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Meltzer WA, Gupta A, Lin PN, Brown RA, Benyamien-Roufaeil DS, Khatri R, Mahurkar AA, Song Y, Taylor RJ, Zalzman M. Reprogramming Chromosome Ends by Functional Histone Acetylation. Int J Mol Sci 2024; 25:3898. [PMID: 38612707 PMCID: PMC11011970 DOI: 10.3390/ijms25073898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Cancers harness embryonic programs to evade aging and promote survival. Normally, sequences at chromosome ends called telomeres shorten with cell division, serving as a countdown clock to limit cell replication. Therefore, a crucial aspect of cancerous transformation is avoiding replicative aging by activation of telomere repair programs. Mouse embryonic stem cells (mESCs) activate a transient expression of the gene Zscan4, which correlates with chromatin de-condensation and telomere extension. Head and neck squamous cell carcinoma (HNSCC) cancers reactivate ZSCAN4, which in turn regulates the phenotype of cancer stem cells (CSCs). Our study reveals a new role for human ZSCAN4 in facilitating functional histone H3 acetylation at telomere chromatin. Next-generation sequencing indicates ZSCAN4 enrichment at telomere chromatin. These changes correlate with ZSCAN4-induced histone H3 acetylation and telomere elongation, while CRISPR/Cas9 knockout of ZSCAN4 leads to reduced H3 acetylation and telomere shortening. Our study elucidates the intricate involvement of ZSCAN4 and its significant contribution to telomere chromatin remodeling. These findings suggest that ZSCAN4 induction serves as a novel link between 'stemness' and telomere maintenance. Targeting ZSCAN4 may offer new therapeutic approaches to effectively limit or enhance the replicative lifespan of stem cells and cancer cells.
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Affiliation(s)
- W. Alex Meltzer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Aditi Gupta
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Phyo Nay Lin
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Robert A. Brown
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Daniel S. Benyamien-Roufaeil
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Raju Khatri
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
| | - Anup A. Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (A.A.M.); (Y.S.)
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (A.A.M.); (Y.S.)
| | - Rodney J. Taylor
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA (A.G.); (P.N.L.); (R.A.B.); (D.S.B.-R.); (R.K.)
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
- Marlene and Stewart Greenbaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D'Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, Hodges TK, Ifeonu O, Jeon M, Kropiwnicki E, Lim MCW, Liming RL, Lumian J, Mahurkar AA, Mandal M, Munro JB, Nadendla S, Richter R, Romano C, Rocca-Serra P, Schor M, Schuler RE, Tangmunarunkit H, Waldrop A, Williams C, Word K, Sansone SA, Ma'ayan A, Wagner R, Foster I, Kesselman C, Brown CT, White O. Making Common Fund data more findable: catalyzing a data ecosystem. Gigascience 2022; 11:6835135. [PMID: 36409836 PMCID: PMC9677336 DOI: 10.1093/gigascience/giac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/16/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022] Open
Abstract
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs' Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.
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Affiliation(s)
| | - Arthur Brady
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Karl Czajkowski
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - Jain Aluvathingal
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Saranya Canchi
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Robert Carter
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Kyle Chard
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Crabtree
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Heather H Creasy
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Mike D'Arcy
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - Victor Felix
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Michelle Giglio
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | | | - Rayna M Harris
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Theresa K Hodges
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Olukemi Ifeonu
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Minji Jeon
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eryk Kropiwnicki
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marisa C W Lim
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - R Lee Liming
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Jessica Lumian
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Anup A Mahurkar
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Meisha Mandal
- RTI International, Research Triangle Park 27709-2194, USA
| | - James B Munro
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Suvarna Nadendla
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Rudyard Richter
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Cia Romano
- University of Southern California Information Sciences Institute, CA 90292, USA.,Interface Guru, Tuscon 85701, USA
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford OX1 3QG, UK
| | - Michael Schor
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
| | - Robert E Schuler
- University of Southern California Information Sciences Institute, CA 90292, USA
| | | | - Alex Waldrop
- RTI International, Research Triangle Park 27709-2194, USA
| | - Cris Williams
- University of Southern California Information Sciences Institute, CA 90292, USA
| | | | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford OX1 3QG, UK
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rick Wagner
- University of California San Diego, San Diego, CA 92093, USA
| | - Ian Foster
- Division of Decision and Information Sciences, University of Chicago and Argonne National Laboratory, Chicago, IL 60637, USA
| | - Carl Kesselman
- University of Southern California Information Sciences Institute, CA 90292, USA
| | - C Titus Brown
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Owen White
- University of Maryland Institute for Genome Sciences, University of Maryland School of Medicine, MD 21201, USA
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3
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Chuang NT, Gardner EJ, Terry DM, Crabtree J, Mahurkar AA, Rivell GL, Hong CC, Perry JA, Devine SE. Mutagenesis of human genomes by endogenous mobile elements on a population scale. Genome Res 2021; 31:2225-2235. [PMID: 34772701 PMCID: PMC8647825 DOI: 10.1101/gr.275323.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of these MEIs on human genomes. However, these projects also have presented major challenges with respect to the scalability and computational costs associated with performing MEI discovery on tens or even hundreds of thousands of samples. To meet these challenges, we have developed a more efficient and scalable version of our mobile element locator tool (MELT) called CloudMELT. We then used MELT and CloudMELT to perform MEI discovery in 57,919 human genomes and exomes, leading to the discovery of 104,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE-annotated features, and disease genes by these MEIs. Our study provides new insights on the L1 source elements that drive MEI mutagenesis and brings forth a better understanding of how this mutagenesis impacts human genomes.
