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Lee B, Nasanovsky L, Shen L, Maglinte DT, Pan Y, Gai X, Schmidt RJ, Raca G, Biegel JA, Roytman M, An P, Saunders CJ, Farrow EG, Shams S, Ji J. Significance Associated with Phenotype Score Aids in Variant Prioritization for Exome Sequencing Analysis. J Mol Diagn 2024; 26:337-348. [PMID: 38360210 DOI: 10.1016/j.jmoldx.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Several in silico annotation-based methods have been developed to prioritize variants in exome sequencing analysis. This study introduced a novel metric Significance Associated with Phenotypes (SAP) score, which generates a statistical score by comparing an individual's observed phenotypes against existing gene-phenotype associations. To evaluate the SAP score, a retrospective analysis was performed on 219 exomes. Among them, 82 family-based and 35 singleton exomes had at least one disease-causing variant that explained the patient's clinical features. SAP scores were calculated, and the rank of the disease-causing variant was compared with a known method, Exomiser. Using the SAP score, the known causative variant was ranked in the top 10 retained variants for 94% (77 of 82) of the family-based exomes and in first place for 73% of these cases. For singleton exomes, the SAP score analysis ranked the known pathogenic variants within the top 10 for 80% (28 of 35) of cases. The SAP score, which is independent of detected variants, demonstrates comparable performance with Exomiser, which considers both phenotype and variant-level evidence simultaneously. Among 102 cases with negative results or variants of uncertain significance, SAP score analysis revealed two cases with a potential new diagnosis based on rank. The SAP score, a phenotypic quantitative metric, can be used in conjunction with standard variant filtration and annotation to enhance variant prioritization in exome analysis.
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Affiliation(s)
- Brian Lee
- Bionano Genomics, San Diego, California
| | | | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dennis T Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Yachen Pan
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ryan J Schmidt
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Gordana Raca
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | | | - Paul An
- Bionano Genomics, San Diego, California
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Emily G Farrow
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | | | - Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California.
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2
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Clarke JL, Cooper LD, Poelchau MF, Berardini TZ, Elser J, Farmer AD, Ficklin S, Kumari S, Laporte MA, Nelson RT, Sadohara R, Selby P, Thessen AE, Whitehead B, Sen TZ. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database (Oxford) 2023; 2023:baad076. [PMID: 37971715 PMCID: PMC10653126 DOI: 10.1093/database/baad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL https://www.agbiodata.org/databases.
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Affiliation(s)
- Jennifer L Clarke
- Department of Statistics and Department of Food Science and Technology, University of Nebraska–Lincoln, 340 Hardin Hall North Wing, Lincoln, NE 68583, USA
| | - Laurel D Cooper
- Department of Botany and Plant Pathology, Oregon State University, 2503 Cordley Hall, Corvallis, OR 97331, USA
| | - Monica F Poelchau
- USDA, Agricultural Research Service, National Agricultural Library, 10301 Baltimore Ave, Beltsville 20705, USA
| | - Tanya Z Berardini
- The Arabidopsis Information Resource and Phoenix Bioinformatic, 39899 Balentine Drive, Suite 200, Newark, CA, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, 2503 Cordley Hall, Corvallis, OR 97331, USA
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Dr. E., Santa Fe, NM 87505, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, 249 Clark Hall, PO Box 646414, Pullman, WA 99164, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Marie-Angélique Laporte
- Digital Inclusion, Bioversity International, Parc Scientifique Agropolis II, 1990 Bd de la Lironde, Montpellier 34397, France
| | - Rex T Nelson
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, 716 Farmhouse Lane, Ames, IA 50011, USA
| | - Rie Sadohara
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Peter Selby
- School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, 215 Garden Avenue, Ithaca, NY 14850, USA
| | - Anne E Thessen
- Department of Biomedical Informatics, University of Colorado Anschutz, 1890 N. Revere Court, Mailstop F600, Aurora CO 80045, USA
| | - Brandon Whitehead
- Data Science and Informatics, Manaaki Whenua—Landcare Research, Ltd., Riddet Road, Massey University, Palmerston North 4472, New Zealand
| | - Taner Z Sen
- USDA, Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany 94710, USA
- Department of Bioengineering, University of California, 306 Stanley Hall, Berkeley, CA 94720, USA
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3
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Ruberte J, Schofield PN, Sundberg JP, Rodriguez-Baeza A, Carretero A, McKerlie C. Bridging mouse and human anatomies; a knowledge-based approach to comparative anatomy for disease model phenotyping. Mamm Genome 2023:10.1007/s00335-023-10005-4. [PMID: 37421464 PMCID: PMC10382392 DOI: 10.1007/s00335-023-10005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/13/2023] [Indexed: 07/10/2023]
Abstract
The laboratory mouse is the foremost mammalian model used for studying human diseases and is closely anatomically related to humans. Whilst knowledge about human anatomy has been collected throughout the history of mankind, the first comprehensive study of the mouse anatomy was published less than 60 years ago. This has been followed by the more recent publication of several books and resources on mouse anatomy. Nevertheless, to date, our understanding and knowledge of mouse anatomy is far from being at the same level as that of humans. In addition, the alignment between current mouse and human anatomy nomenclatures is far from being as developed as those existing between other species, such as domestic animals and humans. To close this gap, more in depth mouse anatomical research is needed and it will be necessary to extent and refine the current vocabulary of mouse anatomical terms.
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Affiliation(s)
- Jesús Ruberte
- Center for Animal Biotechnology and Gene Therapy, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Paul N Schofield
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - John P Sundberg
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Ana Carretero
- Center for Animal Biotechnology and Gene Therapy, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, Canada
- Department of Lab Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
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4
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Cacheiro P, Spielmann N, Mashhadi HH, Fuchs H, Gailus-Durner V, Smedley D, de Angelis MH. Knockout mice are an important tool for human monogenic heart disease studies. Dis Model Mech 2023; 16:288843. [PMID: 36825469 PMCID: PMC10073007 DOI: 10.1242/dmm.049770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Mouse models are relevant to studying the functionality of genes involved in human diseases; however, translation of phenotypes can be challenging. Here, we investigated genes related to monogenic forms of cardiovascular disease based on the Genomics England PanelApp and aligned them to International Mouse Phenotyping Consortium (IMPC) data. We found 153 genes associated with cardiomyopathy, cardiac arrhythmias or congenital heart disease in humans, of which 151 have one-to-one mouse orthologues. For 37.7% (57/151), viability and heart data captured by electrocardiography, transthoracic echocardiography, morphology and pathology from embryos and young adult mice are available. In knockout mice, 75.4% (43/57) of these genes showed non-viable phenotypes, whereas records of prenatal, neonatal or infant death in humans were found for 35.1% (20/57). Multisystem phenotypes are common, with 58.8% (20/34) of heterozygous (homozygous lethal) and 78.6% (11/14) of homozygous (viable) mice showing cardiovascular, metabolic/homeostasis, musculoskeletal, hematopoietic, nervous system and/or growth abnormalities mimicking the clinical manifestations observed in patients. These IMPC data are critical beyond cardiac diagnostics given their multisystemic nature, allowing detection of abnormalities across physiological systems and providing a valuable resource to understand pleiotropic effects.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich, Munich 85764, Germany
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich, Munich 85764, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich, Munich 85764, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Martin Hrabĕ de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Center Munich, Munich 85764, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising 85354, Germany
- German Center for Diabetes Research (DZD), Neuherberg 85764, Germany
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5
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Elucidation of the Landscape of Alternatively Spliced Genes and Features in the Dorsal Striatum of Aggressive/Aggression-Deprived Mice in the Model of Chronic Social Conflicts. Genes (Basel) 2023; 14:genes14030599. [PMID: 36980872 PMCID: PMC10048575 DOI: 10.3390/genes14030599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Both aggressive and aggression-deprived (AD) individuals represent pathological cases extensively studied in psychiatry and substance abuse disciplines. We employed the animal model of chronic social conflicts curated in our laboratory for over 30 years. In the study, we pursued the task of evaluation of the key events in the dorsal striatum transcriptomes of aggression-experienced mice and AD species, as compared with the controls, using RNA-seq profiling. We evaluated the alternative splicing-mediated transcriptome dynamics based on the RNA-seq data. We confined our attention to the exon skipping (ES) events as the major AS type for animals. We report the concurrent posttranscriptional and posttranslational regulation of the ES events observed in the phosphorylation cycles (in phosphoproteins and their targets) in the neuron-specific genes of the striatum. Strikingly, we found that major neurospecific splicing factors (Nova1, Ptbp1, 2, Mbnl1, 2, and Sam68) related to the alternative splicing regulation of cAMP genes (Darpp-32, Grin1, Ptpn5, Ppp3ca, Pde10a, Prkaca, Psd95, and Adora1) are upregulated specifically in aggressive individuals as compared with the controls and specifically AD animals, assuming intense switching between isoforms in the cAMP-mediated (de)phosphorylation signaling cascade. We found that the coding alternative splicing events were mostly attributed to synaptic plasticity and neural development-related proteins, while the nonsense-mediated decay-associated splicing events are mostly attributed to the mRNA processing of genes, including the spliceosome and splicing factors. In addition, considering the gene families, the transporter (Slc) gene family manifested most of the ES events. We found out that the major molecular systems employing AS for their plasticity are the ‘spliceosome’, ‘chromatin rearrangement complex’, ‘synapse’, and ‘neural development/axonogenesis’ GO categories. Finally, we state that approximately 35% of the exon skipping variants in gene coding regions manifest the noncoding variants subject to nonsense-mediated decay, employed as a homeostasis-mediated expression regulation layer and often associated with the corresponding gene expression alteration.
