oklahoma medical research foundation genomics core

Consolidated Core Laboratory

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Illumina Miseq

The Illumina Miseq provides sequencing at a scale perfect for a variety of applications, including amplicons, small genomes, and metagenomics.

Consolidated Core Lab

OU’s Next Generation Sequencing Facility

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The Consolidated Core Lab (CCL) was created to bring economy of scale (often known as shared services), coordination, and collaboration to research areas that require genomic sequencing and related data processing. It is a partnership among the OU Norman campus, OU Health Sciences Center (HSC), and Oklahoma Medical Research Foundation (OMRF). The CCL serves faculty and students and is funded by the Office of the Vice President for Research as well as external grants and contracts.

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Facilitate the advancement of genomics and related sciences by OU faculty and their students. This will be achieved through a traditional “Core” service for basic genomics coupled with the offering of wet-lab bench space, capital equipment availability, training, and consultation.

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• WGS library prep
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All Facilities >> Oklahoma Medical Research Foundation >> OMRF Genomics Core

OMRF Genomics Core

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Oklahoma Medical Research Foundation

825 NE 13th St., MS 57

Oklahoma City, OK 73104

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Graham Wiley

Last Updated: 10/01/2015

The Oklahoma Medical Research Foundation Sequencing and Genotyping Core offers high-throughput sequencing and genotyping services utilizing cutting edge Illumina HiSeq and iScan systems. Our services are available to all outside academic and corporate research entities.

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Services offered:.

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

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Illumina Hiseq 3000 Illumina Nextseq 500 Illumina Miseq Illumina iScan

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SciCrunch Data Imports (data maintained by https://scicrunch.org)

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Bioinformatics core, proteomics core.

Biomedical research has evolved into an increasingly technology-driven endeavor and like the rest of society, has become critically dependent on computational tools and methods for data analysis, archiving and retrieval. This is particularly true as NIH moves into the era of Big Data. The OK-INBRE Bioinformatics Core supports this continuing evolution within the state of Oklahoma, by providing bioinformatics support for both the Oklahoma research and educational enterprises. Collectively, these efforts will enhance the competitiveness of Oklahoma investigators for local, state and national funding, and increase the pool of skilled young biomedical research scientists in Oklahoma. Research Support. Our mission is to enhance Oklahoma research expertise and infrastructure by providing state-of-the-art bioinformatics support to investigators performing biomedical research on the campuses that participate in the Oklahoma IDeA Network. We currently provide bioinformatics research support for over 150 investigators in the state, enriching many scientific disciplines including cancer biology, cell and developmental biology, diabetes and microbial pathogenesis. This breadth demonstrates the wide-ranging power of bioinformatics to advance biomedical research. Our services include DNA sequence data cleanup and analysis of DNA sequence-based experiments including microbial genome sequencing and annotation, RNA-seq and ChIP-seq analysis, 16S rRNA-based microbiomics. Where possible, we will train laboratory personnel in the analysis of these data using commercial software that exploits a graphical user interface, to avoid the necessity of working on the command line to analyze this data. We also provide access to the Ingenuity Pathway Analysis (IPA) software suite, which is essential for exploring whole transcriptome data obtained from eukaryotic cells. If you need access to the IPA software for your project, please contact Dr. Dyer at the email address above to arrange for a user account. In all your studies, we strongly suggest that you contact us before you begin experiments that will require bioinformatics support, so that we can advise on your experimental design. A well-organized experiment is crucial for obtaining a statistically robust outcome for many of these experiments. In addition to these services, we have experience in protein structure modeling, including the analysis of protein interactions with small molecules for drug and inhibitory design. Support for other custom bioinformatics applications is available as needed. Please contact us for more details. As needed, we also will partner with the newly established OK-INBRE Proteomics Core to support your discovery and targeted proteomics experiments. Educational Support.   We provide support for bioinformatics education at Oklahoma IDeA Network Primarily Undergraduate Institutions (PUI) and Community Colleges (CC), by offering didactic coursework and hands-on computing laboratories, such as laboratory exercises in DNA Barcoding and 16S rRNA-based Microbial Ecology. These classes have enriched the educational experiences of undergraduate students, graduate students and high school science teachers in the state. We also provide custom lecture material on other topics such as structural bioinformatics and phylogenetic analysis. Beginning in 2020, we will offer a new course on the OUHSC campus, MI6401 Introduction to Bioinformatics. Holding this course in the summer session will eliminate potential overlap with existing coursework, making the scheduling more flexible and available to a wider selection of graduate students on the OUHSC campus, postdoctoral fellows and OUHSC faculty. This course will not be designed to teach attendees to write code and work extensively on the command line; rather, this is planned as a survey course intended to ensure that students, trainees, and faculty will gain familiarity with the basic tools and databases that are available to researchers for these types of studies.We will make use, where possible, of GUI-based commercial software such as CLC Genomics Workbench.The availability of GUI-driven bioinformatics software greatly enhances the ability of novice researchers to rapidly engage the full power of bioinformatics tools and their capabilities.We have in the planning stages a more formal instruction in writing code (R, Python, etc.) for solving problems in data management and analysis using a more advanced bioinformatics methods. Scheduling MI6401 in the summer also will ease the participation by OK-INBRE PUI and CC faculty; in fact, we plan to develop an on-line version of this course that will be available to PUI and CC faculty. This class will increase faculty familiarity with bioinformatics, and aid in incorporating these materials into coursework on the PUI and CC campuses. It is possible that this course could be included as part of the support offered to PUI and CC faculty who receive OK-INBRE funding for curriculum development. In sum, these bioinformatics educational efforts will stimulate the movement of promising students into the post-graduate education pipeline, foster the career development of young biomedical scientists at all stages of their training, and enable the use of state-of-the-art bioinformatics tools by Oklahoma investigators.

