Tag: eQTL

Short tandem repeat mutations regulate gene expression in colorectal cancer

A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…

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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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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…

Continue Reading 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

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…

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

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….

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

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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INTERVAL RNA-seq Portal | eQTL

INTERVAL RNA-seq Portal | eQTL Gene ID Gene Type Range Lead RsID qVal Z-score Independent eQTL signals Rank Variant RsID Variant PosID AF Dist Beta (joint) P-val (joint) Nominal eQTL summary statistics Variant RsID Variant PosID AF Beta P-val Z-score PheWAS for lead variant (OpenTargets) Trait Author PMID Beta P-val…

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DNA methylation modulated genetic variant effect on gene transcriptional regulation

Background: Expression quantitative trait locus (eQTL) analysis has emerged as an important tool in elucidating the link between genetic variants and gene expression, thereby bridging the gap between risk SNPs and associated diseases. We recently identified and validated a specific case where the methylation of a CpG site influences the…

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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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Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

Abstract Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map…

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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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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…

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

a survey of IGAP genes and SNPs.

Translating Alzheimer’s disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. Publication ,  Journal Article Katsumata, Y; Nelson, PT; Estus, S; Alzheimer’s Disease Neuroimaging Initiative (ADNI), ; Fardo, DW Published in: Neurobiol Aging The International Genomics of Alzheimer’s Project (IGAP) is a consortium for characterizing the genetic landscape…

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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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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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The effect of developmental variation on expression QTLs in a multi parental C. elegans population

doi: 10.1093/g3journal/jkad273. Online ahead of print. Affiliations Expand Affiliations 1 Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH UTRECHT  The Netherlands. 2 Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. 3 Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB…

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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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Is Equital (TLV:EQTL) A Risky Investment?

Howard Marks put it nicely when he said that, rather than worrying about share price volatility, ‘The possibility of permanent loss is the risk I worry about… and every practical investor I know worries about.’ When we think about how risky a company is, we always like to look at…

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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…

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

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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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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JAPAY,DGII,EQTL,ARW,MO,USIO,TGAN,SBEV Earnings-per-Diluted-Share Over Time

You can use any or all of fundamental ratio historical patterns as a complementary method for asset selection as well as a tool for deciding entry and exit points. Many technical investors use fundamentals to limit their universe of possible positions. Check out your portfolio center. Specify up to 10…

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Trans-eQTL hotspots shape complex traits by modulating cellular states

Abstract Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces…

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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…

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

Latent human herpesvirus 6 is reactivated in CAR T cells

Spanjaart, A. M., van der Valk, F. M., van Rooijen, G., Brouwer, M. C. & Kersten, M. J. Confused about confusion. N. Engl. J. Med. 386, 80–87 (2022). Article  PubMed  Google Scholar  Haradhvala, N. J. et al. Distinct cellular dynamics associated with response to CAR-T therapy for refractory B-cell lymphoma….

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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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Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

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Equital (TLV:EQTL) Is Reinvesting At Lower Rates Of Return

Did you know there are some financial metrics that can provide clues of a potential multi-bagger? Typically, we’ll want to notice a trend of growing return on capital employed (ROCE) and alongside that, an expanding base of capital employed. Basically this means that a company has profitable initiatives that it…

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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/

Correction to: A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator | Plant Physiology

This is a correction to: Feng Zhu, Sagar Sudam Jadhav, Takayuki Tohge, Mohamed A Salem, Je Min Lee, James J Giovannoni, Yunjiang Cheng, Saleh Alseekh, Alisdair R Fernie, A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator, Plant Physiology, Volume 190, Issue 1, September 2022,…

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eQTL | Broad Institute

In March of 2020, Broad Institute converted a clinical genetics processing lab into a large-scale COVID-19 testing facility in less than two weeks. We’ve screened more than 1,275 cancer cell lines as part of the Cancer Dependency Map (DepMap). Broad Genomics Platform sequences a whole human genome every four minutes….

