Tag: snp

Job DescriptionThis is a Pre-Fellowship for early career researchers wanting to establish a career in MND translational research and become MND research leaders of the future. The postholder will have a leading role in an exciting new project funded by Motor Neurone Disease Association and MND Scotland. The project is…

How is genetics useful for conservation?5 answersGenetics is useful for conservation in several ways. It allows us to understand and address the loss of genetic diversity in natural populations, which can contribute to extinction risk. Conservation genetics helps investigate the diversity, distribution, and function of genetic variation in populations of…

Isolate characteristics From June 2020 to October 2021, our analysis included a total of 28 isolates from patient and environmental samples, all subjected to Whole Genome Sequencing (WGS) (refer to Table 1). To ensure robustness and minimize the influence of sequencing errors on our findings, all 28 WGS datasets maintained a…

Brent, G. A. Mechanisms of thyroid hormone action. J. Clin. Invest. 9, 3035–3043 (2012). Article  Google Scholar  Iwen, K. A., Oelkrug, R. & Brabant, G. Effects of thyroid hormones on thermogenesis and energy partitioning. J. Mol. Endocrinol. 60, R157–R170 (2018). Article  PubMed  CAS  Google Scholar  Biondi, B. & Wartofsky, L….

Ethics No new aDNA data were generated for this study and we only analysed previously published and publicly available aDNA data. Identifying biological kin is a standard analysis in the aDNA field. Permission for aDNA work on the archaeological samples was granted by the respective excavators, archaeologists, curators and museum…

Sugarcane, a crucial worldwide food and bioenergy crop, accounts for approximately 80% of the world’s sugar production, with its largest cultivation in Brazil and India. As the 5th largest crop by production value and acreage, it presents unique breeding challenges due to its complex polyploid genome, derived from interspecific hybridization….

Sequencing data for a single human genome, at 30× coverage, takes up to 70 gigabytes of storage. Illumina instruments produced 280 million gigabytes of data in 2021 alone, and by 2025, we’ll need storage capacity for 40 billion gigabytes—and that’s just for human genomes. The Genomics & Bioinformatics Service of…

(MENAFN– The Express Wire) Global DNA Analysis in the Government Sector Market 2023 segmented by Manufactures (Lockheed Martin, NEC, M2SYS Technology, MorphoTrust, Ultra Electronics Forensic, NetBio, EyeLock, 3M, A-T Solutions, Stanley Black & Decker), which includes TOC, Fact and Figures, regions. “Final Report will add the analysis of the impact…

Search for specific SNPs in VCF files of patients. 0 I have 490 genomes from 490 patients in VCF format. I created a Multi VCF file from these VCFs. I want to find 2 mutations (Y215C and G325R) in these patients, count the number of patients who have these SNPs…

Almeida OAC, Moreira GCM, Rezende FM et al (2019) Identification of selection signatures involved in performance traits in a paternal broiler line. BMC Genomics 20:1–20. doi.org/10.1186/s12864-019-5811-1 Article  Google Scholar  Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and…

Kershaw, F. et al. The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice. Conserv. Sci. Pract. 4, e12635 (2022). Article  Google Scholar  Waits, L. P. & Paetkau, D. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations…

How to convert and annotate apt-probeset-genotype into PLINK format 2 Dear all, I called SNP genotypes of 100 Affy6 CEL files using apt-probeset-genotype from APT in order to perform a subsequent CNV analysis with PennCNV. As PennCNV doesn’t integrate SNP quality control procedure (move out SNP with genotype call <…

ABL Diagnostics keeps innovating and developing its Research & Development activities through a new line of PCR detection assays, called CRISPRChek, using the disruptive CRISPR technology. First CRISPRChek prototypes to be focusing on HIV & SARS-CoV-2 detection and quantification. Ambitions to position such innovation as an alternative to current qPCR…

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…

Fragment analysis separates and analyzes amplified PCR products according to fragments using a primer marked by a fluorescent label. ‍ Fragment Analysis can have many applications, such as: Linkage mapping Pathogen sub‐typing  Loss of Heterozygosity (LOH)  Animal breeding Genetic diversity Inter‐simple sequence repeat (ISSR)  Human, animal, and plant typing Microsatellite…

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….