OK-INBRE Proteomics Core Director Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, OK 73104 [email protected] Fall 2022 Bioinformatics for Proteomics Workshop

Proteomics Core Goals

The goal of the OK-INBRE Proteomics Core is to provide researchers in Oklahoma and in all IDeA-eligible states access to state-of-the-art instrumentation and expertise for advanced mass spectrometry (MS). The core is equipped with the instrumentation and expertise required to make discovery proteomics and targeted quantitative proteomics experiments available to researchers in Oklahoma. The discovery proteomics experiments will use data dependent analyses to acquire high resolution survey scans to determine peptide mass with high accuracy and collision induced dissociation (CID) spectra to determine the amino acid sequence. Database searches then identify the proteins and find posttranslational modifications. The targeted quantitative proteomics experiments will use selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) to selectively detect and quantify proteins based on peptides formed by trypsin digestion. To ensure statewide awareness of the core’s capabilities and access to these methods, the OKINBRE Proteomics Core laboratory will,  i ) continue to offer educational workshops and develop on-line materials to describe our methods and educate potential users and  ii ) provide vouchers to defray costs associated with pilot projects to enhance utilization of the OK-INBRE Proteomics Core. Finally, the OK-INBRE Proteomics Core will continue to function as the Targeted Quantitative Proteomics component of the  IDeA National Resource for Proteomics  that provides access to advanced proteomics methods and education for Core Directors, trainees, and researchers from all IDeA-eligible states.

Core Facilities

The University of Oklahoma Health Sciences Center has a number of core facilities available to support the wide range of ongoing research taking place on campus.  Among these are the Laboratory of Molecular Biology and Cytometry Research, The Nathan Shock Center of Excellence in the Biology of Aging Cores, and shared resources from The Stephenson Cancer Center and the Oklahoma Medical Research Foundation. 

In addition to these core facilities, researchers have access to Comparative Medicine’s state of the art barrier facility, which is BSL2 equipped and includes a small animal X-ray Irradiator and IVIS Spectrum Imaging system.

The services provided by these various cores include flow cytometry, imaging, mass spectrometry, DNA sequencing, genomics, X-ray crystal screening, structure determination, and histology.  Further details are listed below along with links to the various facilities.

Laboratory of Molecular Biology and Cytometry Research: https://research.ouhsc.edu/Core-Facilities/Laboratory Provides services in the areas of DNA sequencing/genomics, mass spectrometry/proteomics, flow cytometry, imaging and laser microdissection microscopy.

Laboratory of Biomolecular Structure and Function:  https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function#:~:text=The%20Laboratory%20of%20Biomolecular%20Structure,aspects%20of%20their%20macromolecular%20targets  

Provides X-ray crystal screening, X-ray data collection, structure determination and analysis, dynamic light scattering data collection and analysis.

Stephenson Cancer Center Shared Resources: http://stephensoncancercenter.org/Research.aspx Biospecimen acquisition and bank, cancer tissue pathology core, cancer functional genomics, molecular imaging, and biostatistics.