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Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients

Background: More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are…

Continue Reading Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients

Expanding causal genes for Parkinson’s disease via multi-omics analysis

Proteins causally associated with PD in the brain MR analysis of brain dorsolateral prefrontal cortex (dlPFC) pQTLs identified six genetically determined significant proteins on PD after multiple testing corrections (P < 8.55E-05 (0.05/585)). Specifically, the increased abundance of 3 proteins was significantly associated with an increased risk of PD, including GPNMB (OR:1.464,…

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Genomics for monitoring and understanding species responses to global climate change

Smith, T. B. & Bernatchez, L. Evolutionary change in human-altered environments. Mol. Ecol. 17, 1–8 (2008). Article  PubMed  Google Scholar  Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012). Article  PubMed  PubMed Central  Google…

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Systematic differences in discovery of genetic effects on gene expression and complex traits

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Gusev, A. et…

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The eQTL analysis to discover unique eGFR-related SNPs for the Taiwanese population

Chen YC, Wong HS, Wu MY, Chou WH, Kao CC, Chao CH, Chang WC, Wu MS (2022) Genome-wide association study for eGFR in a Taiwanese population. Clin J Am Soc Nephrol 17(11):1598–1608. doi.org/10.2215/CJN.02180222 Article  CAS  PubMed  Google Scholar  Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmuller G (2015) SNiPA:…

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Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Gene expression atlas in fiber development To uncover the genetic regulation of gene expression in fiber development, we collected 376 diverse G. hirsutum accessions for genome and transcriptome analysis. A total of 13.5 Tb of genome resequencing data were generated, with an average depth of 15.6× (Supplementary Table 1). Accessions were…

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eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants

Bajaj D, Upadhyaya HD, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CL, Singh S, Sharma S, Tyagi AK, Chattopdhyay D, Parida SK (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci…

Continue Reading eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

Abstract The impact of genetic regulatory variation active in early pancreatic development on adult pancreatic disease and traits is not well understood. Here, we generate a panel of 107 fetal-like iPSC-derived pancreatic progenitor cells (iPSC-PPCs) from whole genome-sequenced individuals and identify 4,065 genes and 4,016 isoforms whose expression and/or alternative…

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Interrogating the effect of variation in trans-acting factors

Abstract Mutations in trans-acting factors such as transcription factors, chromatin regulators, and DNA repair genes may cause widespread transcriptomic changes or altered genome-wide mutation patterns leading to a variety of phenotypes with varying impact on human health. Functional consequences of these mutations are difficult to systematically evaluate on a large…

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Equital Ltd.’s (TLV:EQTL) stock price dropped 16% last week; retail investors would not be happy

Key Insights Equital’s significant retail investors ownership suggests that the key decisions are influenced by shareholders from the larger public The top 4 shareholders own 51% of the company Institutions own 28% of Equital If you want to know who really controls Equital Ltd. (TLV:EQTL), then you’ll have to look…

Continue Reading Equital Ltd.’s (TLV:EQTL) stock price dropped 16% last week; retail investors would not be happy

Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…

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Fast Eqtl Analysis Tool

Fast Eqtl Analysis Tool 4 I’ve got about 2M imputed SNPs and 35K gene expression probesets, and I’d like to identify all eQTL. Running this under PLINK –linear is going to take a very long time, are there any specialized tools out there to handle this sort of data? eqtl…

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Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses

doi: 10.1093/g3journal/jkad229. Online ahead of print. Affiliations Expand Affiliation 1 Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, 84112, USA. Item in Clipboard Nikki D Russell et al. G3 (Bethesda). 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/g3journal/jkad229. Online ahead of print….

Continue Reading Characterizing genetic variation in the regulation of the ER stress response through computational and cis-eQTL analyses

Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes

Li QS, Shabalin AA, DiBlasi E, Gopal S, Canuso CM, FinnGen ISGC, et al. Genome-wide association study meta-analysis of suicide death and suicidal behavior. Mol. Psychiatry 2023;28:891–900. McGuffin P, Marusic A, Farmer A. What can psychiatric genetics offer suicidology? Crisis. 2001;22:61–65. Article  CAS  PubMed  Google Scholar  Pedersen NL, Fiske A….

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Identification of eQTL from porcine muscle and liver mRNA sequencing

Master’s Dissertation DOI doi.org/10.11606/D.11.2023.tde-02102023-151405 Document Author Freitas, Felipe André Oliveira (Catálogo USP) Full name Felipe André Oliveira Freitas E-mail Institute/School/College Escola Superior de Agricultura Luiz de Queiroz Knowledge Area Animal Science and Pastures Date of Defense Published Piracicaba, 2023 Supervisor Cesar, Aline Silva Mello (Catálogo USP) Committee Cesar, Aline Silva…

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Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification

Timmis, A. et al. European Society of Cardiology: Cardiovascular Disease Statistics 2017. Eur. Heart J. 39, 508–579 (2018). Article  PubMed  Google Scholar  Tsao, C. W. et al. Heart Disease and Stroke Statistics—2022 Update: a report from the American Heart Association. Circulation 145, e153–e639 (2022). Article  PubMed  Google Scholar  Libby, P.,…

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Splitting VCF/BCF file into seperate gene files

Splitting VCF/BCF file into seperate gene files 0 I have a multi-sample bcf file which I would like to split into smaller files per gene so I can use this for some downstream eQTL analysis. I’ve started a bash script which pipes bcftools query -f ‘%SAMPLE\t%POS\t%REF\t%ALT\t%GT\n’ into an awk script…

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tensorQTL interaction issue

Hi, I hope that the question has its place on this board. I am trying to run the mapping of cis eQTL using an interaction term with tensorQTL. I am running into the following index error when running the software: >>> cis.map_nominal(genotype_df, variant_df, … phenotype_df, … phenotype_pos_df, … prefix =…

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eQTL mapping in Brown Swiss bulls to identify variants associated with male fertility

Abstract Fertility is an essential component of the livestock industry. In cattle, numerous QTL for male reproductive success fall within regulatory regions. However, the effects of these loci have not been investigated in detail or on a large scale. Here, we assemble a sizeable cohort of mature bulls to detect…

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eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs

. 2023 Sep 18;19(9):e1010932. doi: 10.1371/journal.pgen.1010932. Online ahead of print. Nurlan Kerimov  1   2 , Ralf Tambets  1 , James D Hayhurst  2   3 , Ida Rahu  1 , Peep Kolberg  1 , Uku Raudvere  1 , Ivan Kuzmin  1 , Anshika Chowdhary  4 , Andreas Vija  1 , Hans J Teras  1 , Masahiro Kanai  5  …

Continue Reading eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs

Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis.

There has been growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by non-coding variants, suggesting genetic regulatory effects may…

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Powerful eQTL mapping through low-coverage RNA sequencing.

Abstract Mapping genetic variants that regulate gene expression (eQTL mapping) in large-scale RNA sequencing (RNA-seq) studies is often employed to understand functional consequences of regulatory variants. However, the high cost of RNA-seq limits sample size, sequencing depth, and, therefore, discovery power in eQTL studies. In this work, we demonstrate that,…

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An eQTL-based Approach Reveals Candidate L1 Transcriptional Regulators in Lymphoblastoid Cells

Abstract Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. The pleiotropic effects L1 induces in host cells (promoting genome instability, inflammation, or cellular senescence) are established, and L1’s associations with aging and aging diseases are widely recognized. However,…

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Genome-wide analysis identifies novel loci influencing plasma apolipoprotein E concentration and Alzheimer’s disease risk

The details of study participants, plasma ApoE measurement, genotyping and imputation, statistical analyses, and functional annotations are given in Online Methods. Association of plasma ApoE concentration with incident dementia and cognition function Whole plasma ApoE concentration at baseline was determined in 3031 participants, of which 2893 were European Americans (EAs),…

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Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Consensus MTG taxonomy across primates The BRAIN Initiative Cell Census Network26 generated high-resolution transcriptomic maps of the MTG in human, chimpanzee, gorilla, macaque and marmoset by applying single-nucleus transcriptomic (snRNA-seq) assays to samples isolated from between three and seven donor brains in each species (plate-based SMART-seq v4 (SSv4) for great…

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An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.

An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. Publication ,  Journal Article Gillies, CE; Putler, R; Menon, R; Otto, E; Yasutake, K; Nair, V; Hoover, P; Lieb, D; Li, S; Eddy, S; Fermin, D; McNulty, MT; Hacohen, N … Published in: Am J Hum Genet Expression quantitative trait loci…

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Transcriptome-wide association studies: recent advances in methods, applications and available databases

TWAS conducts association tests for each gene-trait pair leveraging analysis from eQTL effects and GWAS associations. Based on the idea of TWAS, the basic workflow can be divided into three steps, as illustrated in Fig. 1. It is noted that different models are contained in various stages and should be distinguished…

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How should I adjust covariates in eQTL analysis with an interaction term?