One-letter difference in our DNA determines whether BCG vaccine provides good protection against tuberculosis or not. Researchers at Radboudumc have elucidated how that one letter difference affects the activation and deactivation of the immune system. The discovery, published in Nature Genetics, not only provides more insight into interleukin-driven inflammatory responses,…

Convert bed file from hg19 to GRCH38 1 Hello everyone! I have a list of over 500,000 rs and I would like to obtain the coordinates (BED file) on the GRCH38 reference genome. I am using the UCSC Table Browser tool, but unfortunately, it doesn’t find 90,000 rs, and since…

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…

How to compute Hudson’s/Bhatia’s FST in R OR with vcf? 1 Hi everyone, How can I compute hierarchical Fst with Bhatia’s/Hudson’s estimator using a vcf as input? My data is structured like this: there are individuals within sampling sites, and sampling sites within groups. My vcfs contain SNP data (~1000…

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…

Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…

A PCR–RFLP analysis was performed to identify PTC tasters in a population. The taster allele sequence included a palindromic sequence recognized by a restriction enzyme, whereas the non–taster allele did not due to a SNP in the sequence. The gel shows the results of the analysis from 100 individuals. The…

Register for free to listen to this article Thank you. Listen to this article using the player above. ✖ Want to listen to this article for FREE? Complete the form below to unlock access to ALL audio articles. One-letter difference in our DNA determines whether BCG vaccine…

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

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Büyükköroğlu G, Dora DD, Özdemir F, Hızel C (2018)…

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…

GATK GenomicsDBImport too slow 1 Hello, I have 3264 g.VCFs and an interval list for the reference genome that contains 20000 contigs. The interval list looks like the following: utg19_pilon_pilon:1-42237 utg22_pilon_pilon:1-49947 utg24_pilon_pilon:1-61707 utg30_pilon_pilon:1-459006 utg38_pilon_pilon:1-129173 utg40_pilon_pilon:1-101813 utg58_pilon_pilon:1-143918 utg93_pilon_pilon:1-186249 utg100_pilon_pilon:1-87875 utg104_pilon_pilon:1-49315 I am running the GATK GenomicsDBImport command as follows: gatk –java-options…

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

Phylogenetic analysis of lineage IIb C.1 containing all ten local MPXV from Guangdong To rapidly characterize the phylogeny of the MPXVs involved in the outbreak in Guangdong, we constructed a phylogenetic tree by integrating 10 MPXV sequences from Guangdong into the global MPXV genetic diversity sequences derived from GISAID (Fig. 1a,…

PLINK can’t find my files? 1 Hi, When I run PLINK, I always have this error message: No file (XXX.ped) exists. However, the file exists (of course) and is located at the same place as PLINK on my computer. The software has to be in to work so I…

extract variants from 1000 Genome VCF files 0 Hi everyone, I have a gVCF containing genetic information from different individuals, and I would like to extract specific SNPs. The SNPs of interest are listed in a BED file with the following structure (the end position rapresent the real position of…

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

Introduction Klebsiella pneumoniae (KP), a member of the Enterobacteriaceae family, inhabits aquatic environments and can colonise respiratory and gastrointestinal tracts in humans, making it a significant opportunistic pathogen. It may result in pneumonia, meningitis, urinary tract infections, and bloodstream infections. Hypervirulent Kp (HvKp) is believed to cause severe community-acquired invasive…

The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…

Error: Failed to open /ROH/.log. Try changing the –out parameter. 0 when I used this code in R system(“plink –vcf Pakistan.total.vcf –homozyg –homozyg-window-snp 50 –homozyg-snp 50 –homozyg-window-missing 3 –homozyg-kb 100 –homozyg-density 1000 –allow-extra-chr –out /ROH/plink/n”) I got this error: Error: Failed to open /ROH/plink/n.log. Try changing the –out parameter. How…

This page lists the different DNA sequencing services. 2 main types can be distinguished: Whole exome sequencing is the middle ground between these two types, where a large amount of genes are sequenced, but only those that produce meaningful differences important for practical purposes, which is only 1% of the…

gatk SelectVariants is giving dupilicate allele error while extracting SNPs out of vcf file 1 I am trying to extract snps out of merged vcf file using gatk SelectVariants command but it is giving following error: htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 73: Duplicate allele…

get gene name from rsID 1 I’ve got a list of rs IDs in xlsx format. I need to get the gene name for each rsID. When I use this command, I get the gene name esearch -db snp -query “rs573455” | esummary | xtract -pattern GENE_E -element NAME |…

