Tag: snp

How can I calculate PRS for all samples by using PRSice-2.

How can I calculate PRS for all samples by using PRSice-2. 0 Hi. I am trying to calculate PRS by using PRSice-2. I’d like to know how to handle the model. When I provide same gwas results to PRSice-2’s –base option, is the model always same? I have several thousands…

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Who are the leading innovators in DNA polymorphism detection for the pharmaceutical industry?

The pharmaceutical industry continues to be a hotbed of innovation, with activity driven by the evolution of new treatment paradigms, the gravity of unmet need, as well as the growing importance of technologies such as pharmacogenomics, digital therapeutics, and artificial intelligence (AI). In the last three years alone, there have…

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Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential

Weisman, D. & McKeith, I. Dementia with Lewy Bodies. Semin. Neurol. 27, 042–047 (2007). Article  Google Scholar  Foguem, C. & Manckoundia, P. Lewy Body Disease: Clinical and Pathological “Overlap Syndrome” Between Synucleinopathies (Parkinson Disease) and Tauopathies (Alzheimer Disease). Curr. Neurol. Neurosci. Rep. 2018 18:5 18, 1–9 (2018). CAS  Google Scholar …

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Scientific Manager – Immunology (Nanostring, Exome, RNA, CHIP) job with University of Texas MD Anderson Cancer Center

The Immunology department at MD Anderson Cancer Center seeks to determine the fundamental cellular and molecular mechanisms of a wide range of processes by which the body recognizes and eliminates pathogens and use these findings to unleash the patient’s own immune system against previously treatment-resistant cancers. Treating the immune system…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74. Article  CAS  PubMed  PubMed Central  Google Scholar  Chang CC, Chow CC, Tellier LC, Vattikuti S,…

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Single change in genetic code promotes development of inflammation, high blood pressure and resulting kidney damage

Credit: Circulation Research (2022). DOI: 10.1161/CIRCRESAHA.121.320625 Researchers at Vanderbilt University Medical Center have found that the change in a single letter of the genetic code promotes, in a mouse model, the development of inflammation, high blood pressure and resulting kidney damage. Their findings, featured Oct. 14 on the cover of…

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How to add reference as new sample to vcf?

How to add reference as new sample to vcf? 0 Hello, Do anyone know how to make a vcf file with a new sample from reference genome? I have a vcf file with 200 samples and 2,000 SNP My SNP were called with a reference genome, and I want to…

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Leptin receptor co-expression gene network moderates the effect of early life adversity on eating behavior in children

Gillespie, C. F., Phifer, J., Bradley, B. & Ressler, K. J. Risk and resilience: genetic and environmental influences on development of the stress response. Depress Anxiety 26, 984–992 (2009). CAS  PubMed  PubMed Central  Article  Google Scholar  Silveira, P. P. et al. Cumulative prenatal exposure to adversity reveals associations with a…

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Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

GWAS identifies genetic variations associated with agronomic traits in foxtail millet A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423 Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps…

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Solved the aim of this assignment is to explore the database

Transcribed image text: the aim of this assignment is to explore the database of SNPs and broad the horizon of the students on the role of SNPs databases. each student should look for a SNP in the human genome with a clinical significant effect and report the following details 1)…

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As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

NAME SYNOPSIS DESCRIPTION EXAMPLES BASIC OPTIONS SITE FILTERING OPTIONS INDIVIDUAL FILTERING OPTIONS GENOTYPE FILTERING OPTIONS OUTPUT OPTIONS COMPARISON OPTIONS AUTHOR NAME VCFtools v0.1.12a − Utilities for the variant call format (VCF) and binary variant call format (BCF) SYNOPSIS vcftools [ –vcf FILE | –gzvcf FILE | –bcf FILE]…

Continue Reading As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing

Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS  Article  Google Scholar  Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…

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Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

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Bioconductor – SNPlocs.Hsapiens.dbSNP155.GRCh37 (development version)

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP155.GRCh37     This is the development version of SNPlocs.Hsapiens.dbSNP155.GRCh37; to use it, please install the devel version of Bioconductor. Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly Bioconductor version: Development (3.16) The 929,496,192 SNPs in this package were extracted from…

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All transcript variants in gene MAD1L1 – BIPMed SNP Array

Legend Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column’s header and hold it still. Below, a more detailed description is shown per column. Effect: The variant’s effect on the protein’s function, in the format ‘R/C’ where…

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The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies

Abstract The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced…

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The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

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Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm,…

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Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

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Where can I find a free mtDNA database?