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Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN. Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes. EBioMedicine 2023; 87:104413. [PMID: 36563487 PMCID: PMC9769411 DOI: 10.1016/j.ebiom.2022.104413] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, long COVID is incompletely understood and characterised by a wide range of manifestations that are difficult to analyse computationally. Additionally, the generalisability of machine learning classification of COVID-19 clinical outcomes has rarely been tested. METHODS We present a method for computationally modelling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning. FINDINGS We found six clusters of PASC patients, each with distinct profiles of phenotypic abnormalities, including clusters with distinct pulmonary, neuropsychiatric, and cardiovascular abnormalities, and a cluster associated with broad, severe manifestations and increased mortality. There was significant association of cluster membership with a range of pre-existing conditions and measures of severity during acute COVID-19. We assigned new patients from other healthcare centres to clusters by maximum semantic similarity to the original patients, and showed that the clusters were generalisable across different hospital systems. The increased mortality rate originally identified in one cluster was consistently observed in patients assigned to that cluster in other hospital systems. INTERPRETATION Semantic phenotypic clustering provides a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC. FUNDING NIH (TR002306/OT2HL161847-01/OD011883/HG010860), U.S.D.O.E. (DE-AC02-05CH11231), Donald A. Roux Family Fund at Jackson Laboratory, Marsico Family at CU Anschutz.
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Affiliation(s)
- Justin T Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Elena Casiraghi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; AnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy
| | | | - Johanna J Loomba
- The Integrated Translational Health Research Institute of Virginia (iTHRIV), University of Virginia, Charlottesville, VA, USA
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Bryan Laraway
- Departments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Ben Coleman
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Michael Gargano
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Kenneth J Wilkins
- Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luca Cappelletti
- AnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy
| | - Tommaso Fontana
- AnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy
| | - Nariman Ammar
- Health Science Center, University of Tennessee, Memphis, TN, USA
| | - Blessy Antony
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - J Harry Caufield
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA
| | - Julie A McMurry
- Departments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Williams
- Tufts Medical Center Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA; Tufts University School of Medicine, Institute for Clinical Research and Health Policy Studies, Boston, MA, USA; Northeastern University, OHDSI Center at the Roux Institute, Boston, MA, USA
| | - Richard Moffitt
- Department of Biomedical Informatics and Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | | | | | | | - Kristin Kostka
- Northeastern University, OHDSI Center at the Roux Institute, Boston, MA, USA
| | - Giorgio Valentini
- AnacletoLab, Dipartimento di Informatica, Università Degli Studi di Milano, Milan, Italy
| | | | - Christopher G Chute
- Schools of Medicine, Public Health and Nursing, Johns Hopkins University, Baltimore, MD, USA
| | | | - Melissa A Haendel
- Departments of Biomedical Informatics and Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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7
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Reese JT, Blau H, Bergquist T, Loomba JJ, Callahan T, Laraway B, Antonescu C, Casiraghi E, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN. Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.05.24.22275398. [PMID: 35665012 PMCID: PMC9164456 DOI: 10.1101/2022.05.24.22275398] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Accurate stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, the natural history of long COVID is incompletely understood and characterized by an extremely wide range of manifestations that are difficult to analyze computationally. In addition, the generalizability of machine learning classification of COVID-19 clinical outcomes has rarely been tested. We present a method for computationally modeling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning procedures. Using k-means clustering of this similarity matrix, we found six distinct clusters of PASC patients, each with distinct profiles of phenotypic abnormalities. There was a significant association of cluster membership with a range of pre-existing conditions and with measures of severity during acute COVID-19. Two of the clusters were associated with severe manifestations and displayed increased mortality. We assigned new patients from other healthcare centers to one of the six clusters on the basis of maximum semantic similarity to the original patients. We show that the identified clusters were generalizable across different hospital systems and that the increased mortality rate was consistently observed in two of the clusters. Semantic phenotypic clustering can provide a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.
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8
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Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau‐Frachon S, Dempsey EA, Dufke A, Duyzend MH, el Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz‐Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:231-242. [PMID: 35872606 PMCID: PMC9588534 DOI: 10.1002/ajmg.c.31989] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.
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Affiliation(s)
- Ferdinand Dhombres
- Sorbonne University, GRC26, INSERM, Limics, Armand Trousseau Hospital, Fetal Medicine Department, APHPParisFrance
| | - Patricia Morgan
- American College of Medical Genetics and Genomics, Newborn Screening Translational Research NetworkBethesdaMarylandUSA
| | - Bimal P. Chaudhari
- Institute for Genomic MedicineNationwide Children's HospitalColumbusOhioUSA
| | - Isabel Filges
- University Hospital Basel and University of Basel, Medical GeneticsBaselSwitzerland
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Pablo Lapunzina
- CIBERER and Hospital Universitario La Paz, INGEMM‐Institute of Medical and Molecular GeneticsMadridSpain
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South WalesSydneyNew South WalesAustralia
| | - Umber Agarwal
- Department of Maternal and Fetal MedicineLiverpool Women's NHS Foundation TrustLiverpoolUK
| | - Shagun Aggarwal
- Department of Medical GeneticsNizam's Institute of Medical SciencesHyderabadTelanganaIndia
| | - Claire Beneteau
- Service de Génétique Médicale, UF 9321 de Fœtopathologie et Génétique, CHU de NantesNantesFrance
| | - Pilar Cacheiro
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | - Leigh C. Carmody
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
| | | | - Esther A. Dempsey
- St George's University of London, Molecular and Clinical Sciences Research InstituteLondonUK
| | - Andreas Dufke
- University of Tübingen, Institute of Medical Genetics and Applied GenomicsTübingenGermany
| | | | | | - Jessica L. Giordano
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ragnhild Glad
- Department of Obstetrics and GynecologyUniversity Hospital of North NorwayTromsøNorway
| | - Ieva Grinfelde
- Department of Medical Genetics and Prenatal diagnosisChildren's University HospitalRigaLatvia
| | - Dominic G. Iliescu
- Department of Obstetrics and GynecologyUniversity of Medicine and Pharmacy CraiovaCraiovaDoljRomania
| | - Markus S. Ladewig
- Department of OphthalmologyKlinikum SaarbrückenSaarbrückenSaarlandGermany
| | - Monica C. Munoz‐Torres
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marzia Pollazzon
- Azienda USL‐IRCCS di Reggio EmiliaMedical Genetics UnitReggio EmiliaItaly
| | | | - Carlota Rodo
- Vall d'Hebron Hospital Campus, Maternal & Fetal MedicineBarcelonaSpain
| | - Raquel Gouveia Silva
- Hospital Santa Maria, Serviço de Genética, Departamento de PediatriaHospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de LisboaLisboaPortugal
| | - Damian Smedley
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | | | - Sabrina Toro
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Irene Valenzuela
- Hospital Vall d'Hebron, Clinical and Molecular Genetics AreaBarcelonaSpain
| | - Nicole A. Vasilevsky
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Ronald J. Wapner
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Roni Zemet
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Melissa A Haendel
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Peter N. Robinson
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
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9
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Hou Y, Qi F, Bai X, Ren T, Shen X, Chu Q, Zhang X, Lu X. Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals. BMC Genomics 2020; 21:204. [PMID: 32131728 PMCID: PMC7057487 DOI: 10.1186/s12864-020-6613-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
Background In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection. Results First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild. Conclusions After a comprehensive investigation on genomic diversity and evolutionary trajectories in chickens, we revealed basis, pattern and evolutionary significance of molecular convergence in domesticated bird and mammals, highlighted the genetic basis of a compromise on utmost adaptation to the lives with human at the cost of high risk of neurophysiological changes affecting animals’ fitness in wild.