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Affiliation(s)
- Nelson T Chuang
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Division of Gastroenterology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Eugene J Gardner
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Diane M Terry
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Guillermo L Rivell
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott E Devine
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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4
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Chrysostomou E, Prater KE, Song Y, Orvis J, Kancherla J, Herb B, Ament S, Bravo HC, Mahurkar AA, White O, Garden GA, Hertzano R. NeMO analytics‐AD: The neuroscience multi‐omic visualization and analysis platform, now extended to support Alzheimer’s disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.046097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Yang Song
- University of Maryland School of Medicine Baltimore MD USA
| | - Joshua Orvis
- University of Maryland School of Medicine Baltimore MD USA
| | | | - Brian Herb
- University of Maryland School of Medicine Baltimore MD USA
| | - Seth Ament
- University of Maryland School of Medicine Baltimore MD USA
| | | | | | - Owen White
- University of Maryland School of Medicine Baltimore MD USA
| | | | - Ronna Hertzano
- University of Maryland School of Medicine Baltimore MD USA
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5
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Joshi SS, Tandukar B, Pan L, Huang JM, Livak F, Smith BJ, Hodges T, Mahurkar AA, Hornyak TJ. CD34 defines melanocyte stem cell subpopulations with distinct regenerative properties. PLoS Genet 2019; 15:e1008034. [PMID: 31017901 PMCID: PMC6481766 DOI: 10.1371/journal.pgen.1008034] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/18/2019] [Indexed: 12/16/2022] Open
Abstract
Melanocyte stem cells (McSCs) are the undifferentiated melanocytic cells of the mammalian hair follicle (HF) responsible for recurrent generation of a large number of differentiated melanocytes during each HF cycle. HF McSCs reside in both the CD34+ bulge/lower permanent portion (LPP) and the CD34- secondary hair germ (SHG) regions of the HF during telogen. Using Dct-H2BGFP mice, we separate bulge/LPP and SHG McSCs using FACS with GFP and anti-CD34 to show that these two subsets of McSCs are functionally distinct. Genome-wide expression profiling results support the distinct nature of these populations, with CD34- McSCs exhibiting higher expression of melanocyte differentiation genes and with CD34+ McSCs demonstrating a profile more consistent with a neural crest stem cell. In culture and in vivo, CD34- McSCs regenerate pigmentation more efficiently whereas CD34+ McSCs selectively exhibit the ability to myelinate neurons. CD34+ McSCs, and their counterparts in human skin, may be useful for myelinating neurons in vivo, leading to new therapeutic opportunities for demyelinating diseases and traumatic nerve injury.
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Affiliation(s)
- Sandeep S. Joshi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bishal Tandukar
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Li Pan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jennifer M. Huang
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Ferenc Livak
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Marlene and Stuart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Barbara J. Smith
- Institute for Basic Biomedical Sciences, John Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Theresa Hodges
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Anup A. Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas J. Hornyak
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Marlene and Stuart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Research & Development Service, VA Maryland Health Care System, United States Department of Veterans Affairs, Baltimore, Maryland, United States of America
- Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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6
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Hazen TH, Daugherty SC, Shetty A, Mahurkar AA, White O, Kaper JB, Rasko DA. RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates. Front Microbiol 2015; 6:569. [PMID: 26124752 PMCID: PMC4464170 DOI: 10.3389/fmicb.2015.00569] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/24/2015] [Indexed: 11/13/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) are a leading cause of diarrheal illness among infants in developing countries. E. coli isolates classified as typical EPEC are identified by the presence of the locus of enterocyte effacement (LEE) and the bundle-forming pilus (BFP), and absence of the Shiga-toxin genes, while the atypical EPEC also encode LEE but do not encode BFP or Shiga-toxin. Comparative genomic analyses have demonstrated that EPEC isolates belong to diverse evolutionary lineages and possess lineage- and isolate-specific genomic content. To investigate whether this genomic diversity results in significant differences in global gene expression, we used an RNA sequencing (RNA-Seq) approach to characterize the global transcriptomes of the prototype typical EPEC isolates E2348/69, B171, C581-05, and the prototype atypical EPEC isolate E110019. The global transcriptomes were characterized during laboratory growth in two different media and three different growth phases, as well as during adherence of the EPEC isolates to human cells using in vitro tissue culture assays. Comparison of the global transcriptomes during these conditions was used to identify isolate- and growth phase-specific differences in EPEC gene expression. These analyses resulted in the identification of genes that encode proteins involved in survival and metabolism that were coordinately expressed with virulence factors. These findings demonstrate there are isolate- and growth phase-specific differences in the global transcriptomes of EPEC prototype isolates, and highlight the utility of comparative transcriptomics for identifying additional factors that are directly or indirectly involved in EPEC pathogenesis.