Astrid Böhne1, Zeynep Oğuzhan1, Ioannis Chrysostomakis1, Simon Vitt2, Denis Meuthen2,3, Sebastian Martin1, Sandra Kukowka1 and Timo Thünken2 1Leibniz Institute for the Analysis of Biodiversity Change LIB, Museum Koenig Bonn, 53113 Bonn, Germany; 2Bonn Institute of Organismic Biology (BIOB), Department of Animal Biodiversity, University of Bonn, 53121 Bonn, Germany; 3Evolutionary Biology,…

Alahi MEE, Mukhopadhyay SC (2017) Detection methodologies for pathogen and toxins: a review. Sensors 1885:17 Google Scholar  Aly SM, Sabri DM (2015) Next generation sequencing (NGS): a golden tool in forensic toolkit. Archiwum Medycyny Sądowej i Kryminologii/Archives of Forensic Medicine and Criminology 65(4):260–271 Google Scholar  Amendt J, Richards CS, Campobasso…

PRESS RELEASE Published December 7, 2023 Introduction: “Whole Exome Sequencing Market” New Research Insight Report 2023 | Spread Across 108 Pages Report which provides an in-depth analysis Based on Regions, Applications (Correlation Research of Normal Human, Mendelian Disease and Rare Syndrome Gene Discovery, The Research of Complex Diseases, Mouse Exome…

Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef  CAS  PubMed  Google Scholar  Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef  PubMed Central  PubMed …

Given files genes.bed and snps.bed, you could do something like: $ bedmap –echo –echo-map-id –delim ‘\t’ genes.bed snps.bed > answer.bed The file answer.bed will contain the gene annotation and a semi-colon delimited list of SNP identifiers that overlap each gene. In order to get genes.bed, you could use Gencode v44…

Need help to find FASTA sequence from dbSNP 0 Hello, I am trying to find a fasta sequence to locate SNP using db SNP but I could not find the fasta sequence. The sequence that I want is shown in picture. Could anyone tell me the steps how to reach…

Body: Hello, Biostars Community, I am working on creating a custom database of variants using the VCF from the latest dbSNP alpha release available at ftp.ncbi.nih.gov/snp/population_frequency/latest_release/. I have encountered a couple of issues that I’m hoping someone might help me resolve. Firstly, the chromosome encoding uses RefSeq IDs (e.g., NC_000007.12)…

Introduction Lung cancer remains the leading cause of cancer-related mortality worldwide, and the majority are non-small-cell lung cancer (NSCLC).1,2 Genetic variation is a typical feature of NSCLC that drives cancer initiation and progression.3 Understanding the role of mutated genes in NSCLC is the basis of the development of novel treatment…

The history of paternity testing The history of paternity testing has evolved significantly over the years, with advancements in scientific techniques playing a crucial role in its development. Here is a brief overview of the key milestones in the evolution of paternity testing: Blood Grouping (early 20th century): In the…

locuszoom error 1 Hi there, I downloaded locuszoom in it’s entirty from their github page. I have everything in order but when I attempt to run the following I get an error: locuszoom_test/bin/locuszoom –metal chr7.snx13.marker.locuszoom.metal –ld chr7.imputed.concat.sorted.nomono.80.recode.maf01.pheno.vcf.2.ld.locuszoom.input –refsnp rs1533245 –prefix chr7.snx13.rs1533245 /share/hennlab/progs/locuszoom_test/bin/../src/m2zfast.py:82: SyntaxWarning: invalid escape sequence ‘\d’ RE_SNP_1000G = re.compile(“chr(\d+|[a-zA-z]+):(\d+)$”);…

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…

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…

Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, Dziadek J (2016) Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 29:239–290. doi.org/10.1128/cmr.00055-15 Article  PubMed  PubMed Central  CAS  Google Scholar  Niemann S, Merker M, Kohl T, Supply P…

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

A novel collection of genomes from Cabinda, Angola and Maputo, Mozambique Genomic DNA was extracted using saliva samples collected with informed consent and sequenced using the Illumina HiSeq X™ platform to an average autosomal read depth of ~12X from 300 individuals sampled in Cabinda and 50 individuals sampled in Maputo…

DOI: 10.18129/B9.bioc.semisup   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see semisup. Semi-Supervised Mixture Model Bioconductor version: 3.16 Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis…