How should I adjust covariates in eQTL analysis with an interaction term? 0 Hello, I’m trying to perform eQTL analysis using an interaction term. (maybe with MatrixEQTL) My purpose is to get eQTLs having different effects according to the gender. In my case, it’s impossible to perform analyses separately for…

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Bioinformatics Analyst – School of Medicine, Microbiology/Immunology

Discover Your Career at Emory University: Emory University is a leading research university that fosters excellence and attracts world-class talent to innovate today and prepare leaders for the future. We welcome candidates who can contribute to the diversity and excellence of our academic community. Description: Our labs study epigenetic and…

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Bioinformatics Analysis Homes in on Two Dozen Genes That Could Be Targets for Drugs in Obesity

In a bioinformatic analysis, researchers have identified nearly two dozen genes implicated in obesity that could be targeted by 78 approved and marketed drugs, in a new Journal of Human Genetics study. A team from the National Center for Global Health and Medicine in Tokyo compiled a list of nearly…

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Is Equital Ltd.’s (TLV:EQTL) Recent Stock Performance Influenced By Its Fundamentals In Any Way?

Most readers would already be aware that Equital’s (TLV:EQTL) stock increased significantly by 21% over the past three months. We wonder if and what role the company’s financials play in that price change as a company’s long-term fundamentals usually dictate market outcomes. Specifically, we decided to study Equital’s ROE in…

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Colocalization Coloc – Error in if (min(p) > warn.minp)

Colocalization Coloc – Error in if (min(p) > warn.minp) 0 I have been getting the following error using the most recent version of coloc: Error in if (min(p) > warn.minp) warning(“minimum p value is: “, format.pval(min(p)), : missing value where TRUE/FALSE needed I have checked the datasets and have confirmed…

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eQTL mapping in transgenic alpha-synuclein carrying Caenorhabditis elegans recombinant inbred line

Abstract Protein aggregation of alpha-synuclein (alphaS) is a genetic and neuropathological hallmark of Parkinson disease (PD). Studies in the model nematode Caenorhabditis elegans suggested that variation of alphaS aggregation depends on the genetic background. However, which genes and genetic modifiers underlie individual differences in alphaS pathology remains unknown. To study…

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A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology

INTERVAL study The INTERVAL study was a randomised trial of approximately 45,000 blood donors aged eighteen years or older who were recruited at 25 NHSBT (National Health Service Blood and Transplant) static donor centres across England21. The study was approved by the Cambridge East Research Ethics Committee and we complied…

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Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…

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Modeling tissue co-regulation estimates tissue-specific contributions to disease

Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020). Article  CAS  PubMed  Google Scholar  Ongen, H. et al. Estimating the causal tissues for complex traits and diseases. Nat. Genet. 49, 1676–1683 (2017). Article  CAS  PubMed  Google Scholar …

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Sci-Hub | Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. PLOS Genetics, 13(3), e1006690

Sci-Hub | Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. PLOS Genetics, 13(3), e1006690 | 10.1371/journal.pgen.1006690 ◂ ↓ save Hoffman, J. D., Graff, R. E., Emami, N. C., Tai, C. G., Passarelli, M. N., Hu, D., … Witte, J. S. (2017). Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes…

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Dissecting human population variation in single-cell responses to SARS-CoV-2

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

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Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis

Compston, J. E., McClung, M. R. & Leslie, W. D. Osteoporosis. Lancet 393, 364–376 (2019). Article  CAS  PubMed  Google Scholar  Jha, S., Wang, Z., Laucis, N. & Bhattacharyya, T. Trends in media reports, oral bisphosphonate prescriptions, and hip fractures 1996–2012: an ecological analysis. J. Bone Miner. Res. 30, 2179–2187 (2015)….

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eQTL Study Uncovers New Candidate Genes for Adipose Tissue Biology

Researchers have identified new candidate genes involved in adipose tissue biology through an expression quantitative trait loci study of a Greek population. As they report in BMC Genomics, a team from the Biomedical Sciences Research Center Alexander Fleming in Athens and elsewhere conducted eQTL mapping in subcutaneous and visceral adipose…

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Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics

Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health and disease. Nat Rev Cardiol. 2019;16(2):83–99. Article  PubMed  Google Scholar  Sakers A, De Siqueira MK, Seale P, Villanueva CJ. Adipose-tissue plasticity in health and disease. Cell. 2022;185(3):419–46. Article  CAS  PubMed  Google Scholar  Sun W, von Meyenn F, Peleg-Raibstein…

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Transcriptomic risk scores for attention deficit/hyperactivity disorder

Song P, Zha M, Yang Q, Zhang Y, Li X, Rudan I. The prevalence of adult attention-deficit hyperactivity disorder: A global systematic review and meta-analysis. J Glob Health. 2021;11:1–9. Article  Google Scholar  Faraone SV, Asherson P, Banaschewski T, Biederman J, Buitelaar JK, Ramos-Quiroga JA, et al. Attention-deficit/hyperactivity disorder. Nat Rev…