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Affiliation(s)
- Tracy H Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - Sean C Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - James B Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
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7
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Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, Devine SE. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res 2011; 21:830-9. [PMID: 21460062 DOI: 10.1101/gr.115907.110] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp in length in the genomes of 79 diverse humans. These variants include 819,363 small INDELs that map to human genes. Small INDELs frequently were found in the coding exons of these genes, and several lines of evidence indicate that such variation is a major determinant of human biological diversity. Microarray-based genotyping experiments revealed several interesting observations regarding the population genetics of small INDEL variation. For example, we found that many of our INDELs had high levels of linkage disequilibrium (LD) with both HapMap SNPs and with high-scoring SNPs from genome-wide association studies. Overall, our study indicates that small INDEL variation is likely to be a key factor underlying inherited traits and diseases in humans.
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Affiliation(s)
- Ryan E Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Mahurkar AA, Vivino MA, Trus BL, Kuehl EM, Datiles MB, Kaiser-Kupfer MI. Constructing retinal fundus photomontages. A new computer-based method. Invest Ophthalmol Vis Sci 1996; 37:1675-83. [PMID: 8675411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PURPOSE To develop computer algorithms for reconstructing 24-bit color, wide-angle composite retinal fundus images from a set of adjacent 45 degrees fundus slides. The authors present the description, technical details, and results of the image reconstruction technique. METHODS Patients with retinal degeneration underwent fundus photography with a 45 degrees field-of-view fundus camera. Individual photographic slides were digitized for creating fundus montages. Background variations in individual 45 degrees images were modeled to first- or second-order two-dimensional polynomial functions to generate a background image. The background image was subtracted from the original image to obtain background corrected image. Background corrected images were registered and spatially transformed using a first- or second-order two-dimensional polynomial warp model to reconstruct a composite retinal fundus montage. RESULTS The authors successfully reconstructed 24-bit color, 100 degrees field-of-view, composite retinal fundus images. The computer-reconstructed montages are an improvement over manually generated montages because computer analysis can be performed on the computer-based montages. In addition, background variations and discontinuities between individual photographs observed in manually generated montages are reduced greatly in computer-generated montages. Most important, the computer-generated montages are better aligned than the manually generated photomontages. CONCLUSIONS This method of reconstructing a wide-angle composite retinal fundus image from a set of adjacent small- and wide-angle fundus slides is a new tool for creating montages as large as 100 degrees field of view. The computer-generated montages may be used for documenting and quantifying retinal findings. This can greatly assist studies of retinal manifestations of diseases, such as gyrate atrophy, retinitis pigmentosa, sickle cell disease, and acquired immune deficiency syndrome.
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Affiliation(s)
- A A Mahurkar
- Ophthalmic Genetics and Clinical Services Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892-1860, USA
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9
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Lopez ML, Datiles MB, Podgor MJ, Vivino MA, Mahurkar AA, Lasa SM. Reproducibility study of posterior subcapsular opacities on the NEI retroillumination image analysis system. Eye (Lond) 1994; 8 ( Pt 6):657-61. [PMID: 7867822 DOI: 10.1038/eye.1994.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We developed a semi-automated retroillumination image analysis system which combines speed, ease of operation and interactive analysis. The system measures cataract area and integral of cataract density (ID). For system reproducibility evaluation, 20 eyes with posterior subcapsular opacities were captured twice by two photographers. Variability was estimated under a random effects analysis of variance model. Measurement errors for area and for ID were each small contributors to total variability (the sum of variability between study eyes plus measurement error), being 0.4% and 0.1% respectively. The largest contributor to area measurement error was image analysis variability (97%). For ID measurement error, the variability in images (44%) and in image analysis (46%) were major contributors. The reproducibility is comparable to previously described retroillumination analysis systems. This easy to use system may therefore be useful in clinical research studies including possible clinical trials of anti-cataract drugs.
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Affiliation(s)
- M L Lopez
- Section on Cataract and Cornea, National Institutes of Health, Bethesda, MD 20892
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