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Venlo, the Netherlands, and Deerfield Beach, Florida, Nov. 30, 2023 (GLOBE NEWSWIRE) — QIAGEN (NYSE: QGEN; Frankfurt Prime Standard: QIA) and DNA Labs International announced today that DLI has recently solved two decades-old “cold cases” using QIAGEN solutions. The products involved are ForenSeq Kintelligence System for forensic genetic genealogy, in…

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

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…

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…

Base editors cause unintended indels at the target sites Several types of evolved base editors based on the CRISPR system have been developed for more accurate and efficient genome engineering21,37. Among these, AncBE4max and ABEmax were evolved by modifying codon usage, NLSs, and ancestral deaminase reconstructions21. These modifications greatly improve…

Ipyrad de novo for variant calling 1 Hello everyone, I am trying to run ipyrad to generate a SNP data set de novo (I do not have a good enough reference genome for my species). I have already demultiplexed my raw data and removed the barcodes and adapters. Does anyone…

Where do these snpeff annotation come from? 0 I am annotating a VCF with annotation from snpeff, which I want to use eventually to parse for predicted loss of function variants I want to understand the annotation better and document how they are happening. I run this command: snpEff “hg38″…

GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data 0 Dear all, Is there any best practice for the mouse snp indel vcf files using GATK Mutect2 for mouse whole exome data? For mm10, it seems have several available, for mm39, it seems the newest is from…

I’m trying to get a PRS for a very small subset of samples (~400 training, ~200 testing). Firstly I C+T the training data previous to PRSice. My .log is PRSice 2.3.3 (2020-08-05) github.com/choishingwan/PRSice(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O’ReillyGNU General Public License v3If you use PRSice in…

Hello ! I’m currently trying to develop a local core-genome MLST tool using a combination of a huge genes database and blastn but I came into outputs I can’t explain. Here’s what I have: My genome: genome.fasta My database, comprised of ~1000 genes and n alleles: db/GENE01.fasta: 1500 sequences. db/GENE02.fasta:…

Dear Sam and all, I used PRSice for calculating PRS based on the well-known 30 SNP list that is specific for type 1 diabets. I found that PRSice version 2.6.1 considered only SNPs whose effect allele are alternative alleles in the target file for PRS calculation. All SNPs that thier…

Kumar A, Rasche H, Grüning B, Backofen R. Tool recommender system in Galaxy using deep learning. GigaScience. 2021. doi.org/10.1093/gigascience/giaa152. Article  PubMed  PubMed Central  Google Scholar  The galaxy community: the galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res 50(W1):W345-W35104 2022. (2022). doi.org/10.1093/nar/gkac247 Gil Y, Ratnakar…

Single Nucleotide Polymorphism (SNP) Genotyping Global Market The Business Research Company’s global market reports are now updated with the latest market sizing information for the year 2023 and forecasted to 2032 The Business Research Company’s Single Nucleotide Polymorphism (SNP) Genotyping Global Market Report 2023 identifies The increasing burden of chronic…

Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M. & Cunningham, P. Evidence for two independent domestications of cattle. Proc. Natl Acad. Sci. USA 91, 2757–2761 (1994). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Verdugo Marta, P. et al. Ancient cattle genomics, origins, and rapid turnover…

The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…

About 10-15% of pregnancies fail after conception has been recognized, amounting to 23 million losses a year. Chromosomal anomalies underlie many embryonic and fetal losses, but their exact frequency and localization to the embryo or placenta are still unclear. A new study published in Nature Medicine reports on a chromosomal…

DNA is the unseen constant in our world. Not only do its As, Ts, Cs, and Gs form the basis of all life on earth, but DNA that’s shed from living things will pervade the environment around us and, in some cases, will long outlive us. As a biomaterial, DNA is…

DNA Markers: nuclear DNA SNPs, mtDNA, SNPs, DNA sequences, microsatellites Popular neutral markers: Mitochondrial gene sequences (COI: animal), SNPs (single nucleotide polymorphisms), nuclear sequence (RUBISCO, rDNA: plants) (show SNP heteros have 2 lower peaks), genome resequencing, microsatellites (STR) Microsatellites: tandem repeats of 10-30 copies of 2-4 base pairs (diff in…

Commission, S. P. Pharmacopoeia of the People’s Republic of China (Pharmacopoeia of the People’s Republic of China, 2020). Google Scholar  Sun, X. & Sun, F. Shennong Materia Medica Classic (People’s Health Publishing House, 1963). Google Scholar  Huang, C. Flora of China Vol. 43 (Science Press, 1997). Google Scholar  Hu, J….

SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ====  [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…

Distributed cgMLST scheme and the species tree based on a global dataset of 70,000 Neisseria genomes To set up the new dcgMLST scheme, we established a global collection of genomic sequences for 69,994 Neisseria strains (Supplementary Data 1), consisting of 4411 assembled genomes from GenBank, 65,434 genomes assembled based on short…

Institue for Health Metrics and Evaluation. Global Burden of Disease. vizhub.healthdata.org/gbd-results/ 2019. Troeger, C. E. et al. Quantifying risks and interventions that have affected the burden of diarrhoea among children younger than 5 years: an analysis of the Global Burden of Disease Study 2017. Lancet Infect. Dis. 20, 37–59 (2020)….

Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS  PubMed  PubMed Central  Google Scholar  Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…

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…

TCGA/Broad Institute CNV Files Segment Mean 3 Hello everybody, I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at…

Hi there, Should SNPs that have this sort of name ‘exm_….” be removed from genetic data at the QC stage. Not necessarily, they used this ID cause it was part of their ExomeSNP array, probably because there was no RSID at the time, for example this one: www.ncbi.nlm.nih.gov/projects/SNP/snp_ss.cgi?subsnp_id=ss1958317049 Should SNPs…

RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized…

I’m new to PLINK and I would like to obtain a file with SNPs in approximate linkage equilibrium. Here is my script and the outputs of each step. If someone could tell me if there is an error in the script because at…

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

ABL Diagnostics spreading the DeepChek® technology (suite of Sanger & NGS assays and software systems) to laboratories performing infectious diseases genotyping. The company continues to expand its network of distribution partners in all continents to offer its expertise and innovative solutions to reference microbiology laboratories. Woippy (France) – ABL Diagnostics…

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

a, The diagrammatic sketch of the three components in the solution: DNA@AuNS conjugate, CRISPR/Cas12a complex, and target ssDNA. b, Optical setup, the BS, SPF, and TL are beam splitter, short pass filter, and tube lens (f=200 mm), respectively. Additional details of the setup are provided in the Materials and Methods…

How is negative emotionality connected to neuroticism/negative emoionality? 5 answers What is the roles of Aluminum-activated malate transporter 9 in plants 3 answers What is the roles of Zinc finger CCCH domain-containing protein 2 in plants 3 answers What is the distribution of Oenothera curtiflora? 5 answers What are the…

Working with NCBI downloadable Datasets 0 Hi all, I’m an postgraduate student currently working on an assigment in the field of “Analysis Molecular Data”. We’ve been instructed to examine polymoprhism in the promoter of the gene MMP3 in humans, and how that might affect expression and causality for genetic disorders….

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

Regarding using a “pseudo reference genome” for aligning short reads 0 Hello, my lab is involved in variety identification of plants. Usually we have over 200 varieties which we barcode during the genotyping by sequencing run. This is primarily a “radseq” method, i.e. it is a reduced representation of a…

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

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….

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…

ANNOVAR Error: All variants in a VCF register as “invalid genotype records in input file” 0 Hello, I am running into an error with convert2annovar.pl where it is registering all of the variants in my VCF as invalid. My VCF is 1925 variants plus the header with the following format:…

Concurrent microduplication and microdeletion of the chromosome 22q11.2 region are a rarely reported phenomenon. We describe a case of germline 22q11.21 microduplication syndrome with concurrent mosaic 22q11.2 deletion in a pregnant patient, identified by chromosomal microarray and FISH after noninvasive prenatal genetic screening (cfDNA) results discordant with family history. The…

Houben, R. M. G. J. & Dodd, P. J. The global burden of latent tuberculosis infection: a re-estimation using mathematical modeling. PLoS Med. 13, e1002152 (2016). Article  PubMed  PubMed Central  Google Scholar  Cohen, A., Mathiasen, V. D., Schön, T. & Wejse, C. The global prevalence of latent tuberculosis: a systematic…

Issue with Merging BCF Files: Invalid INFO id Error 0 I am attempting to combine two BCF (Binary Variant Call Format) files into a single file using the command bcftools merge output1.bcf output2.bcf –force-samples -o test.bcf. However, when I try to view the resulting BCF file, I encounter an error…