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Bioinformatics Analyst (EQTL/GWAS/Fine Mapping/Colocalization) – Rangam Infotech Pvt Ltd

Schedule: 9AM-5PM CT or ET Bioinformatician/Computational Biologist – transcriptomics focused Linux & Unix exp needed. Experience in the analysis and integration of NGS data. Prior research experience in studying immunological diseases areas is a plus. Experience working in HPC or Linux platform. Transcriptomic or genetic data exp is a must…

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Zhejiang Nonglin reveals a new mechanism of cell wall xylan acetylation affecting the biomass energy conversion efficiency of poplar

Recently, the research team of Professor Zhang Jin from Zhejiang A&F University published a research paper entitled Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus online in Plant Physiology . Plant lignocellulosic biomass, the secondary cell walls of plants, is an important alternative source…

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Pulling back 6.2% this week, Equital’s TLV:EQTL) three-year decline in earnings may be coming into investors focus

By buying an index fund, investors can approximate the average market return. But if you buy good businesses at attractive prices, your portfolio returns could exceed the average market return. Just take a look at Equital Ltd. (TLV:EQTL), which is up 77%, over three years, soundly beating the market return…

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Mendelian randomization uncovers a protective effect of interleukin-1 receptor antagonist on kidney function

Ramesh, G. & Reeves, W. B. Inflammatory cytokines in acute renal failure. Kidney Int. Suppl. S56–S61. doi.org/10.1111/j.1523-1755.2004.09109.x (2004) Ye, S., Ozgur, B. & Campese, V. M. Renal afferent impulses, the posterior hypothalamus, and hypertension in rats with chronic renal failure. Kidney Int. 51, 722–727 (1997). Article  CAS  PubMed  Google Scholar …

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Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice | BMC Medicine

The strategy and logic of choosing VRK2 SNPs for genetic analyses We retrieved the summary statistics of VRK2 SNPs in 23andMe, UK Biobank, and PGC2 samples [2, 3], and 256 SNPs region were available in all three GWAS datasets (a total of 246,363 cases and 561,190 controls). An overview about…

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Equital (TLV:EQTL) Takes On Some Risk With Its Use Of Debt

Legendary fund manager Li Lu (who Charlie Munger backed) once said, ‘The biggest investment risk is not the volatility of prices, but whether you will suffer a permanent loss of capital.’ It’s only natural to consider a company’s balance sheet when you examine how risky it is, since debt is…

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GWAS Catalog at European Molecular Biology Laboratory (EMBL)

About the team/job We are looking for an experienced Bioinformatician Developer to join the GWAS Catalog development team within the Samples, Phenotypes and Ontologies team. You’ll be working on the GWAS Catalog Summary Statistics Infrastructure, and you’ll have the opportunity to influence the design and development of the system to…

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Trans-Acting Genotypes Associted with mRNA Expression Affect Metabolic and Thermal Tolerance Traits

doi: 10.1093/gbe/evad123. Online ahead of print. Affiliations Expand Affiliation 1 Department of Marine Biology and Ecology, The Rosenstiel School, University of Miami, Miami, FL, USA. Item in Clipboard Melissa K Drown et al. Genome Biol Evol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/gbe/evad123. Online ahead of print….

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Accounting for Isoform Expression in eQTL Mapping Substantially Increases Power

Abstract A core problem in genetics is eQTL mapping, in which genetic variants associated with changes in expression of genes are identified. It is common in eQTL mapping to compute gene expression by aggregating the expression levels of individual isoforms from the same gene and then performing linear regression between…

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Sequence variants affecting the genome-wide rate of germline microsatellite mutations

STR identification and genotyping We used popSTR34 to call genotypes at 5,401,401 autosomal short tandem repeats (STRs) in two large WGS data sets, 53,026 Icelanders and 150,119 participants in the UK Biobank (UKB), sequenced to an average coverage of 39.2× (min: 19.7, max: 608.3) and 32.5× (min: 23.6, max: 128.1),…

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Download | RatGTEx

See the About page for processing and data format specifications. Gene info Gene expression Median TPM per gene per tissue Used for heatmap visualizations log2(count+1) Used to compute allelic fold change Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC…

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Should genotype PCA in eQTL analysis be performed using all SNPs? or can be with a subset of SNPs?