MitoVariome A freely available database of 5344 mtDNA sequences from around the world. Geni.com. Geni.com introduced DNA matching in July 2016. Customers can integrate their Y-DNA, mtDNA and autosomal DNA results from Family Tree DNA with their Geni tree. [0] One may also ask, What is ancient mtDNA database? Welcome…

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Bioinformatics Analyst in Minneapolis, MN for University of Minnesota, Twin Cities

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

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UK Biobank Copy Number-Based GWAS Discovers New Associations With Human Traits

NEW YORK – A new set of analytical tools is making it possible to systematically search for links between copy number variants and complex human traits or conditions, according to a study by a pair of investigators at the European Molecular Biology Laboratory’s European Bioinformatics Institute. “[W]e present a robust…

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Genotyping Market Analysis, Insights by Emerging Trends, Future Growth, Revenue Analysis, Demand

Genotyping is the process of studying DNA sequence to determine genetic constitution in the genotypes of living organisms, such as humans, plants, animals, and microorganisms. Human genotyping helps in determining fatherhood or motherhood. Genotyping of micro-organisms, including viruses and bacteria, helps in prevention of spreading of pathogens by tracking down…

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Gene Amplification Technologies Market Analysis Report 2022 –

Acumen Research and Consulting has announced the addition of the “Gene Amplification Technologies Market” report to their offering. The Gene Amplification Technologies Market Report 2030 is an in depth study analyzing the current state of the Gene Amplification Technologies Market. It provides brief overview of the market focusing on definitions,…

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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Sampson, J. N. et al. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed  PubMed Central  Article  CAS  Google Scholar  Bosse, Y. & Amos, C. I. A decade of GWAS results in lung cancer. Cancer Epidemiol….

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Get gene names from rs SNP ids for mmusculus_gene_ensembl

Get gene names from rs SNP ids for mmusculus_gene_ensembl 1 I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my…

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Extracting Beta, SE and P-Value from GLM model

Extracting Beta, SE and P-Value from GLM model 1 Hi there, I want to extract beta from a glm model analysis, my variables are as follows: test.data ID Phenotype snp 1442211 0.947595614262281 2 1501431 0.828960485290687 2 1676115 1.43030605455755 2 1700393 0.77901178220667 2 2028223 0.981493321966468 2 2075852 0.734295870666147 2 2601302 0.829567302722706…

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SMAD4 rs10502913 | COPD

1Department of Pulmonary and Critical Care Medicine, Sinopharm Tongmei General Hospital, Datong, People’s Republic of China; 2China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China; 3Department of Emergency, Chinese PLA General Hospital -Fourth Medical Center, Beijing, People’s Republic of China; 4School…

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Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

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Postdoctoral Researcher in Computational Biology at Karolinska Institute, Sweden 2022

Postdoctoral Researcher in Computational Biology is available for doctoral degree candidates in Bioinformatics, Computer science, Mathematics, Biostatistics, Neuroscience, or similar field at the Department of Clinical Neuroscience, Karolinska Institute, Sweden 2022 Qualification Details Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent…

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How to modify VCF file?