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Affiliation(s)
- Yali Hou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,China National Center for Bioinformation, Beijing, People's Republic of China.
| | - Furong Qi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xue Bai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.,China National Center for Bioinformation, Beijing, People's Republic of China
| | - Tong Ren
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xu Shen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, People's Republic of China
| | - Xiquan Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, People's Republic of China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China.
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10
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Ebiki M, Okazaki T, Kai M, Adachi K, Nanba E. Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. Yonago Acta Med 2019; 62:244-252. [PMID: 31582890 DOI: 10.33160/yam.2019.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/17/2019] [Indexed: 12/24/2022]
Abstract
Background During the investigation of causative variants of Mendelian disorders using next-generation sequencing, the enormous number of possible candidates makes the detection process complex, and the use of multidimensional methods is required. Although the utility of several variant prioritization tools has been reported, their effectiveness in Japanese patients remains largely unknown. Methods We selected 5 free variant prioritization tools (PhenIX, hiPHIVE, Phen-Gen, eXtasy-order statistics, and eXtasy-combined max) and assessed their effectiveness in Japanese patient populations. To compare these tools, we conducted 2 studies: one based on simulated data of 100 diseases and another based on the exome data of 20 in-house patients with Mendelian disorders. To this end we selected 100 pathogenic variants from the "Database of Pathogenic Variants (DPV)" and created 100 variant call format (VCF) files that each had pathogenic variants based on reference human genome data from the 1000 Genomes Project. The later "in-house" study used exome data from 20 Japanese patients with Mendelian disorders. In both studies, we utilized 1-5 terms of "Human Phenotype Ontology" as clinical information. Results In our analysis based on simulated disease data, the detection rate of the top 10 causative variants was 91% for hiPHIVE, and 88% for PhenIX, based on 100 sets of simulated disease VCF data. Also, both software packages detected 82% of the top 1 causative variants. When we used data from our in-house patients instead, we found that these two programs (PhenIX and hiPHIVE) produced higher detection rates than the other three systems in our study. The detection rate of the top 1 causative variant was 71.4% for PhenIX, 65.0% for hiPHIVE. Conclusion The rates of detecting causative variants in two Exomizer software packages, hiPHIVE and PhenIX, were higher than for the other three software systems we analyzed, with respect to Japanese patients.
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Affiliation(s)
- Mitsutaka Ebiki
- The Development of Innovative Future Medical Treatment, Graduate School of Medical Sciences, Tottori University, Yonago 683-8504, Japan.,KUSUNOKI SCALE INC., Yonago 683-0832, Japan
| | - Tetsuya Okazaki
- Division of Child Neurology, Department of Brain and Neurosciences, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan.,Division of Clinical Genetics, Tottori University Hospital, Yonago 683-8504, Japan, ‖Technical Department, Tottori University, Yonago 683-8503, Japan
| | - Masachika Kai
- Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
| | - Kaori Adachi
- Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
| | - Eiji Nanba
- Division of Clinical Genetics, Tottori University Hospital, Yonago 683-8504, Japan, ‖Technical Department, Tottori University, Yonago 683-8503, Japan.,Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
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11
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Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC, Gourdine JP, Gargano M, McMurry J, Danis D, Mungall CJ, Smedley D, Haendel M, Robinson PN. Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. CURRENT PROTOCOLS IN HUMAN GENETICS 2019; 103:e92. [PMID: 31479590 PMCID: PMC6814016 DOI: 10.1002/cphg.92] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. The HPO is frequently used to create a set of terms that accurately describe the observed clinical abnormalities of an individual being evaluated for suspected rare genetic disease. This profile is compared with computational disease profiles in the HPO database with the aim of identifying genetic diseases with comparable phenotypic profiles. The computational analysis can be coupled with the analysis of whole-exome or whole-genome sequencing data through applications such as Exomiser. This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sebastian Köhler
- Charité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
- Einstein Center Digital Future, Berlin 10117, Germany
- Monarch Initiative, monarchinitiative.org
| | | | | | | | - Julius OB Jacobsen
- Monarch Initiative, monarchinitiative.org
- Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Nicole Vasilevsky
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
| | - Leigh C Carmody
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - JP Gourdine
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
| | - Michael Gargano
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Julie McMurry
- Monarch Initiative, monarchinitiative.org
- Oregon State University, Corvallis, OR, USA
| | - Daniel Danis
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Christopher J Mungall
- Monarch Initiative, monarchinitiative.org
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Damian Smedley
- Monarch Initiative, monarchinitiative.org
- Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Melissa Haendel
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
- Oregon State University, Corvallis, OR, USA
| | - Peter N Robinson
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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12
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Large-scale neuroanatomical study uncovers 198 gene associations in mouse brain morphogenesis. Nat Commun 2019; 10:3465. [PMID: 31371714 PMCID: PMC6671969 DOI: 10.1038/s41467-019-11431-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/13/2019] [Indexed: 01/03/2023] Open
Abstract
Brain morphogenesis is an important process contributing to higher-order cognition, however our knowledge about its biological basis is largely incomplete. Here we analyze 118 neuroanatomical parameters in 1,566 mutant mouse lines and identify 198 genes whose disruptions yield NeuroAnatomical Phenotypes (NAPs), mostly affecting structures implicated in brain connectivity. Groups of functionally similar NAP genes participate in pathways involving the cytoskeleton, the cell cycle and the synapse, display distinct fetal and postnatal brain expression dynamics and importantly, their disruption can yield convergent phenotypic patterns. 17% of human unique orthologues of mouse NAP genes are known loci for cognitive dysfunction. The remaining 83% constitute a vast pool of genes newly implicated in brain architecture, providing the largest study of mouse NAP genes and pathways. This offers a complementary resource to human genetic studies and predict that many more genes could be involved in mammalian brain morphogenesis. Brain morphogenesis is an important process contributing to higher-order cognition, however our knowledge about its biological basis is largely incomplete. Here, authors analyzed 118 neuroanatomical parameters in 1,566 mutant mouse lines to identify 198 genes whose disruptions yield neuroanatomical phenotypes
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13
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Ferris E, Abegglen LM, Schiffman JD, Gregg C. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance. Cell Rep 2019. [PMID: 29514101 PMCID: PMC6294302 DOI: 10.1016/j.celrep.2018.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genomewide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.
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Affiliation(s)
- Elliott Ferris
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Lisa M Abegglen
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84132-3401, USA; Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Joshua D Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84132-3401, USA; Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA; New York Stem Cell Foundation, New York, NY, USA.
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14
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Roitsch T, Cabrera-Bosquet L, Fournier A, Ghamkhar K, Jiménez-Berni J, Pinto F, Ober ES. Review: New sensors and data-driven approaches-A path to next generation phenomics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:2-10. [PMID: 31003608 PMCID: PMC6483971 DOI: 10.1016/j.plantsci.2019.01.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/15/2018] [Accepted: 01/09/2019] [Indexed: 05/19/2023]
Abstract
At the 4th International Plant Phenotyping Symposium meeting of the International Plant Phenotyping Network (IPPN) in 2016 at CIMMYT in Mexico, a workshop was convened to consider ways forward with sensors for phenotyping. The increasing number of field applications provides new challenges and requires specialised solutions. There are many traits vital to plant growth and development that demand phenotyping approaches that are still at early stages of development or elude current capabilities. Further, there is growing interest in low-cost sensor solutions, and mobile platforms that can be transported to the experiments, rather than the experiment coming to the platform. Various types of sensors are required to address diverse needs with respect to targets, precision and ease of operation and readout. Converting data into knowledge, and ensuring that those data (and the appropriate metadata) are stored in such a way that they will be sensible and available to others now and for future analysis is also vital. Here we are proposing mechanisms for "next generation phenomics" based on our learning in the past decade, current practice and discussions at the IPPN Symposium, to encourage further thinking and collaboration by plant scientists, physicists and engineering experts.
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Affiliation(s)
- Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czech Republic
| | | | - Antoine Fournier
- Arvalis, Institut du végétal, 45, voie Romaine 41240 Beauce la Romaine, France
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Tennent Drive, Fitzherbert, Palmerston North 4410, New Zealand
| | - José Jiménez-Berni
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Cientificas (CSIC) Avenida Menéndez Pidal, Campus Alameda del Obispo, 14004 Córdoba, Spain
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, México C.P. 56237, Mexico
| | - Eric S Ober
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE, UK.