Should genotype PCA in eQTL analysis be performed using all SNPs? or can be with a subset of SNPs? 0 Hello, I’m a beginner in eQTL analysis. Now I’m using a published variant dataset, and I want to detect eQTLs from a list of variants located in enhancer elements. As…

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EQTL news, real time EQTL stock news, Equitech Intl news today

Securities trading is offered to self-directed customers by Webull Financial LLC, a broker dealer registered with the Securities and Exchange Commission (SEC). Webull Financial LLC is a member of the Financial Industry Regulatory Authority (FINRA), Securities Investor Protection Corporation (SIPC), The New York Stock Exchange (NYSE), NASDAQ and Cboe EDGX…

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Integration of eQTL and Machine Learning Methods to Dissect Causal Genes with Pleiotropic effects in Genetic Regulation Networks of Seed Cotton Yield

Abstract Expression quantitative trait loci (eQTL) provide a powerful means of investigating the biological basis of genome-wide association study (GWAS) results and exploring complex traits or phenotypes. In addition to identifying the causal gene in cis, eQTL analysis also reveals a large number of trans-regulated genes located on different chromosomes,…

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GASPACHO: A Game-Changer in Investigating Genetic Susceptibility to COVID-19

Researchers have developed a new technique called GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity) that allows researchers to track changes in gene expression along the innate immune response, revealing previously unknown culprits for illness risk. Scientists have discovered a gene variation linked to an increased susceptibility to COVID-19…

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Research Fellow (Biological Sciences) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description (1) The Allergy and Molecular Immunology Laboratory / (2) Molecular Breeding Laboratory at the Lee Hiok Kwee Functional Genomics Laboratories, Department of Biological Sciences led by Associate Professor CHEW Fook Tim, is currently looking for (a) Molecular Biologist and (b) Bioinformatician / Geneticist / Statistician, to work on…

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A Game-Changer in Unraveling Genetic Susceptibility to COVID-19

Researchers have utilized a novel tool named GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity) to discover a mechanism for COVID-19 susceptibility related to genetic variations. This tool enables scientists to track changes in gene expression along the innate immune response, shedding light on previously hard-to-identify factors contributing to…

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eQTL and sQTL from 16 cattle tissues (linear mixed model).

Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle” (www.biorxiv.org/content/10.1101/2022.05.30.494093v1) Summary stats of cis and trans eQTL and sQTL mapped from 16 cattle tissues (N~5000) using linear mixed model. Multi-tissue eQTL and sQTL (from meta-analysis) are also included. For details, please read “esQTLSumdataXiang2022/README.txt”…

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Study Compares Abilities of Various Genetic Approaches to Identify Drug Targets

NEW YORK – Researchers compared many major gene prioritization approaches to uncover which can best identify approved drug targets. In a study published in Cell Genomics on Thursday, researchers from Switzerland and The Netherlands compared how well different approaches such as genome-wide association studies (GWAS), quantitative trait loci (QTL) analyses,…

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Some Investors May Be Worried About Equital’s (TLV:EQTL) Returns On Capital

If you’re looking for a multi-bagger, there’s a few things to keep an eye out for. Ideally, a business will show two trends; firstly a growing return on capital employed (ROCE) and secondly, an increasing amount of capital employed. Basically this means that a company has profitable initiatives that it…

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New tool uncovers COVID-19 susceptibility mec

Researchers have discovered a mechanism for COVID-19 susceptibility using a newly created tool. The tool, GASPACHO, captures dynamic changes in gene expression along the innate immune response, allowing researchers to identify genes and molecular pathways associated with disease risk that have previously been too complex to detect or interpret.  Using…

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New tool uncovers COVID-19 susceptibility mechanism

Schematics of experiment and statistical analysis. a, Experimental design using the in vitro fibroblast system. b, GASPACHO framework. Expression data and relevant metadata (known confounding factors) as well as donor (cell line) structure are used to construct a GPLVM to extract the target cell state, while dissecting cell cycle effect…

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Transforming Diagnosis and Therapeutics Using Cancer Genomics

Nogrady B (2020) How cancer genomics is transforming diagnosis and treatment. Nature 579(7800):S10–S10 CrossRef  CAS  PubMed  Google Scholar  Tabin CJ et al (1982) Mechanism of activation of a human oncogene. Nature 300(5888):143–149 CrossRef  CAS  PubMed  Google Scholar  Health NIO (2016) The human genome project completion: Frequently asked questions. National Human…

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