Tag: GWAS

Polygenic Risk Score Performance Improved With Expression-Related Rare Variant Insights

NEW YORK – A team from Stanford University and other centers in the US and China have demonstrated that polygenic risk scores (PRS) based on common variants can be bolstered by incorporating clues from rare variants linked to significant gene expression shifts, dubbed expression outliers. “As individual PRS estimates are…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

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genetic epidemiology postdoc

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

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Scientist, Bioinformatics – Urgent Hiring at Tonix Pharmaceuticals Inc

Job Description We are searching for a capable Scientist, Bioinformatics to join our high calibre team at Tonix Pharmaceuticals Inc in Chatham, NJ 07928.Growing your career as a Full Time Scientist, Bioinformatics is a fantastic opportunity to develop exceptional skills.If you are strong in presentation, adaptability and have the right…

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Remove related individuals pre or post ld-pruning before GWAS?

Remove related individuals pre or post ld-pruning before GWAS? 0 I’m doing a GWAS on a dataset that contains some related individuals. To avoid false positives, I’m removing related individuals from the dataset as well as doing LD pruning. However, I am unsure what order should the algorithm follow and…

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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Could DNA be linked to Premature Aging in Cancer Survivors?

In this interview, we speak to Dr. Zhaoming Wang about his latest research that investigated accelerated aging in childhood cancer survivors and the underlying genetics causing this. Please could you introduce yourself and tell us what inspired your latest research? I’m an associate member of the faculty at St. Jude…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

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Extact SNPs ID’s and their Values with IID, Additive and dominance components

Extact SNPs ID’s and their Values with IID, Additive and dominance components 0 I’m dealing with GWAS data and I have 2M records of the .bed file, I’m New to P-link, Can anyone please help me with the Plink command which can Extract all SNPs Id’s and their Values with…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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Polygenic Transcriptome Risk Scores for COPD Show Improved Cross-Ancestry Portability

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

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Solved based on the Manhattan plot of GWAS study looking at

Transcribed image text: Based on the Manhattan plot of GWAS study looking at alleles associated with breast cancer in a Japanese population (below). what can you conclude about the SNP rs 1177 (Choose the best answer.) GWAS of breast cancer in Japanese population 78117 60 5334 18366 r3589 are dortor…

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adRn-s/ukbbgwas – githubhot

Explore SNVs associations with traits of UK BioBank. GWAS study results where made publicly available courtesy of Neale’s Lab on August 1st, 2018. For more information please visit: www.nealelab.is/uk-biobank INSTALL In R: devtools::install_github(“adRn-s/ukbbgwas”). DEV(s) Dependencies Mandatory and optional dependencies can all be handled with bioconda. Here’s a complete YAML specification…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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dx: error: unrecognized arguments: running swiss army knife plink2

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

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Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Aysu Okbay, Hyeokmoon Kweon & Philipp D. Koellinger Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia Yeda Wu, Julia Sidorenko, Jian Yang, Loic Yengo & Peter M. Visscher National Bureau of Economic Research, Cambridge, MA, USA Nancy Wang, Hariharan Jayashankar, Michael Bennett, Grant Goldman, Tamara Gjorgjieva, Steven…

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Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

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Bioinformatics Scientist – GWAS – Invitae

Invitae is a rapidly growing, purposeful company. Our mission is to empower doctors and patients with genetic information to help them make informed medical decisions at all stages of life. The Integrated Risk Assessment Platform plays a meaningful role in rapidly growing our understanding of genomic health and personalized medicine….

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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What software to use for GWAS with repeated longitudinal quantitative phenotype data?

What software to use for GWAS with repeated longitudinal quantitative phenotype data? 0 I have quantitative data that has been collected at 4 different time points. Before treatment, 1 month after, 1 year after and 2 year after. I have generated Linear Mixed Models in R to obtain the residuals….