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15
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Tadenev ALD, Burgess RW. Model validity for preclinical studies in precision medicine: precisely how precise do we need to be? Mamm Genome 2019; 30:111-122. [PMID: 30953144 PMCID: PMC6606658 DOI: 10.1007/s00335-019-09798-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022]
Abstract
The promise of personalized medicine is that each patient’s treatment can be optimally tailored to their disease. In turn, their disease, as well as their response to the treatment, is determined by their genetic makeup and the “environment,” which relates to their general health, medical history, personal habits, and surroundings. Developing such optimized treatment strategies is an admirable goal and success stories include examples such as switching chemotherapy agents based on a patient’s tumor genotype. However, it remains a challenge to apply precision medicine to diseases for which there is no known effective treatment. Such diseases require additional research, often using experimentally tractable models. Presumably, models that recapitulate as much of the human pathophysiology as possible will be the most predictive. Here we will discuss the considerations behind such “precision models.” What sort of precision is required and under what circumstances? How can the predictive validity of such models be improved? Ultimately, there is no perfect model, but our continually improving ability to genetically engineer a variety of systems allows the generation of more and more precise models. Furthermore, our steadily increasing awareness of risk alleles, genetic background effects, multifactorial disease processes, and gene by environment interactions also allows increasingly sophisticated models that better reproduce patients’ conditions. In those cases where the research has progressed sufficiently far, results from these models appear to often be translating to effective treatments for patients.
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Affiliation(s)
- Abigail L D Tadenev
- The Center for Precision Genetics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Robert W Burgess
- The Center for Precision Genetics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
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16
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Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B. Computational aspects underlying genome to phenome analysis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:182-198. [PMID: 30500991 PMCID: PMC6849790 DOI: 10.1111/tpj.14179] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
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Affiliation(s)
- Anthony M. Bolger
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Hendrik Poorter
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | - Kathryn Dumschott
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Marie E. Bolger
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Sonia Osorio
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasCampus de Teatinos29071MálagaSpain
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology (PGSB)Helmholtz Zentrum München (HMGU)Ingolstädter Landstraße 185764NeuherbergGermany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstraße 306466SeelandGermany
| | - Björn Usadel
- Institute for Biology I, BioSCRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Forschungszentrum Jülich (FZJ) Institute of Bio‐ and Geosciences (IBG‐2) Plant SciencesWilhelm‐Johnen‐Straße52428JülichGermany
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17
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Han SK, Kim D, Lee H, Kim I, Kim S. Divergence of Noncoding Regulatory Elements Explains Gene–Phenotype Differences between Human and Mouse Orthologous Genes. Mol Biol Evol 2018; 35:1653-1667. [DOI: 10.1093/molbev/msy056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Heetak Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Inhae Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Korea
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18
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Song C, Liu BP, Zhang YP, Peng Z, Wang J, Collier AD, Echevarria DJ, Savelieva KV, Lawrence RF, Rex CS, Meshalkina DA, Kalueff AV. Modeling consequences of prolonged strong unpredictable stress in zebrafish: Complex effects on behavior and physiology. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:384-394. [PMID: 28847526 DOI: 10.1016/j.pnpbp.2017.08.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/17/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Abstract
Chronic stress is the major pathogenetic factor of human anxiety and depression. Zebrafish (Danio rerio) have become a novel popular model species for neuroscience research and CNS drug discovery. The utility of zebrafish for mimicking human affective disorders is also rapidly growing. Here, we present a new zebrafish model of clinically relevant, prolonged unpredictable strong chronic stress (PUCS). The 5-week PUCS induced overt anxiety-like and motor retardation-like behaviors in adult zebrafish, also elevating whole-body cortisol and proinflammatory cytokines - interleukins IL-1β and IL-6. PUCS also elevated whole-body levels of the anti-inflammatory cytokine IL-10 and increased the density of dendritic spines in zebrafish telencephalic neurons. Chronic treatment of fish with an antidepressant fluoxetine (0.1mg/L for 8days) normalized their behavioral and endocrine phenotypes, as well as corrected stress-elevated IL-1β and IL-6 levels, similar to clinical and rodent data. The CNS expression of the bdnf gene, the two genes of its receptors (trkB, p75), and the gfap gene of glia biomarker, the glial fibrillary acidic protein, was unaltered in all three groups. However, PUCS elevated whole-body BDNF levels and the telencephalic dendritic spine density (which were corrected by fluoxetine), thereby somewhat differing from the effects of chronic stress in rodents. Together, these findings support zebrafish as a useful in-vivo model of chronic stress, also calling for further cross-species studies of both shared/overlapping and distinct neurobiological responses to chronic stress.
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Affiliation(s)
- Cai Song
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China; Graduate Institute of Neural and Cognitive Science, China Medical University and Hospital, Taichung 00001, Taiwan.
| | - Bai-Ping Liu
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China
| | - Yong-Ping Zhang
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China
| | - Zhilan Peng
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China
| | - JiaJia Wang
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China
| | - Adam D Collier
- ZENEREI Institute and the International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA 70458, USA
| | - David J Echevarria
- ZENEREI Institute and the International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA 70458, USA; Department of Psychology, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Katerina V Savelieva
- ZENEREI Institute and the International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA 70458, USA
| | - Robert F Lawrence
- Afraxis, Inc. 6605 Nancy Ridge Rd. Suite 224, San Diego, CA 92121, USA
| | - Christopher S Rex
- Afraxis, Inc. 6605 Nancy Ridge Rd. Suite 224, San Diego, CA 92121, USA
| | - Darya A Meshalkina
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 3960002, Russia
| | - Allan V Kalueff
- Institute for Marine Drugs and Nutrition, Zhanjiang City Key Laboratory, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 3452001, Guangdong, China; ZENEREI Institute and the International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA 70458, USA; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 3960002, Russia; Ural Federal University, Ekaterinburg 620002, Russia.
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19
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Taboada M, Rodriguez H, Gudivada RC, Martinez D. A new synonym-substitution method to enrich the human phenotype ontology. BMC Bioinformatics 2017; 18:446. [PMID: 29017443 PMCID: PMC5635572 DOI: 10.1186/s12859-017-1858-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/02/2017] [Indexed: 12/29/2022] Open
Abstract
Background Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technologies in bioinformatics, providing resources for improved natural language processing tasks. However, biomedical ontology-based named entity recognition continues to be a major research problem. Results This paper presents an automated synonym-substitution method to enrich the Human Phenotype Ontology (HPO) with new synonyms. The approach is mainly based on both the lexical properties of the terms and the hierarchical structure of the ontology. By scanning the lexical difference between a term and its descendant terms, the method can learn new names and modifiers in order to generate synonyms for the descendant terms. By searching for the exact phrases in MEDLINE, the method can automatically rule out illogical candidate synonyms. In total, 745 new terms were identified. These terms were indirectly evaluated through the concept annotations on a gold standard corpus and also by document retrieval on a collection of abstracts on hereditary diseases. A moderate improvement in the F-measure performance on the gold standard corpus was observed. Additionally, 6% more abstracts on hereditary diseases were retrieved, and this percentage was 33% higher if only the highly informative concepts were considered. Conclusions A synonym-substitution procedure that leverages the HPO hierarchical structure works well for a reliable and automatic extension of the terminology. The results show that the generated synonyms have a positive impact on concept recognition, mainly those synonyms corresponding to highly informative HPO terms. Electronic supplementary material The online version of this article (10.1186/s12859-017-1858-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Taboada
- Department of Electronics & Computer Science, University of Santiago de Compostela, Campus Vida, Santiago de Compostela, 15705, Spain.
| | - Hadriana Rodriguez
- Department of Electronics & Computer Science, University of Santiago de Compostela, Campus Vida, Santiago de Compostela, 15705, Spain
| | | | - Diego Martinez
- Department of Applied Physics, University of Santiago de Compostela, 15705, Santiago de Compostela, Campus Vida, Spain
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20
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Sandor C, Beer NL, Webber C. Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PLoS Comput Biol 2017; 13:e1005816. [PMID: 29059180 PMCID: PMC5667928 DOI: 10.1371/journal.pcbi.1005816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 11/02/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Type 2 Diabetes (T2D) constitutes a global health burden. Efforts to uncover predisposing genetic variation have been considerable, yet detailed knowledge of the underlying pathogenesis remains poor. Here, we constructed a T2D phenotypic-linkage network (T2D-PLN), by integrating diverse gene functional information that highlight genes, which when disrupted in mice, elicit similar T2D-relevant phenotypes. Sensitising the network to T2D-relevant phenotypes enabled significant functional convergence to be detected between genes implicated in monogenic or syndromic diabetes and genes lying within genomic regions associated with T2D common risk. We extended these analyses to a recent multiethnic T2D case-control exome of 12,940 individuals that found no evidence of T2D risk association for rare frequency variants outside of previously known T2D risk loci. Examining associations involving protein-truncating variants (PTV), most at low population frequencies, the T2D-PLN was able to identify a convergent set of biological pathways that were perturbed within four of five independent T2D case/control ethnic sets of 2000 to 5000 exomes each. These same pathways were found to be over-represented among both known monogenic or syndromic diabetes genes and genes within T2D-associated common risk loci. Our study demonstrates convergent biology amongst variants representing different classes of T2D genetic risk. Although convergence was observed at the pathway level, few of the contributing genes were found in common between different cohorts or variant classes, most notably between the exome variant sets which suggests that future rare variant studies may be better focusing their power onto a single population of recent common ancestry.
