Tag: ROH

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…

Li Z, Gao Y, Cao Y et al (2023) Extracellular RNA in Melanoma: advances, challenges, and opportunities. Front Cell Dev Biol 11:1141543. doi.org/10.3389/fcell.2023.1141543 Article  PubMed  PubMed Central  Google Scholar  Hamid O, Cowey CL, Offner M, Faries M, Carvajal RD (2019) Efficacy, Safety, and tolerability of approved combination BRAF and MEK…

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…

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…

RUH ROH! While first the “we stand with Ukraine” provided a decent distraction, it didn’t stop the wave of awakening taking place globally. Now, with the “I stand with Israel,” we’ve the same issue. Despite the hits of distraction coming thick and fast, more and more medical professionals are waking up to…

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article  PubMed  Google Scholar  Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …

Machado-Ferreira E, Vizzoni VF, Balsemao-Pires E, Moerbeck L, Gazeta GS, Piesman J, et al. Coxiella symbionts are widespread into hard ticks. Parasitol Res. 2016;115:4691–9. doi.org/10.1007/s00436-016-5230-z. Article  PubMed  Google Scholar  Jung M, Kho JW, Lee WG, Roh JY, Lee DH. Seasonal occurrence of Haemaphysalis longicornis (Acari: Ixodidae) and Haemaphysalis flava, vectors…

Encuesta Nacional de Salud 2000 Since 1988, Mexico has established periodical National Health Surveys (Encuesta Nacional de Salud (ENSA), originally conceived as National Nutrition Surveys) for surveillance of Mexican population-based nutrition and health metrics. In this study, we use data and samples collected from the survey carried out in 2000,…

Abstract After the completion of the human genome project, there have been many advances in the field of genetics. With next generation sequencing, patients can undergo genomic analysis through whole exome or whole genome testing. These comprehensive tests can shorten the diagnostic odyssey and guide medical management and thereby potentially…

Farber, D. L., Netea, M. G., Radbruch, A., Rajewsky, K. & Zinkernagel, R. M. Immunological memory: lessons from the past and a look to the future. Nat. Rev. Immunol. 16, 124–128 (2016). Article  PubMed  Google Scholar  Netea, M. G. et al. Defining trained immunity and its role in health and…

1. Introduction The alarming decline of biodiversity worldwide necessitates urgent conservation measures, particularly for wild, endangered, and understudied species. According to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, of the 5973 mammal species assessed, 1340 were classified as threatened with extinction, including 233 critically…

(a) The scatter graph showing the results from the principal component analysis (PCA) using the whole genomes of dogs, dingoes, and wolves. (b) The proportion of genetic admixture in each canine genome is shown. This analysis was performed assuming four ancestries for canines (K = 4). Credit: Ecology and Evolution (2023). DOI:…

I am running into an issue when importing data with detectRUNS in R. The following commands to import PLINK files have not been successful, and result in blank data frames. genotypeFilePath <- system.file(“extdata”, “genome.ped”,package=”detectRUNS”) mapFilePath <- system.file(“extdata”, “genome.map”, package=”detectRUNS”) head(genotypeFilePath) [1] “” The PLINK data are correctly formatted. OR I…

Barker DJ. The origins of the developmental origins theory. J Intern Med. 2007;261:412–7. Article  CAS  PubMed  Google Scholar  Barker DJ, Gluckman PD, Godfrey KM, Harding JE, Owens JA, Robinson JS. Fetal nutrition and cardiovascular disease in adult life. Lancet. 1993;341:938–41. Article  CAS  PubMed  Google Scholar  Cain MA, Salemi JL, Tanner…

An SJ, Kim TJ, Yoon BW (2017) Epidemiology, risk factors, and clinical features of intracerebral hemorrhage: an update. J Stroke 19:3–10 Article  PubMed  PubMed Central  Google Scholar  Cordonnier C, Demchuk A, Ziai W, Anderson CS (2018) Intracerebral haemorrhage: current approaches to acute management. Lancet 392:1257–1268 Article  PubMed  Google Scholar  Kim…

Ahmed I, Yokota A, Fujiwara T (2007) Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil. Int J Syst Evol Microbiol 57(4):796–802 Article  CAS  PubMed  Google Scholar  Ali A, Liaqat S, Tariq H, Abbas S, Arshad M, Li W-J, Ahmed I (2021a) Neonatal calf diarrhea:…

Maroli M, Feliciangeli MD, Bichaud L, Charrel RN, Gradoni L. Phlebotomine sandflies and the spreading of leishmaniases and other diseases of public health concern. Med Vet Entomol. 2013;27:123–47. CAS  PubMed  Google Scholar  Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. Historical overview of the…

Overview of the Dog10K collection. a Sample collection and sample filtering for (b) the varied demographic, genome function, and architecture examined in the program. QC, quality control. ROH, runs of homozygosity. OMIA, Online Mendelian Inheritance in Animals. Credit: Genome Biology (2023). DOI: 10.1186/s13059-023-03023-7 An international research consortium has generated and…