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Dissertations.se: CHIP-SEQ

Showing result 1 – 5 of 34 swedish dissertations containing the word ChIP-Seq. Author : Ola Wallerman; Claes Wadelius; Jussi Taipale; Uppsala universitet; []Keywords : MEDICAL AND HEALTH SCIENCES; MEDICIN OCH HÄLSOVETENSKAP; MEDICIN OCH HÄLSOVETENSKAP; MEDICAL AND HEALTH SCIENCES; ChIP; ChIP-chip; ChIP-seq; transcription factors; motif discovery; nucleosome positioning; HepG2; genome-wide;…

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CD Genomics: Bioinformatics-Analysis Division Provides Genotyping Analysis Service for Studying Genetic Variations

New York, USA – February 23, 2022 – The Bioinformatics-analysis division is a new division of CD Genomics that provides reliable next-generation and third-generation high-throughput sequencing data analysis, comprehensive technology services, database construction, and other related data analysis services. CD Genomics recently launched various types of genotyping analysis services, including…

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Research Associate

Research Associate Dr. Brent Richards is seeking a Research Associate to assist in the creation and management of a research program to improve clinical care through the use of computational genomics. The job will take place at the Lady Davis Institute of the Jewish General Hospital, a McGill University teaching…

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Deep learning and genomics: predicting gene expression from DNA sequence

The human genome is enormously complex. Before the first draft of the genome was completed in 2003, there was an optimism that knowing its sequence could smoothly translate into cures and treatments for various diseases. Unfortunately, the scientific community quickly discovered that having the DNA sequence is still many steps…

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PostDoc Plant Bioinformatics job with SKOLKOVO INSTITUTE OF SCIENCE AND TECHNOLOGY

<p><strong>Want to participate to the outstanding new area of agro-genomics ? To put into the practice how the genetic diversity and genome-assisted breeding in crops contribute to provide healthy and high quality food in a sustainable way to humankind? Strong in bioinformatics and interested in working with very large datasets…

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Postdoctoral Fellow – Genomics and Bioinformatics

An open position for a Postdoctoral Fellow in human molecular genetics/genomics field is available in the laboratory of Rinki Ratnapriya, Ph.D. at the Department of Ophthalmology, Baylor College of Medicine, Houston, TX. The successful applicant will work on functional characterization of AMD-GWAS signals to understand the molecular basis of observed…

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dbSNP – Wikipedia @ WordDisk

The Single Nucleotide Polymorphism Database[1] (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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GWAS and ExWAS of blood Mitochondrial DNA copy number identifies 71 loci and highlights a potential causal role in dementia

Background: Mitochondrial DNA copy number (mtDNA-CN) is an accessible blood-based measurement believed to capture underlying mitochondrial function. The specific biological processes underpinning its regulation, and whether those processes are causative for disease, is an area of active investigation. Methods: We developed a novel method for array-based mtDNA-CN estimation suitable for…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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Senior Bioinformatics Scientist (Statistical Geneticist) – Research – Cambridge, UK in San Diego, California

Senior Bioinformatics Scientist – Cambridge, UK Candidates wishing to work remotely from the Netherlands, France, or Belgium may also be considered. Overview Since 2001, the cost of DNA sequencing has dropped more than 100,000-fold, from $100,000,000 USD per human genome to less than $600 USD today. This is resulting in…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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Polygenetic Risk Score Calculation

Polygenetic Risk Score Calculation 1 Hello all, My company has Whole exome sequencing (WES) data for individuals lying around and was wondering if this can be used to generate Polygenetic Risk Scores (PRS)? From what I researched online, it seems to be more so used for GWAS and not WES….

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Diverse Ancestry GWAS Yields More Accurate Heart Disease Risk Scores

Big genomic data visualization. DNA test, genom map. Graphic concept for your design A multi-ancestry genome-wide association study (GWAS),  led by scientists from the Global Lipids Genetics Consortium (GLGC) recently analyzed genomic data from nearly 1.65 million individuals to narrow down the number of genomic variants strongly associated with blood…

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How to merge vcf files

How to merge vcf files 3 Hi, I have 90 VCF files which I am looking to merge into one VCF file. I am trying to use VCFtools to merge these files. For that I am following the below process but while using vcf-merge command is not able to merge…

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Bioinformatics Scientist – Bethesda | Mendeley Careers

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the National Human Genome Research Institute (NHGRI), The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it is on site in…

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Best software for hQTL analysis with the aim of performing MR analysis

I would like to perform QTL analysis on a list of BAM files that I have containing the locations of histone mark reads. Ultimately my aim is to perform Mendellian randomisation, with these hQTLs as the exposure, against a different phenotype as the outcome. The outcome effects are expressed as…

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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ewout J. N. Groen, Michael…

