1
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Danis D, Bamshad MJ, Bridges Y, Cacheiro P, Carmody LC, Chong JX, Coleman B, Dalgleish R, Freeman PJ, Graefe ASL, Groza T, Jacobsen JOB, Klocperk A, Kusters M, Ladewig MS, Marcello AJ, Mattina T, Mungall CJ, Munoz-Torres MC, Reese JT, Rehburg F, Reis BCS, Schuetz C, Smedley D, Strauss T, Sundaramurthi JC, Thun S, Wissink K, Wagstaff JF, Zocche D, Haendel MA, Robinson PN. A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308104. [PMID: 38854034 PMCID: PMC11160806 DOI: 10.1101/2024.05.29.24308104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present phenopacket-store. Version 0.1.12 of phenopacket-store includes 4916 phenopackets representing 277 Mendelian and chromosomal diseases associated with 236 genes, and 2872 unique pathogenic alleles curated from 605 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.
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Affiliation(s)
- Daniel Danis
- The Jackson Institute for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle WA 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98195, USA
| | - Yasemin Bridges
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Leigh C Carmody
- The Jackson Institute for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle WA 98195, USA
| | - Ben Coleman
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- The Jackson Institute for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA
| | - Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Peter J Freeman
- Division of Informatics, Imaging and Data Science, The University of Manchester, Manchester, UK
| | - Adam S L Graefe
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tudor Groza
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA 6009, Australia
- SingHealth Duke-NUS Institute of Precision Medicine, 5 Hospital Drive Level 9, Singapore 169609, Singapore
- Telethon Kids Institute, Nedlands, WA 6009, Australia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Adam Klocperk
- Department of Immunology, 2nd Faculty of Medicine, Charles University and University Hospital in Motol, Prague, Czech Republic
| | - Maaike Kusters
- Department of Paediatric Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- University College London Institute of Child Health, London, United Kingdom
| | - Markus S Ladewig
- Department of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany
| | - Anthony J Marcello
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA 98195, USA
| | - Teresa Mattina
- Medica Genetics University of Catania Italy
- Morgagni foundation and Clinic, Catania, Italy
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Ccampus
| | - Justin T Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Filip Rehburg
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Bárbara C S Reis
- Department of Immunology, National Institute of Women's, Children's and Adolescents' Health Fernandes Figueira, Rio de Janeiro, Brazil
- High Complexity Laboratory, National Institute of Women's, Children's and Adolescents' Health Fernandes Figueira, Rio de Janeiro, Brazil
| | - Catharina Schuetz
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- University Center for Rare Diseases, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Timmy Strauss
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- University Center for Rare Diseases, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Sylvia Thun
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kyran Wissink
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Utrecht University, Utrecht, the Netherlands
| | | | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark's Hospitals, London, UK
| | | | - Peter N Robinson
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- The Jackson Institute for Genomic Medicine, 10 Discovery Drive, Farmington CT 06032, USA
- ELLIS-European Laboratory for Learning and Intelligent Systems
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2
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AlMail A, Jamjoom A, Pan A, Feng MY, Chau V, D'Gama AM, Howell K, Liang NSY, McTague A, Poduri A, Wiltrout K, Bassett AS, Christodoulou J, Dupuis L, Gill P, Levy T, Siper P, Stark Z, Vorstman JAS, Diskin C, Jewitt N, Baribeau D, Costain G. Consensus reporting guidelines to address gaps in descriptions of ultra-rare genetic conditions. NPJ Genom Med 2024; 9:27. [PMID: 38582909 PMCID: PMC10998895 DOI: 10.1038/s41525-024-00408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/27/2024] [Indexed: 04/08/2024] Open
Abstract
Genome-wide sequencing and genetic matchmaker services are propelling a new era of genotype-driven ascertainment of novel genetic conditions. The degree to which reported phenotype data in discovery-focused studies address informational priorities for clinicians and families is unclear. We identified reports published from 2017 to 2021 in 10 genetics journals of novel Mendelian disorders. We adjudicated the quality and detail of the phenotype data via 46 questions pertaining to six priority domains: (I) Development, cognition, and mental health; (II) Feeding and growth; (III) Medication use and treatment history; (IV) Pain, sleep, and quality of life; (V) Adulthood; and (VI) Epilepsy. For a subset of articles, all subsequent published follow-up case descriptions were identified and assessed in a similar manner. A modified Delphi approach was used to develop consensus reporting guidelines, with input from content experts across four countries. In total, 200 of 3243 screened publications met inclusion criteria. Relevant phenotypic details across each of the 6 domains were rated superficial or deficient in >87% of papers. For example, less than 10% of publications provided details regarding neuropsychiatric diagnoses and "behavioural issues", or about the type/nature of feeding problems. Follow-up reports (n = 95) rarely contributed this additional phenotype data. In summary, phenotype information relevant to clinical management, genetic counselling, and the stated priorities of patients and families is lacking for many newly described genetic diseases. The PHELIX (PHEnotype LIsting fiX) reporting guideline checklists were developed to improve phenotype reporting in the genomic era.