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Affiliation(s)
- Cynthia Sandor
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola L. Beer
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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21
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22
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Epistasis in Neuropsychiatric Disorders. Trends Genet 2017; 33:256-265. [PMID: 28268034 DOI: 10.1016/j.tig.2017.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022]
Abstract
The contribution of epistasis to human disease remains unclear. However, several studies have now identified epistatic interactions between common variants that increase the risk of a neuropsychiatric disorder, while there is growing evidence that genetic interactions contribute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in patients. This review discusses the current evidence for epistatic events and genetic interactions in neuropsychiatric disorders, how paradigm shifts in the phenotypic classification of patients would empower the search for epistatic effects, and how network and cellular models might be employed to further elucidate relevant epistatic interactions.
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23
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Ramoni RB, Mulvihill JJ, Adams DR, Allard P, Ashley EA, Bernstein JA, Gahl WA, Hamid R, Loscalzo J, McCray AT, Shashi V, Tifft CJ, Wise AL, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernick D, Bernstein JA, Bican A, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brownstein CA, Brush M, Burke EA, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eastwood R, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Iglesias B, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Martin C, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Robertson AK, Rodan LH, Rosenfeld JA, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease. Am J Hum Genet 2017; 100:185-192. [PMID: 28157539 PMCID: PMC5294757 DOI: 10.1016/j.ajhg.2017.01.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/30/2016] [Indexed: 01/07/2023] Open
Abstract
Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.
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24
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Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2016; 45:D865-D876. [PMID: 27899602 PMCID: PMC5210535 DOI: 10.1093/nar/gkw1039] [Citation(s) in RCA: 501] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nicole A Vasilevsky
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark Engelstad
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erin Foster
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julie McMurry
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ségolène Aymé
- Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia
| | - Susan M Bello
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Cornelius F Boerkoel
- Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia
| | - Laura E DeMare
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Andrew D Devereau
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Courtney Hum
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Roger James
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Roland Krause
- LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan
| | - Annie Olry
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Willem H Ouwehand
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ana Rath
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Segal
- SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA
| | | | - Richard Sever
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Catherine Turner
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Marijcke W M Veltman
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Tom Vulliamy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Julie von Ziegenweidt
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK
| | - Andreas Zankl
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.,Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia
| | - Stephan Züchner
- JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Julius O B Jacobsen
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Damian Smedley
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa Haendel
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA .,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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25
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Li Y, Zhao Q, Wang Y, Man T, Zhou L, Fang X, Pei H, Chi L, Liu J. Ultrasensitive Signal-On Detection of Nucleic Acids with Surface-Enhanced Raman Scattering and Exonuclease III-Assisted Probe Amplification. Anal Chem 2016; 88:11684-11690. [DOI: 10.1021/acs.analchem.6b03267] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yingying Li
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qingcheng Zhao
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yandong Wang
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tiantian Man
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Lu Zhou
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xu Fang
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hao Pei
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Lifeng Chi
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jian Liu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
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26
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Robinson PN, Mungall CJ, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud 2016; 1:a000372. [PMID: 27148566 PMCID: PMC4850887 DOI: 10.1101/mcs.a000372] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities-an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research.
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Affiliation(s)
- Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;; Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, Oregon 97239, USA
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27
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Trzaskowski M, Lichtenstein P, Magnusson PK, Pedersen NL, Plomin R. Application of linear mixed models to study genetic stability of height and body mass index across countries and time. Int J Epidemiol 2016; 45:417-423. [PMID: 26819444 PMCID: PMC4864877 DOI: 10.1093/ije/dyv355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background:
It is now possible to estimate genetic correlations between two independent samples when there is no overlapping phenotypic information. We applied the latest bivariate genomic methods to children in the UK and older adults in Sweden to ask two questions. Are the same variants driving individual differences in anthropometric traits in these two populations, and are these variants as important in childhood as they are later in life?
Methods:
A sample of 3152 11-year-old children in the UK was compared with a sample of 6813 adults with an average age of 65 in Sweden. Genotypes were imputed from 1000 genomes with combined 9 767 136 single nucleotide polymorphisms meeting quality control criteria in both samples. Two cross-sample GCTA-GREML analyses and linkage disequilibrium (LD) score regressions were conducted to assess genetic correlations across more than 50 years: child versus adult height and child versus adult body mass index (BMI). Consistency of effects was tested using the recently proposed polygenic scoring method.
Results:
For height, GCTA-GREML and LD score indicated strong genetic stability between children and adults, 0.58 (0.16) and 1.335 (1.09), respectively. For BMI, both methods produced similarly strong estimates of genetic stability 0.75 (0.26) and 0.855 (0.49), respectively. In height, adult polygenic score explained 60% of genetic variance in childhood and 10% of variance in BMI.
Conclusions:
Here we replicated and extended previous findings of longitudinal genetic stability in anthropometric traits to cross-cultural dimensions, and showed that for height but not BMI these variants are as important in childhood as they are in adulthood.
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Affiliation(s)
- Maciej Trzaskowski
- King's College London, Institute of Psychiatry, Psychology & Neuroscience, London, UK and
| | - Paul Lichtenstein
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Patrik K Magnusson
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Nancy L Pedersen
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Robert Plomin
- King's College London, Institute of Psychiatry, Psychology & Neuroscience, London, UK and
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28
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Collier N, Groza T, Smedley D, Robinson PN, Oellrich A, Rebholz-Schuhmann D. PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. Database (Oxford) 2015; 2015:bav104. [PMID: 26507285 PMCID: PMC4622021 DOI: 10.1093/database/bav104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/24/2015] [Accepted: 08/27/2015] [Indexed: 11/27/2022]
Abstract
Analysis of scientific and clinical phenotypes reported in the experimental literature has been curated manually to build high-quality databases such as the Online Mendelian Inheritance in Man (OMIM). However, the identification and harmonization of phenotype descriptions struggles with the diversity of human expressivity. We introduce a novel automated extraction approach called PhenoMiner that exploits full parsing and conceptual analysis. Apriori association mining is then used to identify relationships to human diseases. We applied PhenoMiner to the BMC open access collection and identified 13,636 phenotype candidates. We identified 28,155 phenotype-disorder hypotheses covering 4898 phenotypes and 1659 Mendelian disorders. Analysis showed: (i) the semantic distribution of the extracted terms against linked ontologies; (ii) a comparison of term overlap with the Human Phenotype Ontology (HP); (iii) moderate support for phenotype-disorder pairs in both OMIM and the literature; (iv) strong associations of phenotype-disorder pairs to known disease-genes pairs using PhenoDigm. The full list of PhenoMiner phenotypes (S1), phenotype-disorder associations (S2), association-filtered linked data (S3) and user database documentation (S5) is available as supplementary data and can be downloaded at http://github.com/nhcollier/PhenoMiner under a Creative Commons Attribution 4.0 license. Database URL: phenominer.mml.cam.ac.uk.
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Affiliation(s)
- Nigel Collier
- The University of Cambridge, Cambridge, CB3 9DB, UK, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK,
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Damian Smedley
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitatsmedizin Berlin, 13353 Berlin, Germany and
| | - Anika Oellrich
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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29
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Madhukar NS, Elemento O, Pandey G. Prediction of Genetic Interactions Using Machine Learning and Network Properties. Front Bioeng Biotechnol 2015; 3:172. [PMID: 26579514 PMCID: PMC4620407 DOI: 10.3389/fbioe.2015.00172] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 12/04/2022] Open
Abstract
A genetic interaction (GI) is a type of interaction where the effect of one gene is modified by the effect of one or several other genes. These interactions are important for delineating functional relationships among genes and their corresponding proteins, as well as elucidating complex biological processes and diseases. An important type of GI - synthetic sickness or synthetic lethality - involves two or more genes, where the loss of either gene alone has little impact on cell viability, but the combined loss of all genes leads to a severe decrease in fitness (sickness) or cell death (lethality). The identification of GIs is an important problem for it can help delineate pathways, protein complexes, and regulatory dependencies. Synthetic lethal interactions have important clinical and biological significance, such as providing therapeutically exploitable weaknesses in tumors. While near systematic high-content screening for GIs is possible in single cell organisms such as yeast, the systematic discovery of GIs is extremely difficult in mammalian cells. Therefore, there is a great need for computational approaches to reliably predict GIs, including synthetic lethal interactions, in these organisms. Here, we review the state-of-the-art approaches, strategies, and rigorous evaluation methods for learning and predicting GIs, both under general (healthy/standard laboratory) conditions and under specific contexts, such as diseases.