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METAL GWAS

METAL GWAS 0 I’m using METAL to perform meta-analysis of GWAS, but one of the public summary data I downloaded did not have effect allele frequency. I am wondering if i can perform METAl without effect allele frequency or is there anything I can do to fix this problem? frequency…

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Decode Genetics Plasma Proteome Study Improves Understanding of Disease Pathogenesis

NEW YORK – Researchers at Decode Genetics (a subsidiary of Amgen), the University of Iceland, and Reykjavik University have conducted a population-scale study of plasma proteins, genomics, and transcriptomics data to create a new resource that could be used to further elucidate disease pathogenesis. In a study published in Nature…

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Job: Research Associate (Bioinformatics-Bio-Data Science)

Job Description A Research Associate (Bioinformatics/Bio-Data Science/Machine Learning) position is currently available in the Bio-Data Science and Education Laboratory, School of Biological Sciences, Nanyang Technological University, Singapore (gohwils.github.io/biodatascience/). The project is concerned with developing predictive models for early detection of mental illness in youth cohorts in Singapore and New Zealand…

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Large-scale integration of the plasma proteome with genetics and disease

1. Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47, D1005–D1012 (2019). CAS  Google Scholar  2. Loos, R. J. F. 15 years of genome-wide association studies and no signs of slowing down. Nat. Commun. 11, 5900…

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GPA-Tree: Statistical Approach for Functional-Annotation-Tree-Guided Prioritization of GWAS Results

Motivation: In spite of great success of genome-wide association studies (GWAS), multiple challenges still remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), each with small or moderate effect sizes. Second, our understanding of the functional mechanisms through which genetic variants are associated with complex traits…

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Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information

Where To Get The Genetic Map For The Haplotype Reference Consortium to phase the data externally using SHAPEIT software with family information 0 The Sanger Imputation Service does not offer a pipeline that utilizes the family information during phasing. Therefore, our pipeline (previously) has been to previously use genetic maps…

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How to calculate beta and SE from z-score , p-value and frequency

How to calculate beta and SE from z-score , p-value and frequency 0 Hi all, I have (an imputed) GWAS that only has z-score and p-values. I want to convert z-score into beta and SE. My ultimate goal is to use log(odds ratio) with its corresponding standard error to run…

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An Introduction to BioTechniques and Next-Generation Sequencing

Share Tweet Share Share Email An overview of the latest in next-generation sequencing techniques and technologies. Next-generation sequencing (NGS), or ‘high-throughput sequencing’, is a catch-all term that refers to various modern sequencing techniques. These techniques enable the rapid sequencing of the base pairs…

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Correlation between MYO9B gene polymorphism and IBD

Introduction Inflammatory bowel disease (IBD) is chronic and recurrent intestinal inflammation of unknown etiology. Epidemiological data indicate that the incidence of IBD is high in Western regions, such as the Americas and Europe, and low in Asian regions. However, IBD has become increasingly common in Asia in recent years with…

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Polygenetic risk score construction in UKBB

Polygenetic risk score construction in UKBB 0 Hi, all. I am learning to construct a polygenetic score in UKBB using published GWAS summary statistics. So I was trying to apply for certain SNPs in the AMS. When applying for SNPs one by one, I was asked to enter SNP (Affy)…

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Gwas Help.

Gwas Help. 0 GWAS: I only have information on single allele in every samples. Example: At pos 657, sample 1 has T, sample 2 has C, sample3 has T and so on. To conduct a GWAS, should I consider it as homozygous? Ex. C should be treated as CC for…

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michigan imputation server

michigan imputation server 0 Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use mimimac3 (–format GT,DS,GP) and in the output file “.dose.vcf.gz” are present all the three formats. I’m new on this kind of…

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Bioinformatics Analysis

News:Bioinformatics Analysis 0 Increasingly, bioinformatics analysis is a bottleneck in the research process. Datasets continue to grow in size and complexity and typically require the intelligent use of many different tools to be queried effectively. With competitive rates, our skilled Data Analysis group are able to help move your bioinformatics…

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minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing when that autopkgtest is run with the binary packages of minimac4 from unstable. It passes when run with only packages from testing. In…

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How to classify the SNPs/gene loci as reported or novel?