Cohort structure We collected sequencing data and information about age, sex, and phenotypes from 152 families (44 simplex with one, 79 multiplex with two, 24 with three, and five with four or more). The cohort characteristics are depicted in Fig. 2A (details in File S2 [12]). Most affected individuals were younger than…

Introduction Diffuse large B-cell lymphoma (DLBCL) is a group of B cell-derived malignant tumors with obvious heterogeneity.1 After obtaining standardized treatment, a sizeable portion of DLBCL patients can be cured and survive for a long time. However, roughly one-third of DLBCL patients experience drug resistance and disease recurrence.2,3 Therefore, it…

Buckley, C. E. & St Johnston, D. Apical-basal polarity and the control of epithelial form and function. Nat. Rev. Mol. Cell Biol. 23, 559–577 (2022). Article  CAS  PubMed  Google Scholar  Buchheit, C. L., Weigel, K. J. & Schafer, Z. T. Cancer cell survival during detachment from the ECM: multiple barriers…

In this study, for the first time, we presented an overview of the ROH patterns of the Kazakh national dog breed Tazy from a genome-wide perspective. According to the obtained results, there was strong evidence of distant inbreeding in this breed about 50 generations ago, as most ROH fell into…

Boer, M., Duchnik, E., Maleszka, R. & Marchlewicz, M. Structural and biophysical characteristics of human skin in maintaining proper epidermal barrier function. Postepy Dermatol. Alergol. 33, 1–5 (2016). PubMed  PubMed Central  Google Scholar  Watt, F. M. & Fujiwara, H. Cell-extracellular matrix interactions in normal and diseased skin. Cold Spring Harb….

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860–4. Article  CAS  PubMed  Google Scholar  Blackmore M, Letourneau PC. Changes within maturing neurons limit axonal regeneration in the developing spinal cord. J Neurobiol. 2006;66:348–60. Article  CAS  PubMed  Google Scholar …

doi: 10.1007/978-1-0716-3084-6_12. Affiliations Expand Affiliation 1 Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. tyroh@postech.edu. Item in Clipboard Tae-Young Roh. Methods Mol Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-3084-6_12. Affiliation 1 Department of Life Sciences, Pohang University of Science…

Entry EC 1.4.3.19                 Enzyme                                  Name Class Oxidoreductases;Acting on the CH-NH2 group of donors;With oxygen as acceptorBRITE hierarchy Sysname glycine:oxygen oxidoreductase (deaminating) Reaction(IUBMB) glycine + H2O + O2 = glyoxylate + NH3 + H2O2 (overall reaction) [RN:R00366]; (1a) glycine + O2 = 2-iminoacetate + H2O2 [RN:R07463]; (1b) 2-iminoacetate + H2O = glyoxylate +…

Environmental factors are one of the forces influencing agricultural and the livestock sectors. Animals exposed to stressful environments exhibit various adaptive mechanisms, such as behavioural, physiological, endocrine, cellular, metabolic and biochemical for minimising the stressful conditions. Thus, adaptation is the natural strategy to ensure both welfare and efficiency. The action…

Sample collection We obtained the short read sequences for 33 brown bear genomes, four polar bears (Ursus maritimus) and two American black bears (Ursus americanus), publicly available from NCBI’s SRA repository (Table S1 and Fig. 1a)12,13,15,16,40,51,65. Next, we selected from our private collections a total of 95 additional samples for sequencing, among…

In the absence of a standardized definition of ocular myasthenia gravis (OMG) from established diagnostic criteria, researchers of a new retrospective, single-center study say that OMG should be considered in patients with both ptosis and diplopia, particularly vertical diplopia. Further, they suggest that high acetylcholine receptor auto-antibody (AchR Ab) titer,…

Filtering methods for samtools or GATK 1 Hello everyone! I just started my PhD and my level of expertise is fairly low about bioinformatics! Is there any advice regarding different covarege levels?( 10x vs 50x or more ). I would need simple instructions for filtering using either samtools or GATK….

Tuttle KR, Bakris GL, Bilous RW, Chiang JL, de Boer IH, Goldstein-Fuchs J, et al. Diabetic kidney disease: a report from an ADA Consensus Conference. Diabetes Care. 2014;37(10):2864–83. Article  Google Scholar  Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B, et al. Chronic kidney disease: global dimension…

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

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

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…

plotting roh from bcftools 0 Heys, I am following this small tutorial on how to calculate ROHs from a vcf file using bcftools (samtools.github.io/bcftools/howtos/roh-calling.html) and I am getting this txt file: # This file was produced by: bcftools roh(1.10.2+htslib-1.10.2-3) # The command line was: bcftools roh -G30 –AF-dflt 0.4 my_file.vcf…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

Interpreting output of BCFtools RoH 0 Hello! I am using BCFtools RoH for the first time, and I am having some trouble understanding its output file. The input is a gvcf file with genotype calls for one sample only, and I want to infer where there might be autozygous tracts….