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Affiliation(s)
- Neel S Madhukar
- Department of Physiology and Biophysics, Meyer Cancer Center, Institute for Precision Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College , New York, NY , USA ; Tri-Institutional Training Program in Computational Biology and Medicine , New York, NY , USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Meyer Cancer Center, Institute for Precision Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College , New York, NY , USA ; Tri-Institutional Training Program in Computational Biology and Medicine , New York, NY , USA
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences and Graduate School of Biomedical Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai , New York, NY , USA
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30
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Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat 2015; 36:979-84. [PMID: 26269093 PMCID: PMC5473253 DOI: 10.1002/humu.22857] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/22/2015] [Indexed: 11/10/2022]
Abstract
The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.
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Affiliation(s)
| | - Nicole L. Washington
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jeremy Nguyen-Xuan
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Condit
- San Diego Supercomputing Center, UC San Diego, La Jolla, California, USA
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Mouse Informatics group, Hinxton, UK
| | - Sebastian Köhler
- Charité - Universitätsmedizin Berlin, Institute for Medical and Human Genetics, Berlin, Germany
| | - Tudor Groza
- Garvan Institute, Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Kent Shefchek
- Department of Biomedical Informatics and Clinical Epidemiology, Oregon Health and Science University
| | - Harry Hochheiser
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Peter N. Robinson
- Charité - Universitätsmedizin Berlin, Institute for Medical and Human Genetics, Berlin, Germany
| | - Suzanna E. Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Melissa A. Haendel
- Department of Biomedical Informatics and Clinical Epidemiology, Oregon Health and Science University
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31
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Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, Simon M, Wang L, Winnenburg R, Dumontier M. The digital revolution in phenotyping. Brief Bioinform 2015; 17:819-30. [PMID: 26420780 PMCID: PMC5036847 DOI: 10.1093/bib/bbv083] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 12/22/2022] Open
Abstract
Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support 'bench to bedside' efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, by means of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data.
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32
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Applications of comparative evolution to human disease genetics. Curr Opin Genet Dev 2015; 35:16-24. [PMID: 26338499 DOI: 10.1016/j.gde.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 12/15/2022]
Abstract
Direct comparison of human diseases with model phenotypes allows exploration of key areas of human biology which are often inaccessible for practical or ethical reasons. We review recent developments in comparative evolutionary approaches for finding models for genetic disease, including high-throughput generation of gene/phenotype relationship data, the linking of orthologous genes and phenotypes across species, and statistical methods for linking human diseases to model phenotypes.
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33
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Steinberg J, Honti F, Meader S, Webber C. Haploinsufficiency predictions without study bias. Nucleic Acids Res 2015; 43:e101. [PMID: 26001969 PMCID: PMC4551909 DOI: 10.1093/nar/gkv474] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 04/07/2015] [Accepted: 04/29/2015] [Indexed: 11/12/2022] Open
Abstract
Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied 'gold standard' haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.
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Affiliation(s)
- Julia Steinberg
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Frantisek Honti
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Stephen Meader
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
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34
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Krawitz P, Buske O, Zhu N, Brudno M, Robinson PN. The genomic birthday paradox: how much is enough? Hum Mutat 2015; 36:989-97. [PMID: 26239817 DOI: 10.1002/humu.22848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/15/2015] [Indexed: 12/18/2022]
Abstract
Genomic matchmaking databases (GMDs) allow participants to submit genomic and phenotypic data with the goal of identifying previously uncharacterized disease-associated genes by "matching" to other comparable cases. Current estimates suggest that there are at least 3,000 Mendelian disease-associated genes that have not yet been characterized as such, but the true number may be substantially higher. Therefore, GMDs are addressing a pressing medical need, and it is important to ask how they should be designed and how much data they should strive to contain in order to identify a certain number of these genes. In this work, we argue that genomic matchmaking has similarities to the so-called "birthday paradox," which refers to the observation that within a group of just 23 persons, two people will have the same birthday with probability greater than 50%. We develop a series of simulations to provide a rough estimate of the number of cases required and to explore the influence of parameters such as genetic heterogeneity, mode of inheritance, background variation, precision of phenotypic descriptions, disease prevalence, and the accuracy of bioinformatics pathogenicity prediction programs on the performance of genomic matchmaking.
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Affiliation(s)
- Peter Krawitz
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.,Berlin Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Orion Buske
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 3G4, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Na Zhu
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 3G4, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.,Berlin Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin 13353, Germany.,Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
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35
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Poot M, Haaf T. Mechanisms of Origin, Phenotypic Effects and Diagnostic Implications of Complex Chromosome Rearrangements. Mol Syndromol 2015; 6:110-34. [PMID: 26732513 DOI: 10.1159/000438812] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2015] [Indexed: 01/08/2023] Open
Abstract
Complex chromosome rearrangements (CCRs) are currently defined as structural genome variations that involve more than 2 chromosome breaks and result in exchanges of chromosomal segments. They are thought to be extremely rare, but their detection rate is rising because of improvements in molecular cytogenetic technology. Their population frequency is also underestimated, since many CCRs may not elicit a phenotypic effect. CCRs may be the result of fork stalling and template switching, microhomology-mediated break-induced repair, breakage-fusion-bridge cycles, or chromothripsis. Patients with chromosomal instability syndromes show elevated rates of CCRs due to impaired DNA double-strand break responses during meiosis. Therefore, the putative functions of the proteins encoded by ATM, BLM, WRN, ATR, MRE11, NBS1, and RAD51 in preventing CCRs are discussed. CCRs may exert a pathogenic effect by either (1) gene dosage-dependent mechanisms, e.g. haploinsufficiency, (2) mechanisms based on disruption of the genomic architecture, such that genes, parts of genes or regulatory elements are truncated, fused or relocated and thus their interactions disturbed - these mechanisms will predominantly affect gene expression - or (3) mixed mutation mechanisms in which a CCR on one chromosome is combined with a different type of mutation on the other chromosome. Such inferred mechanisms of pathogenicity need corroboration by mRNA sequencing. Also, future studies with in vitro models, such as inducible pluripotent stem cells from patients with CCRs, and transgenic model organisms should substantiate current inferences regarding putative pathogenic effects of CCRs. The ramifications of the growing body of information on CCRs for clinical and experimental genetics and future treatment modalities are briefly illustrated with 2 cases, one of which suggests KDM4C (JMJD2C) as a novel candidate gene for mental retardation.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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36
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Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ. Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 2015. [PMID: 26220875 DOI: 10.1002/dvg.22878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscape's semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.
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Affiliation(s)
- Prashanti Manda
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - Hilmar Lapp
- US National Evolutionary Synthesis Center, Durham, North Carolina.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota
| | - Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
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37
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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38
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39
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Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet 2015; 97:111-24. [PMID: 26119816 PMCID: PMC4572507 DOI: 10.1016/j.ajhg.2015.05.020] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.
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Affiliation(s)
- Tudor Groza
- School of Information Technology and Electrical Engineering, University of Queensland, St. Lucia, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dawid Moldenhauer
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; University of Applied Sciences, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Nicole Vasilevsky
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gareth Baynam
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6840, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Office of Population Health Genomics, Public Health and Clinical Services Division, Department of Health, Perth, WA 6004, Australia; Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; Telethon Kids Institute, Perth, WA 6008, Australia
| | - Tomasz Zemojtel
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Lynn Marie Schriml
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Warren Alden Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tim Beck
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Drashtti Vasant
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Andreas Zankl
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Academic Department of Medical Genetics, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia
| | - Nicole L Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany.
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40
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Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome 2015; 26:548-55. [PMID: 26092691 PMCID: PMC4602072 DOI: 10.1007/s00335-015-9577-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/20/2015] [Indexed: 11/30/2022]
Abstract
New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient’s set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene.