How to classify the SNPs/gene loci as reported or novel? 1 I have a big list of significant SNPs (>30K) from a GWAS/meta-analysis. Can you please suggest what are some best ways to find the respective gene names and further classify them as already reported and novel ones? Thanks in…

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SHAPEIT using VCF unphased genotype input

I can get SHAPEIT to work with the default Plink PED/MAP format input files, but not with a VCF as input. As an example, here I use the demo data that comes with SHAPEIT, which runs well. DEMO=/Users/michaelflower/bin/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/example shapeit -B $DEMO/gwas.bed $DEMO/gwas.bim $DEMO/gwas.fam -M $DEMO/genetic_map.txt -O “$DIR”/shapeit/gwas.phased However, when I…

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Senior Bioinformatics Scientist in Cambridge, Cambridgeshire | The Tec Recruitment Group Limited

Senior Bioinformatics Scientist – Cambridge Remote/hybrid working option Role overview: You will be part of an industry leading Genomics company, who are working in the development and accessibility of sequencing products to push the boundaries of drug discovery and therapy development. You will be part of a global team of…

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How can get significant results from the GWAS summary statistics results

How can get significant results from the GWAS summary statistics results 0 How can I use the GWAS summary statistics results and get the most significant genes and SNPs? summary GWAS PGS statistics • 41 views • link updated 47 minutes ago by gokberk &utrif; 70 • written 2 hours…

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Allele coding in BGENIE GWAS output

Allele coding in BGENIE GWAS output 1 Hi all, I have a quick question about BGENIE GWAS summary stats. In the summary statistics, alleles are coded as a_0 and a_1, looks like as the following: chr rsid pos a_0 a_1 af info pheno1_beta pheno1_se pheno1_t … 22 22:16050075:A:G 16050075 A…

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How to analyze genotype data and imputed data in GWAS study

How to analyze genotype data and imputed data in GWAS study 0 Dear users, I am new to GWAS study, I have a concern about genetic association procedures. After having real genotyped data from the experiment ( we use the array for genotyping), we need to impute the genotype data….

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Need help understanding a GWAS in an article. : bioinformatics

Hello r/bioinformatics. I’m a student studying plant selection (with an interest in bioinformatics) and right now for a course work (yeah I know using reddit for homework is frowned upon) I need to showcase an example of GWAS used to identify biotic stress. So I found this example of GWAS…

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Genomics Core Policies on Attribution and Cost Recovery

Mission and GoalThe Genomics Core at KUMC serves as a resource for providing expert and timely genomics services for single cell applications, Next Generation sequencing and microarray analysis. The Genomics Core offers services to investigators both within and outside KUMC on a fee for service basis. The Genomics Core’s mission…

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Bioconductor – cageminer

DOI: 10.18129/B9.bioc.cageminer     Candidate Gene Miner Bioconductor version: Release (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally,…

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UC Davis Bioinformatics Core Workshops

Hello researchers! Join the UC Davis Bioinformatics Core for a hands-on multi-day online and in-person workshops! We’re excited to announce the new Metagenomics and Metatranscriptmics workshop this December 2021. We would also to share a sneak peak of our 2022 workshops which will be offered on-site and remote. You can…

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How to make .ped and .map files

How to make .ped and .map files 0 Hello I have a dataset but I need to create .ped and .map files (as I understand) in order to use plink to run a GWAS. However, I do not know what files I need to use in order to create them,…

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How to run a GWAS in command line with Plink2?

How to run a GWAS in command line with Plink2? 0 I am trying to run a GWAS in the command line with plink version 2, however when I run the following command plink2 –file hapmap1 I get the following error Error: Unrecognized flag (‘–file’) I am trying to follow…

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Linked supergenes underlie split sex ratio and social organization in an ant

Significance Some social insects exhibit split sex ratios, wherein a subset of colonies produce future queens and others produce males. This phenomenon spawned many influential theoretical studies and empirical tests, both of which have advanced our understanding of parent–offspring conflicts and the maintenance of cooperative breeding. However, previous studies assumed…

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Polygenic scores in diabetic individuals across UKBB

Polygenic scores in diabetic individuals across UKBB 1 Hi all, I am calculating PRS for a binary trait (T2D) across UKBB individuals. I am using external GWAS from PRS catalog in order to acquire weights for the base file. I have noticed the weights are given in the form of…

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PLINK Dosage file without family ID error

PLINK Dosage file without family ID error 0 Hi, I am simply trying to extract a small set of SNPs from a .dos dosage file using plink1.9. However, I get the error: Line 1 of yourfile.dos has fewer tokens than expected I have checked that the .fam file and the…