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Affiliation(s)
- Ali AlMail
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Ahmed Jamjoom
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Department of Pediatrics, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amy Pan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Min Yi Feng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vann Chau
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Division of Neurology, Hospital for Sick Children, Toronto, ON, Canada
| | - Alissa M D'Gama
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Katherine Howell
- Department of Neurology, Royal Children's Hospital, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Nicole S Y Liang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
| | - Amy McTague
- Department of Neurology, Great Ormond Street Hospital, London, UK
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kimberly Wiltrout
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Anne S Bassett
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | | | - Lucie Dupuis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Gill
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Tess Levy
- Division of Psychiatry, Ichan School of Medicine at Mount Sinai, New York City, NY, USA
| | - Paige Siper
- Division of Psychiatry, Ichan School of Medicine at Mount Sinai, New York City, NY, USA
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Service, Melbourne, VIC, Australia
| | - Jacob A S Vorstman
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Hospital for Sick Children, Toronto, ON, Canada
| | - Catherine Diskin
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Natalie Jewitt
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Danielle Baribeau
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, Hospital for Sick Children, Toronto, ON, Canada.
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.
| | - Gregory Costain
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON, Canada.
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada.
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3
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Duyzend MH, Cacheiro P, Jacobsen JO, Giordano J, Brand H, Wapner RJ, Talkowski ME, Robinson PN, Smedley D. Improving prenatal diagnosis through standards and aggregation. Prenat Diagn 2024; 44:454-464. [PMID: 38242839 PMCID: PMC11006584 DOI: 10.1002/pd.6522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024]
Abstract
Advances in sequencing and imaging technologies enable enhanced assessment in the prenatal space, with a goal to diagnose and predict the natural history of disease, to direct targeted therapies, and to implement clinical management, including transfer of care, election of supportive care, and selection of surgical interventions. The current lack of standardization and aggregation stymies variant interpretation and gene discovery, which hinders the provision of prenatal precision medicine, leaving clinicians and patients without an accurate diagnosis. With large amounts of data generated, it is imperative to establish standards for data collection, processing, and aggregation. Aggregated and homogeneously processed genetic and phenotypic data permits dissection of the genomic architecture of prenatal presentations of disease and provides a dataset on which data analysis algorithms can be tuned to the prenatal space. Here we discuss the importance of generating aggregate data sets and how the prenatal space is driving the development of interoperable standards and phenotype-driven tools.
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Affiliation(s)
- Michael H. Duyzend
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Pilar Cacheiro
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jessica Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J. Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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4
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Rueda M, Leist IC, Gut IG. Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data. J Biomed Inform 2024; 149:104558. [PMID: 38035971 DOI: 10.1016/j.jbi.2023.104558] [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: 07/11/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Efficient sharing and integration of phenotypic data is crucial for advancing biomedical research and enhancing patient outcomes in precision medicine and public health. To achieve this, the health data community has developed standards to promote the harmonization of variable names and values. However, the use of diverse standards across different research centers can hinder progress. Here we present Convert-Pheno, an open-source software toolkit that enables the interconversion of common data models for phenotypic data such as Beacon v2 Models, CDISC-ODM, OMOP-CDM, Phenopackets v2, and REDCap. Along with the software, we have created a detailed documentation that includes information on deployment and installation.
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Affiliation(s)
- Manuel Rueda
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain.
| | - Ivo C Leist
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat de Barcelona (UB), Barcelona, Spain
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5
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Policiuc L, Nutu A, Zanoaga O, Mehterov N, Braicu C, Berindan-Neagoe I. Current aspects in biobanking for personalized oncology investigations and treatments. Med Pharm Rep 2023; 96:235-245. [PMID: 37577017 PMCID: PMC10419688 DOI: 10.15386/mpr-2647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Background/Aim A biobank is an organization that gathers, refines, preserves and provides access to biospecimens along with relevant clinical data that can be used in applied or clinical research. Biobanking is a critical component of the scientific foundation for personalized medicine; this implies the accessibility of high-quality human biospecimens, such as blood, tissue, and other body fluids, along with the patient clinical data that goes with them. Methods This paper summarizes the function of biobanks in oncology and the requirements for biobank development in translational and clinical research. Results Biobanks raise numerous ethical issues that government agencies address by enacting particular laws. To develop personalized medicine, biobanks are crucial, given that the availability of an extensive collection of patient samples with thoroughly annotated clinical and pathological data is an essential necessity. Also, data related to biobanking raises complex ethical, legal, and social issues, particularly concerning the protection of donor privacy and the appropriate use of collected samples. International standards have been developed to address these issues to ensure biobanking practices' quality, safety, and integrity. Conclusions Biobanking is vital in advancing biomedical research, supporting clinical applications, and enhancing our understanding of human health and disease. Using real-world data and biobanking can accelerate medical research, support personalized medicine initiatives, and improve patient care.
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Affiliation(s)
- Liliana Policiuc
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Oana Zanoaga
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Nikolay Mehterov
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
- Department of Dental Prosthetics, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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