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Affiliation(s)
- Melissa A Haendel
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Nicole Vasilevsky
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Matthew Brush
- University Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Harry S Hochheiser
- Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Julius Jacobsen
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anika Oellrich
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Nicole Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sebastian Köhler
- Computational Biology Group, Institute for Medical Genetics and Human Genetics, Universitatsklinikum Charité, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Peter N Robinson
- Computational Biology Group, Institute for Medical Genetics and Human Genetics, Universitatsklinikum Charité, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Damian Smedley
- Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Orgogozo V, Morizot B, Martin A. The differential view of genotype-phenotype relationships. Front Genet 2015; 6:179. [PMID: 26042146 PMCID: PMC4437230 DOI: 10.3389/fgene.2015.00179] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022] Open
Abstract
An integrative view of diversity and singularity in the living world requires a better understanding of the intricate link between genotypes and phenotypes. Here we re-emphasize the old standpoint that the genotype-phenotype (GP) relationship is best viewed as a connection between two differences, one at the genetic level and one at the phenotypic level. As of today, predominant thinking in biology research is that multiple genes interact with multiple environmental variables (such as abiotic factors, culture, or symbionts) to produce the phenotype. Often, the problem of linking genotypes and phenotypes is framed in terms of genotype and phenotype maps, and such graphical representations implicitly bring us away from the differential view of GP relationships. Here we show that the differential view of GP relationships is a useful explanatory framework in the context of pervasive pleiotropy, epistasis, and environmental effects. In such cases, it is relevant to view GP relationships as differences embedded into differences. Thinking in terms of differences clarifies the comparison between environmental and genetic effects on phenotypes and helps to further understand the connection between genotypes and phenotypes.
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Affiliation(s)
- Virginie Orgogozo
- CNRS, UMR 7592, Institut Jacques Monod, Université Paris DiderotParis, France
| | - Baptiste Morizot
- Aix Marseille Université, CNRS, CEPERC UMR 7304Aix en Provence, France
| | - Arnaud Martin
- Department of Molecular Cell Biology, University of CaliforniaBerkeley, CA, USA
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42
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Roux J, Rosikiewicz M, Robinson-Rechavi M. What to compare and how: Comparative transcriptomics for Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:372-82. [PMID: 25864439 PMCID: PMC4949521 DOI: 10.1002/jez.b.22618] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/19/2015] [Indexed: 12/30/2022]
Abstract
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 The Authors. J. Exp. Zool. (Mol. Dev. Evol.) published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julien Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Marta Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Andrews T, Meader S, Vulto-van Silfhout A, Taylor A, Steinberg J, Hehir-Kwa J, Pfundt R, de Leeuw N, de Vries BBA, Webber C. Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PLoS Genet 2015; 11:e1005012. [PMID: 25781962 PMCID: PMC4362763 DOI: 10.1371/journal.pgen.1005012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/17/2015] [Indexed: 12/05/2022] Open
Abstract
Readily-accessible and standardised capture of genotypic variation has revolutionised our understanding of the genetic contribution to disease. Unfortunately, the corresponding systematic capture of patient phenotypic variation needed to fully interpret the impact of genetic variation has lagged far behind. Exploiting deep and systematic phenotyping of a cohort of 197 patients presenting with heterogeneous developmental disorders and whose genomes harbour de novo CNVs, we systematically applied a range of commonly-used functional genomics approaches to identify the underlying molecular perturbations and their phenotypic impact. Grouping patients into 408 non-exclusive patient-phenotype groups, we identified a functional association amongst the genes disrupted in 209 (51%) groups. We find evidence for a significant number of molecular interactions amongst the association-contributing genes, including a single highly-interconnected network disrupted in 20% of patients with intellectual disability, and show using microcephaly how these molecular networks can be used as baits to identify additional members whose genes are variant in other patients with the same phenotype. Exploiting the systematic phenotyping of this cohort, we observe phenotypic concordance amongst patients whose variant genes contribute to the same functional association but note that (i) this relationship shows significant variation across the different approaches used to infer a commonly perturbed molecular pathway, and (ii) that the phenotypic similarities detected amongst patients who share the same inferred pathway perturbation result from these patients sharing many distinct phenotypes, rather than sharing a more specific phenotype, inferring that these pathways are best characterized by their pleiotropic effects. Developmental disorders occur in ∼3% of live births, and exhibit a broad range of abnormalities including: intellectual disability, autism, heart defects, and other neurological and morphological problems. Often, patients are grouped into genetic syndromes which are defined by a specific set of mutations and a common set of abnormalities. However, many mutations are unique to a single patient and many patients present a range of abnormalities which do not fit one of the recognized genetic syndromes, making diagnosis difficult. Using a dataset of 197 patients with systematically described abnormalities, we identified molecular pathways whose disruption was associated with specific abnormalities among many patients. Importantly, patients with mutations in the same pathway often exhibited similar co-morbid symptoms and thus the commonly disrupted pathway appeared responsible for the broad range of shared abnormalities amongst these patients. These findings support the general concept that patients with mutations in distinct genes could be etiologically grouped together through the common pathway that these mutated genes participate in, with a view to improving diagnoses, prognoses and therapeutic outcomes.
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Affiliation(s)
- Tallulah Andrews
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Stephen Meader
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Avigail Taylor
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Julia Steinberg
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bert B. A. de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- * E-mail: (BBAdV); (CW)
| | - Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (BBAdV); (CW)
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Stewart AM, Nguyen M, Poudel MK, Warnick JE, Echevarria DJ, Beaton EA, Song C, Kalueff AV. The failure of anxiolytic therapies in early clinical trials: what needs to be done. Expert Opin Investig Drugs 2015; 24:543-56. [PMID: 25727478 DOI: 10.1517/13543784.2015.1019063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Anxiety spectrum disorders (ASDs) are highly prevalent psychiatric illnesses that affect millions of people worldwide. Strongly associated with stress, common ASDs include generalized anxiety disorder, panic, social anxiety, phobias and drug-abuse-related anxiety. In addition to ASDs, several other prevalent psychiatric illnesses represent trauma/stressor-related disorders, such as post-traumatic stress disorder and acute stress disorder. Anxiolytic drugs, commonly prescribed to treat ASDs and trauma/stressor-related disorders, form a highly heterogenous group, modulating multiple neurotransmitters and physiological mechanisms. However, overt individual differences in efficacy and the potential for serious side-effects (including addiction and drug interaction) indicate a need for further drug development. Yet, over the past 50 years, there has been relatively little progress in the development of novel anxiolytic medications, especially when promising candidate drugs often fail in early clinical trials. AREAS COVERED Herein, the authors present recommendations of the Task Force on Anxiolytic Drugs of the International Stress and Behavior Society on how to improve anxiolytic drug discovery. These recommendations cover a wide spectrum of aspects, ranging from methodological improvements to conceptual insights and innovation. EXPERT OPINION In order to improve the success of anxiolytic drugs in early clinical trials, the goals of preclinical trials may need to be adjusted from a clinical perspective and better synchronized with those of clinical studies. Indeed, it is important to realize that the strategic goals and approaches must be similar if we want to have a smoother transition between phases.
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Affiliation(s)
- Adam Michael Stewart
- ZENEREI Institute , 309 Palmer Court, Slidell, LA , USA +1 240 328 2275 ; +1 240 328 2275 ;
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Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM. PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. Sci Rep 2015; 5:8117. [PMID: 25631385 PMCID: PMC4822650 DOI: 10.1038/srep08117] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/19/2014] [Indexed: 12/19/2022] Open
Abstract
We describe a new method, PhenomeExpress, for the analysis of transcriptomic datasets to identify pathogenic disease mechanisms. Our analysis method includes input from both protein-protein interaction and phenotype similarity networks. This introduces valuable information from disease relevant phenotypes, which aids the identification of sub-networks that are significantly enriched in differentially expressed genes and are related to the disease relevant phenotypes. This contrasts with many active sub-network detection methods, which rely solely on protein-protein interaction networks derived from compounded data of many unrelated biological conditions and which are therefore not specific to the context of the experiment. PhenomeExpress thus exploits readily available animal model and human disease phenotype information. It combines this prior evidence of disease phenotypes with the experimentally derived disease data sets to provide a more targeted analysis. Two case studies, in subchondral bone in osteoarthritis and in Pax5 in acute lymphoblastic leukaemia, demonstrate that PhenomeExpress identifies core disease pathways in both mouse and human disease expression datasets derived from different technologies. We also validate the approach by comparison to state-of-the-art active sub-network detection methods, which reveals how it may enhance the detection of molecular phenotypes and provide a more detailed context to those previously identified as possible candidates.