Hi community, I have a question: the SNP position in vcf file is from GRCh37/hg19, I need to change the position to GRCh38. So, I used UCSC liftover to replace the hg19 pos by GRCh38 pos and deleted some SNPs, then sorted the pos and saved to a new vcf…

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Table 5 | Scripting Analyses of Genomes in Ensembl Plants

arabidopsis_thaliana The 1001 Genomes Project [18] arabidopsis_thaliana Nordborg [19] brachypodium_distachyon Jaiswal_lab_OSU [20] hordeum_vulgare International Barley Sequencing Consortium (IBSC) [21,22,23] hordeum_vulgare Ensembl Plants [24] hordeum_vulgare Illumina iSelect SNP chip [22] malus_domestica fruitbreedomics.com [25] oryza_glaberrima Glab (OGE) oryza_glaberrima Barthii (OGE) oryza_glumipatula Oryza Genome Evolution (OGE) oryza_indica dbSNP [26] oryza_sativa www.ebi.ac.uk/eva [27,28,29,30] oryza_sativa…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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08 compare visualization results of different annotation software

stay In the first two sections , We compared the differences vcf Use of annotation software , And convert the demerit recorded after the annotation into maf File format , because snpeff The comment result cannot be converted to maf, So we will compare later ANNOVAR、VEP、GATK Funcatator The results of…

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TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies

doi: 10.1093/genetics/iyac088. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. 2 Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA. 3 Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA. 4 Gilead…

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  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,…

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how to predict gene expression from genotype file using already developed elastic net model

how to predict gene expression from genotype file using already developed elastic net model 0 Hello everyone, I want to predict gene expression from genotype file and already developed elastic net model. My model file look like this: GENE RSID1 RSID2 VALUE ENSG00000107937.18 rs7475652 rs7475652 0.531316876443232 ENSG00000107937.18 rs7475652 rs7918643 -0.1434806647803035…

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Help with PCA plot from SNPRelate

Hello, BioStars community! I am working on a datase of 50 samples(between cases and controls) with genotyping data for ~200 SNPs. I ran SNPRelate PCA analysis without adding population data and tried to plot its results. My PCA plot seems a bit “strange” since the observations did not come together…

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BAM file and no RNAME or POS information? : bioinformatics

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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Dissertations.se: HETEROPLASMY

Showing result 1 – 5 of 7 swedish dissertations containing the word Heteroplasmy. Author : Guilherme Costa Baião; Lisa Klasson; Alistair Darby; Uppsala universitet; []Keywords : NATURAL SCIENCES; NATURVETENSKAP; NATURVETENSKAP; NATURAL SCIENCES; Wolbachia; Drosophila; Drosophila paulistorum; Differential Gene Expression; Reproductive Incompatibility; Reproductive Isolation; Comparative Genomics; Transcriptomics; RNA-Seq; Heteroplasmy; Mitochondria; Genomic…

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A Highly Sensitive and Specific Detection Method for Mycobacterium tuberculosis Fluoroquinolone Resistance Mutations Utilizing the CRISPR-Cas13a System

Objectives CRISPR-Cas13a system-based nucleic acid detection methods are reported to have rapid and sensitive DNA detection. However, the screening strategy for crRNAs that enables CRISPR-Cas13a single-base resolution DNA detection of human pathogens remains unclear. Methods A combined rational design and target mutation-anchoring CRISPR RNA (crRNA) screening strategy was proposed. Results…

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Mediation analysis of local chromatin state and gene expression data in human cell lines.

SNP associations with (a) SLFN5 and (b) GPR63 expression (top) and nearby chromatin accessibility (bottom) for variants on the genes’ chromosome. Peak SNPs are labeled. Mediation results for the (c) SLFN5 eQTL and (d) GPR63 eQTL. Log posterior odds from Bayesian model selection (top), -log10 p-values from Sobel test (middle),…

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difficulty filtering vcf file with vcftools

difficulty filtering vcf file with vcftools 1 I had a large VCF file named “common_known_variants.vcf ” which contains all known human variants downloaded from ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz -O common_known_variants.vcf.gz I’m trying to extract the known variants from only chromosomes 1,2,3,9,22, and X and write them in a new vcf file with the…

