity Are you interested in joining a revolutionary Biotech start-up that is using their ground-breaking AI platform to change the way we discover drugs? This established start-up with over $30M in…

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How To Get Chromosome Position Given Rs Number?

How To Get Chromosome Position Given Rs Number? 3 I have a list of a few hundred SNPs given by rs number. I want to get the chromosome and position for each SNP. For example: input: rs4477212 output: chr1:82154 snp chromosome position • 29k views you can download this information…

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The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

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Quality control on imputed genotypes for GWAS / application of PGS

Quality control on imputed genotypes for GWAS / application of PGS 0 Hi everyone, I want to run a GWAS on imputed genotypes from UKB. Unfortunately, I only found tutorials that describe the quality control of genotypes in preparation for a GWAS. Are there tutorials for imputed datasets? I suppose…

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Alternatives to snpflip to find ambigious and flipped snps

Alternatives to snpflip to find ambigious and flipped snps 0 Hello everyone, I having an issue with strand flips when trying to perform imputation. In the past on an old HPC I used it supported snpflip, a tool which would recognize ambigious snps as well as snps that have been…

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St. Jude Children’s Research Hospital hiring Senior Bioinformatics Analyst/Bioinformatics Analyst in Memphis, Tennessee, United States

St. Jude Children’s Research Hospital is looking for a highly motivated Senior Bioinformatics Analyst/Bioinformatic Analyst to contribute to genetic research projects in the Department of Epidemiology and Cancer Control. Our research leverages comprehensive biomedical data from childhood cancer survivors participating in two world-leading cohort studies, CCSS (ccss.stjude.org/ ) and SJLIFE…

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Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders

Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article  PubMed  Google Scholar  Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….

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Why do we remove multi-allele when conducting a GWAS or NGS-sequencing analysis?

Why do we remove multi-allele when conducting a GWAS or NGS-sequencing analysis? 1 Hi, Dear all! I am new to GWAS, there exists one question made me sad. I wonder why do we need to remove multi-allele when we conduct a GWAS or NGS-sequencing analysis like WES. I have tried…

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Bioinformatics Research Associate, Genomics and Genetics

Job:Bioinformatics Research Associate, Genomics and Genetics 0 @jp-carter-15371 Last seen 7 hours ago Nashville, TN The Bioinformatics Research Associate is part of the Creative Data Solutions (CDS) Shared Resource at Vanderbilt University and is a key individual contributor responsible for performing bioinformatics analyses of genomic data sets, developing and implementing…

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Integrative transcriptome- and DNA methylation analysis of brain tissue from the temporal pole in suicide decedents and their controls

World Health Organization. Facts sheet: suicide. www.who.int/news-room/fact-sheets/detail/suicide. National Institute of Mental Health. Suicide. www.nimh.nih.gov/health/statistics/suicide. Nock MK, Hwang I, Sampson N, Kessler RC, Angermeyer M, Beautrais A, et al. Cross-national analysis of the associations among mental disorders and suicidal behavior: findings from the WHO world mental health surveys. PLoS Med. 2009;6:e1000123….

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Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau

Abebe TD, Naz AA, Léon J (2015) Landscape genomics reveal signatures of local adaptation in barley (Hordeum vulgare L.). Front Plant Sci 6:813 Article  PubMed  PubMed Central  Google Scholar  Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 Article  CAS  PubMed …

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Open Archive of Plant Images and Traits

The world of agriculture is constantly evolving, with new technologies continuously shaping the way we understand and interact with plants. One such advancement is the development of high-throughput plant phenotypic collection technology, which has revolutionized the field of plant phenomics. Through this technology, scientists are able to gather vast amounts…

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Genes that shape facial features

After turning up hundreds of genes with hard-to-predict effects, some scientists are now probing the grander developmental processes that shape face geometry When Eric Mueller, who was adopted, first saw a photograph of his birth mother, he was overcome by how alike their faces were. It was, he wrote, “the…

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Scientists develop open archive of plant images and related phenotypic traits

Graphical abstract. Credit: Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad975 Plant images contain a wealth of information that reflects key phenotypic characteristics such as color, shape, growth, and health status of plants. High-throughput plant phenotypic collection technology has been widely applied in plant phenomics, generating numerous images and image-based traits (i-traits)…

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About the item name of UCSC GWAS catalog

hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gwasCatalog.sql `bin` smallint(5) unsigned NOT NULL, `chrom` varchar(255) NOT NULL, `chromStart` int(10) unsigned NOT NULL, `chromEnd` int(10) unsigned NOT NULL, `name` varchar(255) NOT NULL, `pubMedID` int(10) unsigned NOT NULL, `author` varchar(255) NOT NULL, `pubDate` varchar(255) NOT NULL, `journal` varchar(255) NOT NULL, `title` varchar(1024) NOT NULL, `trait` varchar(255) NOT NULL, `initSample`…

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Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

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Looking to compute R-squared with P-value for LocusZoom plot

Looking to compute R-squared with P-value for LocusZoom plot 0 Looking to compute R-squared values for a list of SNPs associated with specific phenotypes. Interested in having both p-values and R-squared scores for each SNP. Any advice on how to do this efficiently? After Rsqure and the p-value. I want…

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University of Minnesota Medical School hiring Postdoctoral Associate in Bioinformatics and Computational Biology in Minneapolis, MN