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ICH GCP – CRA jobs – Senior Scientist Bioinformatics

Parexel International Corporation USA – Any Region – Home Based The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for…

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Relationship between Standard Error and P-value

GWAS – Relationship between Standard Error and P-value 1 Is there a relationship between the p-values obtained in a GWAS and the standard error of the effect size of a SNP that can that can be explained either explicitly or intuitively? Methods for prediction based on effect sizes, such as…

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Postdoc in the area of bioinformatics / genomics

Category Research / Academic Location Wageningen Do you want to use as researcher your expertise in analyses of whole genome sequences to contribute to research to identify functional genetic variants in pigs to improve genomic selection? Do you want to work together with national and international breeding organisations? We have…

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Senior Scientist Bioinformatics at Parexel

The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for the BGM strategy and interpretation to other SBUs and clients….

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X-chromosome variants are associated with aldosterone producing adenomas.

Dutta RK, Larsson M, Arnesen T, Heie A, Walz M, Alesina P, Gimm O, Söderkvist P Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18] Aldosterone-producing adenomas (APAs) are a major cause of primary aldosteronism (PA) and are characterized by constitutively producing aldosterone, which leads to hypertension. Several mutations have been…

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(LDSC) – Munge Error – ValueError: could not convert string to float: OR

Hi everyone, I am trying to munge some data for later use in ldsc and I come into this error: /home/expcard/Projects/GWAS_SCA/GWAS_NTR/LDSC/ldsc/munge_sumstats.py –sumstats /home/dominicz/LDSC/SCAMILIFELINESforMETALnoSNPFinalLDSCmunge.txt –N 18236 –chunksize 500000 –out /home/dominicz/LDSC/SCAMILIFELINESforMETALnoSNPFinalLDSC.munge.txt –merge-alleles /home/dominicz/LDSC/w_hm3.snplist LD Score Regression (LDSC) Version 1.0.1 (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane Broad Institute of MIT and Harvard…

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Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat

Background: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat…

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deflated QQ plot but lambda >1

deflated QQ plot but lambda >1 1 Dear All, What might be the reason for a deflated QQ-plot but lambda showing > 1 value. GWAS (case-control using glm-logistic regression adjusting for PC1-PC3 and three covariates) was done in plink2.0, and QQ plot using QQman package TIA package plink deflation GWAS…

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Genome Engineering Research Scientist

Genome Engineering Research Scientist – 94152 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Environmental Genomics and Systems Biology Division (biosciences.lbl.gov/divisions/egsb/) has an opening for a Genome Engineering Research Scientist to join the team. In this exciting role, you will work as part of the Center for Advanced…

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ALSPAC Bioinformatics and Biobank Data Manager

The role The Avon Longitudinal Study of Parents and Children (ALSPAC) is a longitudinal population study following the lives of thousands of study participants living in and around Bristol and elsewhere is the UK. ALSPAC is run as a resource and researchers from all over the world access data and…

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Bioinformatics Programmer/Analyst – Job at RTI Research Triangle Institute in Washington, DC

The GenOmics, Bioinformatics, and Translational Research Center at RTI International has an opening for a Bioinformatics Programmer/Analyst interested in applying their computational and analytical skills within a team of researchers who leverage high-dimensional, multi-omic data sets to discover biomarkers of human health and disease. Who we are:Our team is a…

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PLINK and population stratification with known subpopulations

PLINK and population stratification with known subpopulations 0 I want to perform a genome wide association study (GWAS) with PLINK 1.9. I have whole genome sequencing SNP calls for ~100 patients where I know in advance that there is a skew towards subpopulations of African and South American descents, with…

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How to check the allele strand of variants?