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Latest dbSNP VCF

This is the directory you’re looking for: ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/ curl -s ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.39.gz | zcat | head ##fileformat=VCFv4.2 ##fileDate=20210513 ##source=dbSNP ##dbSNP_BUILD_ID=155 ##reference=GRCh38.p13 ##phasing=partial ##INFO=<ID=RS,Number=1,Type=Integer,Description=”dbSNP ID (i.e. rs number)”> ##INFO=<ID=GENEINFO,Number=1,Type=String,Description=”Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Restriction Fragment Length Polymorphism – Top Future point

In molecular biology , restriction fragment length polymorphism ( RFLP ) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms , in order to distinguish individuals, populations, or species or to indicate the locations of For in the gene within a sequence. The term may refer…

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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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snp – Reference variant detected as altered one in bam file

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

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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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aCGH – Allie: Result by abbreviation

1  array comparative genomic hybridization(1473 times) Neoplasms(306 times) FISH (238 times)CNVs (135 times)MLPA (72 times) 2003 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. 2  array CGH(43 times) Neoplasms(12 times) CNVs (7 times)FISH (3 times)ID (3 times) 2003 Combined array comparative genomic hybridization and…

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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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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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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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wrong number of fields ?

Error occurence after merging files with bcftools: wrong number of fields ? 1 I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff, SnpSift. first pair vcf -> only variations| CASES and CONTROLS second pair vcf -> variations + SnpEff | CASES and CONTROLS third pair vcf->…

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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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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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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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How to Select data for a SNP for all samples using PLINK

How to Select data for a SNP for all samples using PLINK 0 Hello Folks, I’m very new to this plink. The below task has been assigned, any reference/blogs/Articles much appreciated. Q: Be able to select data for an SNP for all samples using PLINK please help plink • 49…

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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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Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups…

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rna seq – RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. Objective Our ultimate goal with this genotypic data is to search for variants (both SNPs and indels)…

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Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

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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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Understanding signatures of positive natural selection in human zinc transporter genes

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

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Understanding the number of intersection in bedtools jaccard

Understanding the number of intersection in bedtools jaccard 1 Hello, I am using bedtools jaccard to compare two vcf files, as: bedtools jaccard -a ancestors.calls.norm.snp.vcf.gz -b GC078310.calls.norm.snp.vcf.gz intersection union-intersection jaccard n_intersections 1606899 1806667 0.889427 1536700 What I do not get is why n_intersections is equal to 1536700. Especially, the difference…

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R: PC gamma

PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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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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AutoKinship at GEDmatch by Genetic Affairs

Genetic Affairs has created a new version of AutoKinship at GEDmatch. The new AutoKinship report adds new features, allows for more kits to be included in the analysis, and integrates multiple reports together: AutoCluster – the autoclusters we all know and love AutoSegment – clusters based on segments AutoTree –…

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Phylogenomic analysis of CTX-M-15-producing Enterobacter hormaechei belonging to the high-risk ST78 from animal infection: Another successful One Health clone?

Available online 18 February 2022 doi.org/10.1016/j.jgar.2022.02.010Get rights and content Highlights • ESBL-positive Enterobacter cloacae complex members are critical priority pathogens. • E. hormaechei belonging to sequence type (ST) ST78 is an emergent high-risk clone. • Phylogenomic data of an E. hormaechei ST78/CTX-M-15 infecting a calf is presented. • E. hormaechei…

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EQTL visualization

EQTL visualization 0 I have generated file from MATRIXEQTL . I would like to visualize haploblocks, plots for MATRIXEQTL. I am having SNP.txt, Gene expression.txt. How can I visualize Chromosome specific eQTL list EQTL plot • 53 views • link 17 hours ago by Nai &utrif; 20 Login before adding…

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Genomic analysis on Galaxy using Azure CycleCloud

Cloud computing and digital transformation have been powerful enablers for genomics. Genomics is expected to be an exabase-scale big data domain by 2025, posing data acquisition and storage challenges on par with other major generators of big data. Embracing digital transformation offers a practically limitless ability to meet the genomic…