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Affiliation(s)
- Jamie Soul
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Timothy E Hardingham
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Raymond P Boot-Handford
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jean-Marc Schwartz
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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46
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Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. Finding our way through phenotypes. PLoS Biol 2015; 13:e1002033. [PMID: 25562316 PMCID: PMC4285398 DOI: 10.1371/journal.pbio.1002033] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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Affiliation(s)
- Andrew R. Deans
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Suzanna E. Lewis
- Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Eva Huala
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
- Phoenix Bioinformatics, Palo Alto, California, United States of America
| | - Salvatore S. Anzaldo
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - James P. Balhoff
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - David C. Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, United States of America
| | - Judith A. Blake
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - J. Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Bruno Chanet
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Laurel D. Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mélanie Courtot
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sándor Csösz
- MTA-ELTE-MTM, Ecology Research Group, Pázmány Péter sétány 1C, Budapest, Hungary
| | - Hong Cui
- School of Information Resources and Library Science, University of Arizona, Tucson, Arizona, United States of America
| | - Wasila Dahdul
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, India
| | - T. Alexander Dececchi
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Agnes Dettai
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Rui Diogo
- Department of Anatomy, Howard University College of Medicine, Washington D.C., United States of America
| | - Robert E. Druzinsky
- Department of Oral Biology, College of Dentistry, University of Illinois, Chicago, Illinois, United States of America
| | - Michel Dumontier
- Stanford Center for Biomedical Informatics Research, Stanford, California, United States of America
| | - Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Frank Friedrich
- Biocenter Grindel and Zoological Museum, Hamburg University, Hamburg, Germany
| | - George V. Gkoutos
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Melissa Haendel
- Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Luke J. Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Terry F. Hayamizu
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Yongqun He
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Heather M. Hines
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nizar Ibrahim
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Laura M. Jackson
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Christina James-Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Guillaume Lecointre
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, Paris, France
| | - Hilmar Lapp
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
| | - Carolyn J. Lawrence
- Department of Genetics, Development and Cell Biology and Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | | | - John G. Lundberg
- Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Pennsylvania, United States of America
| | - James Macklin
- Eastern Cereal and Oilseed Research Centre, Ottawa, Ontario, Canada
| | - Austin R. Mast
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | | | - István Mikó
- Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christopher J. Mungall
- Genome Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Anika Oellrich
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Martín J. Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales - CONICET, Buenos Aires, Argentina
| | - Stefan Richter
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany
| | - Peter N. Robinson
- Institut für Medizinische Genetik und Humangenetik Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Alan Ruttenberg
- School of Dental Medicine, University at Buffalo, Buffalo, New York, United States of America
| | - Katja S. Schulz
- Smithsonian Institution, National Museum of Natural History, Washington, D.C., United States of America
| | - Erik Segerdell
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Katja C. Seltmann
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - Michael J. Sharkey
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Aaron D. Smith
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, New York, United States of America
| | - Chelsea D. Specht
- Department of Plant and Microbial Biology, Integrative Biology, and the University and Jepson Herbaria, University of California, Berkeley, California, United States of America
| | - R. Burke Squires
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert W. Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Anne Thessen
- The Data Detektiv, 1412 Stearns Hill Road, Waltham, Massachusetts, United States of America
| | | | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Peter D. Vize
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Lars Vogt
- Universität Bonn, Institut für Evolutionsbiologie und Ökologie, Bonn, Germany
| | - Christine E. Wall
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Ramona L. Walls
- iPlant Collaborative University of Arizona, Thomas J. Keating Bioresearch Building, Tucson, Arizona, United States of America
| | - Monte Westerfeld
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Robert A. Wharton
- Department of Entomology, Texas A & M University, College, Station, Texas, United States of America
| | - Christian S. Wirkner
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, Rostock, Germany
| | - James B. Woolley
- Department of Entomology, Texas A & M University, College, Station, Texas, United States of America
| | - Matthew J. Yoder
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Aaron M. Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, Cincinnati, Ohio, United States of America
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
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Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. Clinical interpretation of CNVs with cross-species phenotype data. J Med Genet 2014; 51:766-772. [PMID: 25280750 DOI: 10.1136/jmedgenet-2014-102633] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human genes, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. METHODS Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. RESULTS We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype relations. CONCLUSIONS Integrating and visualising cross-species phenotype information on the affected genes may help in routine diagnostics of CNVs.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Uwe Schoeneberg
- Foundation Institute Molecular Biology and Bioinformatics, Freie Universitaet Berlin, Berlin, Germany
| | | | - Sandra C Doelken
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jonas Ibn-Salem
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany
| | | | - Damian Smedley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Melissa A Haendel
- Department of Medical Informatics and Epidemiology and OHSU Library, Oregon Health & Science University, Portland, USA
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universitaet Berlin, Berlin, Germany
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48
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Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol 2014; 15:423. [PMID: 25315429 PMCID: PMC4180961 DOI: 10.1186/s13059-014-0423-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 07/24/2014] [Indexed: 12/21/2022] Open
Abstract
Background Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These topological domains form the regulatory backbone of the genome and are separated by regulatory boundary elements or barriers. Copy-number variations can potentially alter the topological domain architecture by deleting or duplicating the barriers and thereby allowing enhancers from neighboring domains to ectopically activate genes causing misexpression and disease, a mutational mechanism that has recently been termed enhancer adoption. Results We use the Human Phenotype Ontology database to relate the phenotypes of 922 deletion cases recorded in the DECIPHER database to monogenic diseases associated with genes in or adjacent to the deletions. We identify combinations of tissue-specific enhancers and genes adjacent to the deletion and associated with phenotypes in the corresponding tissue, whereby the phenotype matched that observed in the deletion. We compare this computationally with a gene-dosage pathomechanism that attempts to explain the deletion phenotype based on haploinsufficiency of genes located within the deletions. Up to 11.8% of the deletions could be best explained by enhancer adoption or a combination of enhancer adoption and gene-dosage effects. Conclusions Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0423-1) contains supplementary material, which is available to authorized users.
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Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med 2014; 6:252ra123. [PMID: 25186178 PMCID: PMC4512639 DOI: 10.1126/scitranslmed.3009262] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Less than half of patients with suspected genetic disease receive a molecular diagnosis. We have therefore integrated next-generation sequencing (NGS), bioinformatics, and clinical data into an effective diagnostic workflow. We used variants in the 2741 established Mendelian disease genes [the disease-associated genome (DAG)] to develop a targeted enrichment DAG panel (7.1 Mb), which achieves a coverage of 20-fold or better for 98% of bases. Furthermore, we established a computational method [Phenotypic Interpretation of eXomes (PhenIX)] that evaluated and ranked variants based on pathogenicity and semantic similarity of patients' phenotype described by Human Phenotype Ontology (HPO) terms to those of 3991 Mendelian diseases. In computer simulations, ranking genes based on the variant score put the true gene in first place less than 5% of the time; PhenIX placed the correct gene in first place more than 86% of the time. In a retrospective test of PhenIX on 52 patients with previously identified mutations and known diagnoses, the correct gene achieved a mean rank of 2.1. In a prospective study on 40 individuals without a diagnosis, PhenIX analysis enabled a diagnosis in 11 cases (28%, at a mean rank of 2.4). Thus, the NGS of the DAG followed by phenotype-driven bioinformatic analysis allows quick and effective differential diagnostics in medical genetics.
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Affiliation(s)
- Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland. Labor Berlin-Charité Vivantes GmbH, Humangenetik, Föhrer Straße 15, 13353 Berlin, Germany
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Luisa Mackenroth
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter Krawitz
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Luitgard Graul-Neumann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sandra Doelken
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Nancy Christine Oien
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michal R Schweiger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Cologne Center for Genomics, University of Cologne, D-50931 Cologne, Germany
| | - Ulrike Krüger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Götz Frommer
- Agilent Technologies, Hewlett-Packard-Straße 8, 76337 Waldbronn, Germany
| | - Björn Fischer
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Ricarda Flöttmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Amin Ardeshirdavani
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Yves Moreau
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa Haendel
- University Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Sciences University, Portland, OR 97327, USA
| | - Damian Smedley
- Mouse Informatics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany. Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.
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Lobo D, Feldman EB, Shah M, Malone TJ, Levin M. Limbform: a functional ontology-based database of limb regeneration experiments. Bioinformatics 2014; 30:3598-600. [PMID: 25170026 DOI: 10.1093/bioinformatics/btu582] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY The ability of certain organisms to completely regenerate lost limbs is a fascinating process, far from solved. Despite the extraordinary published efforts during the past centuries of scientists performing amputations, transplantations and molecular experiments, no mechanistic model exists yet that can completely explain patterning during the limb regeneration process. The lack of a centralized repository to enable the efficient mining of this huge dataset is hindering the discovery of comprehensive models of limb regeneration. Here, we introduce Limbform (Limb formalization), a centralized database of published limb regeneration experiments. In contrast to natural language or text-based ontologies, Limbform is based on a functional ontology using mathematical graphs to represent unambiguously limb phenotypes and manipulation procedures. The centralized database currently contains >800 published limb regeneration experiments comprising many model organisms, including salamanders, frogs, insects, crustaceans and arachnids. The database represents an extraordinary resource for mining the existing knowledge of functional data in this field; furthermore, its mathematical nature based on a functional ontology will pave the way for artificial intelligence tools applied to the discovery of the sought-after comprehensive limb regeneration models.
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Affiliation(s)
- Daniel Lobo
- Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Erica B Feldman
- Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Michelle Shah
- Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Taylor J Malone
- Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Michael Levin
- Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
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