  OU Vision Research Facilities: https://ouvision.ouhsc.edu/Vision-Cores Cellular imaging, live animal imaging, and genotyping.

Diabetes COBRE Core: http://www.ouhsc.edu/Endocrinology/CoBRE/Cores.asp Histology, image acquisition and analysis, diabetic human repository, and diabetic animal core.

Nathan Shock Center of Excellence in the Biology of Aging: http://aging.ouhsc.edu/   Multiplexing protein quantification, targeted DNA methylation and mitochondrial heteroplasmy, integrated redox biology, and bioinformatics core.

Oklahoma Shared Clinical & Translational Resources:  http://osctr.ouhsc.edu/Research%20Resources   Research navigator service for investigators new to clinical research, biostatistics and epidemiology research design consultation, clinical trial assistance, and assistance in the development of registries and repositories of clinical research information.

Oklahoma Medical Research Foundation: https://omrf.org/research-faculty/core-facilities/ Biacore, imaging, myositis testing, nuclear magnetic resonance, DNA sequencing, clinical genomics, biorepository, patient-derived xenograft (PDX) models, flow cytometry, serum analyte, human phenotyping, and quantitative analysis.

Department of Microbiology and Immunology University of Oklahoma Health Sciences Center 940 Stanton L. Young Blvd., BMSB 1053 Oklahoma City, OK 73104

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Our department has a mix of clinical faculty members with funded research programs and full-time experimental pathologists, including faculty members who are members of the Stephenson Cancer Center .  Our partnership with the Stephenson Cancer Center allows us to further expand the research opportunities and collaboration for each faculty.

The Experimental Pathology faculty members are involved in research focusing on the molecular basis of human diseases.  Research interests include Molecular pathology, cancer biology, cell biology, neurobiology, protein chemistry, myeloproliferative disorders, inflammation, Alzheimer's disease, aging, hematopoiesis, intracellular trafficking, apoptosis, and signal transduction. 

A  Molecular Pathology Core laboratory  equipped with many pieces of the latest molecular biological instrumentation, and other OUHSC campus-wide facilities, such as the Flow and Image Cytometry Laboratory and Laboratory for Genomics and Bioinformatics, provide both the expertise and facilities necessary for conducting cutting-edge biomedical research.  

The research facilities on the OUHSC campus have grown to include the Biomedical Research Center , the recently acquired 700,000+ square foot complex at University Research Park , and additional laboratory space within our administrative office building, the Biomedical Sciences Building.  The growth of our research space provides access to high-end biomedical equipment shared by other departments.  In addition, our faculty regularly utilize resources and collaborate with P.I.'s at Oklahoma Medical Research Foundation and Presbyterian Health Foundation .

A Doctoral Degree in Experimental Pathology labeled the Graduate Program in Biomedical Sciences (or GPiBS) is offered by the  Graduate Program , which shares an interdisciplinary core curriculum with the other basic science departments in the College of Medicine.  Members of the Experimental Pathology group are involved in teaching medical, dental, and graduate students, and play prominent roles in numerous College of Medicine and university committees.

WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly

Affiliations.

• 1 Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
• 2 Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
• 3 Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.
• 4 Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany.
• 5 MVZ Labor Krone, Filialpraxis für Humangenetik, Bielefeld, Germany.
• 6 Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.
• 7 Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
• 8 Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
• 9 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
• 10 Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany.
• 11 Institut für Humangenetik, Westfälische Wilhelms-Universität Münster, Münster, Germany.
• 12 CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany.
• 13 Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands.
• 14 Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany.
• 15 Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
• 16 Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.
• 17 Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
• 18 Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.
• 19 Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany.
• 20 DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany.
• PMID: 35790048
• DOI: 10.1002/humu.24430

Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme's active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.

Keywords: ARS; CRISPR/Cas9; SARS1; WARS1; aminoacyl-tRNA synthetase; aminoacylation; intellectual disability; microcephaly; tRNA; zebrafish.

© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.

Publication types

• Research Support, Non-U.S. Gov't
• Amino Acyl-tRNA Synthetases* / genetics
• Charcot-Marie-Tooth Disease* / genetics
• Microcephaly* / genetics
• Microcephaly* / pathology
• RNA, Transfer
• Tryptophan-tRNA Ligase* / genetics
• Zebrafish / genetics
• Amino Acyl-tRNA Synthetases
• Tryptophan-tRNA Ligase
• WARS1 protein, human
• SARS1 protein, human