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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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A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Dataset for manuscript “The use of comparative genomic analysis for the development of subspecies-specific PCR assays for the Mycobacterium abscessus complex” by Winifred Akwani et al. A core genome MLST scheme was developed for Mycobacterium abscessus complex (MABC) subspecies M. abscessus, M. bolletii and M. massiliense, using chewBBACA version 2.8.5…

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snp.plotter_ input files

snp.plotter_ input files 0 Dear friends I’m running an LD analysis using the package of snp.plotter in R The problem that I’m facing right now is the files that I need to use for running the analysis My first question is why there is no template for the config.file??? what…

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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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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Frontiers | Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study

Introduction Congenital heart disease (CHD) refers to a group of anatomic heart and great vessel malformations that arise during the embryologic development of the fetus. CHD is one of the most prevalent birth defects, affecting around 2.50 out of every 1,000 births in China (1), and it imposes a substantial…

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qctool to merge two bgen file fails with no clear reason to

Hi, I am trying to merge two bgen files using qctool as explained here. I am using qctool_v2.2.0. The command works but ends with an error: ❱ qctool -g bug/in2.bgen -s bug/in2.sample -merge-in bug/in1.bgen bug/in1.sample -og bla.bgen -os bla.sample Welcome to qctool (version: 2.2.0, revision: unknown) (C) 2009-2020 University of…

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GATK HaplotypeCaller with interval list

I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows: 12 33029845 33030845 + rs24767598 13 40586682 40587682 + rs24748362 18 24373857 24374857 + rs8856159 21 50381146 50382146 +…

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Active Motif Incorporated Announces the Acquisition of Amaryllis Nucleics and their proprietary RNASeq workflow

CARLSBAD, Calif., Jan. 27, 2022 /PRNewswire/ — Active Motif Incorporated, a company with the vision of bringing epigenetics more deeply into precision medicine, announced that it has purchased Amaryllis Nucleics, a Bay Area-based start-up company focused on proprietary RNA Sequencing methods. Amaryllis Nucleics provides Active Motif with a streamlined, low-cost…

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DNA Labs International Launches the Newest Technology for Forensic Genetic Genealogy

MiSeq FGx platform by Verogen DEERFIELD BEACH, Fla. (PRWEB) January 26, 2022 DNA Labs International, which specializes in forensic DNA analysis including forensic genetic genealogy (FGG) for law enforcement agencies, government forensic labs, and attorneys, is announcing the release of their newest technology, Single Nucleotide Polymorphism (SNP) testing with…

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To use rflp analysis to detect a snp. the snp must _______.

To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. cause disease occur in homozygous form occur within a restriction enzyme recognition sequence be present in…

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Download full list of SNPs and their coordinates in hg38

Download full list of SNPs and their coordinates in hg38 3 What is the best / standard place to get a full list of SNPs and their coordinates in hg38? I downloaded the SNPsnap database, but just realized that those coordinates are in hg19. I’m trying to figure out how…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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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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High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

Abstract The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with…

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Do we need to apply the same p-value threshold on all 22 chromsomes?

Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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What is SNP array testing?

What is SNP array testing? The SNP array test looks for changes in specific areas of a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. How does SNP array work? SNP array is a type of…

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Associate Scientist, Bioinformatics – jobRxiv

Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center?  This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University…

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SNP associated contigs

SNP associated contigs 0 I am using usegalaxy.org for SNP analysis. After mapping with bowtie2 I got BAM file including QNAME FLAG RNAME POS and on variant calling I got Chrom Pos ID Ref Alt. Showing Variant position on reference genome. I want to get those sequences associated to SNP….

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Bioinformatics, Computer Science, Biology – Transcriptomic, Genomic Assays (f/m/d) – Evotec International GmbH – Biologie & Life Sciences

Evotec is a life science company with a unique business model focused on delivering highly effective new therapeutics to the patients. The Company leverages its multimodality platform, the “Data-driven R&D Autobahn to Cures”, for proprietary projects and within a network of partners including Pharma, Biotech, academics, and other healthcare stakeholders….

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