Required Qualifications: • A PhD degree in related field (Bioinformatics, Computer Science, Statistics, etc.) • Strong quantitative data analysis background (machine learning, biostatistics, etc.) and/or computational genomics/genetics experiences (spatial transcriptomics, single-cell sequencing, high-throughput omics sequencing data analysis, TWAS/GWAS, etc.) or other relevant areas. • Strong programming skills: (e.g., R, Python,…

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significant SNPs from per-phenotype GWAS summary statistics

significant SNPs from per-phenotype GWAS summary statistics 0 I performed an analysis for a specific gene/region of interest using GWAS summary statistics for a binary phenotype (+/- disease). Using the corrected p values in the summary statistics and mapping in FUMA, I found a significant missense/coding SNP, with p=0.025. Other…

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Postdoc in Computational Biology at the Cardiac Genetics Group

Faculty of Health and Medical SciencesUniversity of Copenhagen The Cardiac Genetics Group is looking for a highly motivated and dynamic bioinformatics postdoc for a 2-year position to commence 1st of March 2024 or soon thereafter.  You will be part of our team leading research on elucidation the genetic mechanisms underlying complex…

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University of Oklahoma hiring Postdoctoral Researcher in Bioinformatics & Computational Biology in Norman, OK

Description Description The candidate is responsible for analyzing and mining multi-omics data using computational techniques, such as deep learning, generalized linear mixed models, and biological network analysis. This may require development of new computer algorithms and/or construction of computational workflows on computer clusters. The types of multi-omics data will include…

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Locally annotating SNP IDs and Gene names of called variants

Locally annotating SNP IDs and Gene names of called variants 0 I have GWAS results after variant calling. The VCF file only had CHR (1:22) and POS (12345678 etc) information but the ID column has all “.”, namely no rsIDs in it. After GWAS analysis I have a list of…

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HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…

Continue Reading HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases

eQTL colocalization analysis highlights novel susceptibility genes in Autism Spectrum Disorders (ASD)

Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders (NDDs) characterized by difficulties in social interaction and communication, repetitive behavior, and restricted interests. ASD has proven to have a strong genetic component. However, defining causal genes is still one of the main challenges in GWAS, since the vast majority…

Continue Reading eQTL colocalization analysis highlights novel susceptibility genes in Autism Spectrum Disorders (ASD)

Recent GWAS studies have made extensive use of large eQTL data sets to functionally annotate index SNPs. With a large number of association signals located outside coding regions there has been an intense search among sequence variants affecting gene expression at the transcriptional level. However, little progress has been made in mapping regulatory variants that affect protein levels at the translational or post-translational level. It is now possible to undertake a protein QTL scan for focused sets of e.g. oxidized proteins by mass spectrometry. We have established a collaboration with a longitudinal, family-based study in France, the Stanislas cohort, which comprises circa 1000 nuclear families (4,295 individuals) and has follow up data for 10 years (three visits). We have undertaken a pilot study in a focus set of 257 subjects from 79 families with the aim to integrate GWAS, transcriptomic and DNA methylation data with proteomic data on a set of 100 proteins measured in PBMCs. We have already generated GWAS data using Illumina’s core-exome chip as well as DNA methylation profiles with the 450K array. We propose to use RNA seq to generate transcriptomic data of the corresponding PBMCs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset Description Recent GWAS studies have made extensive use of large eQTL data sets to functionally annotate index SNPs. With a large number of association signals located outside coding regions there has been an intense search among sequence variants affecting gene expression at the transcriptional level. However, little progress has…

Continue Reading Recent GWAS studies have made extensive use of large eQTL data sets to functionally annotate index SNPs. With a large number of association signals located outside coding regions there has been an intense search among sequence variants affecting gene expression at the transcriptional level. However, little progress has been made in mapping regulatory variants that affect protein levels at the translational or post-translational level. It is now possible to undertake a protein QTL scan for focused sets of e.g. oxidized proteins by mass spectrometry. We have established a collaboration with a longitudinal, family-based study in France, the Stanislas cohort, which comprises circa 1000 nuclear families (4,295 individuals) and has follow up data for 10 years (three visits). We have undertaken a pilot study in a focus set of 257 subjects from 79 families with the aim to integrate GWAS, transcriptomic and DNA methylation data with proteomic data on a set of 100 proteins measured in PBMCs. We have already generated GWAS data using Illumina’s core-exome chip as well as DNA methylation profiles with the 450K array. We propose to use RNA seq to generate transcriptomic data of the corresponding PBMCs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Bacterial SNPs in the human gut microbiome associate with host BMI

Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016). Article  CAS  PubMed  Google Scholar  Manichanh, C. et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55, 205–211 (2006). Article  CAS  PubMed …

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Senior Bioinformatics Scientist Job in Cambridgeshire, Career, Permanent Jobs in Insmed EU

Company Description Insmed Innovation UK Ltd, formerly Adrestia Therapeutics, is a leader in synthetic rescue therapies for genetically defined diseases and is part of Insmed Incorporated, a global biopharmaceutical company on a mission to transform the lives of patients living with serious and rare diseases. Our most valuable resource…

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Cannot proceed with –glm regression on phenotype ‘platelet_count’, since covariate correlation matrix could not be inverted (VIF_INFINITE)

Hi, I am trying to run GWAS on the Platelet Count phenotype.I am using sex, age, assessment center, genotype measurement, and 40 PCs as a covariance matrix.  I removed NA from the phenotype file, and I fitted it to the covariance matrix so it contains the same IDs.I calculated the…

Continue Reading Cannot proceed with –glm regression on phenotype ‘platelet_count’, since covariate correlation matrix could not be inverted (VIF_INFINITE)