How to check the allele strand of variants? 1 Hi all, I have a list of variants obtained from various GWAS studies, it is important for me that all variant alleles (alternate allele) located on the forward strand. Could you please kindly tell me how I can check this issue…

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Post Doctorate Fellow Job at Tata Memorial Centre – Bioinformatics

The Tata Memorial Centre is a Comprehensive Cancer Centre with a mission to achieve the highest standards in patients care, cancer prevention, cancer research and professional development for oncology and allied disciplines. TMC is an autonomous Grant-In-Aid Institute of the Department of Atomic Energy, Government of India. TMC is affiliated…

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Checking chromosome builds for genotyping data

Checking chromosome builds for genotyping data 0 Hi, I have several studies worth of data (In both PLINK and vcf format), and I was wondering if anyone knew of an online tool which I could use to check my chromosome build i.e GRCh37 vs GRCh38. (I thought I used one…

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Looking Back 20 Years After the Unveiling of the First Human Genome Sequence

I’m about to begin revising the 14th edition of my human genetics textbook. In normal times, I’d have amassed technical articles and case reports, as well as notes from meetings and interviews, choosing topics to add or ax and updating or replacing examples as the new edition takes shape. But…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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Further and More Detailed Study of Domestic Cat Genome | McDonnell Boehnen Hulbert & Berghoff LLP

The advent of technology making feasible elucidation of whole genomic sequencing over the past 30 years has led to reports of many if not most important or interesting animal genomes (including the most celebrated results of the Human Genome Project) (see, e.g., “Nautilus pompilius Genome Determined“; “Giraffe Genome Reveals Relevant…

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Molecular Signature of PWS Linked to Episodes of Psychosis, Study Finds

Prader–Willi syndrome (PWS) is associated with a specific molecular signature — a set of genes that can be used as markers for a certain trait — in the brain that is linked to episodes of psychosis, or a loss of contact with reality, a mouse study found. According to the…

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CSIRO Postdoctoral Fellowship in Transformational Bioinformatics at CSIRO Australia

The Opportunity   Kick-start your research career in Bioinformatics Contribute to the development of genome-based analytics and clinical applications Join CSIRO – Australia’s leading scientific research organisation!    CSIRO Early Research Career (CERC) Postdoctoral Fellowships provide opportunities to scientists and engineers who have completed their doctorate and have less than three years…

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How to make Q-Q plots for different models at a single chart using R?

How to make Q-Q plots for different models at a single chart using R? 1 Hello everyone! I am trying to make a Q-Q plot to visualise p-values obtained from different models afterr runing GWAS analysis. The key thing is that I want to reflect p-values from the different models…

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Polygenic Risk Score Analysis for an individual genome

Polygenic Risk Score Analysis for an individual genome 2 Hello, I am developing a model for PRS calculation. For PRS, you need the base data and target data. I have got these datasets however, it is not clear how the model can be used to predict the susceptibility of a…

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GWAS Studies

GWAS Studies 0 How to create a .ped file for use in PLink? I have the following csv file: Chromosome Position Sample1 Sample 2 ……….. Sample n Chr Pos Sam1 Sam2 Sam3, Sam 4, ……Sample_n 1 11 A T T, A, A, T, …… 2 141 G G G, T,…

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Bioinformatics Scientist (Genome) in Bethesda, MD

Position Objective: Provide services as a Bioinformatics Scientist in support of the overall functions of the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH). Duties and Responsibilities: + Generate and optimize programs and scripts for the analysis of data; create programs and algorithms and develop…

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GWAS data from PGC

GWAS data from PGC 0 this is my first time using the GWAS data, I downloaded some data from PGS and I Have some questions. 1- there are a lot of SNP to the same gene with different P-values, why does this occur? and if I want to use one…

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How do I know the SNPS which are removed when clumping are in a LD block or SNPs not existed in 1000 Genome

How do I know the SNPS which are removed when clumping are in a LD block or SNPs not existed in 1000 Genome 0 Hi everyone, I’m not sure how to know why my SNPs are being removed applying clumping when reading the exposure data (in MR analysis). I would…

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Mitochondrial DNA sequence variation and risk of meningioma

This article was originally published here J Neurooncol. 2021 Oct 20. doi: 10.1007/s11060-021-03878-5. Online ahead of print. ABSTRACT BACKGROUND: Risk factors for meningioma include female gender, African American race, high body mass index (BMI), and exposure to ionizing radiation. Although genome-wide association studies (GWAS) have identified two nuclear genome risk…

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Research Associate (Bioinformatics-Bio-Data Science) [R00003753] at Nanyang Technological University Singapore

Job Description A Research Associate (Bioinformatics/Bio-Data Science/Machine Learning) position is currently available in the Bio-Data Science and Education Laboratory, School of Biological Sciences, Nanyang Technological University, Singapore (gohwils.github.io/biodatascience/). The project is concerned with developing predictive models for early detection of mental illness in youth cohorts in Singapore and New Zealand…

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