A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

Danis, Daniel; Bamshad, Michael J.; Bridges, Yasemin; Caballero-Oteyza, Andrés; Cacheiro, Pilar; Carmody, Leigh C.; Chimirri, Leonardo; Chong, Jessica X.; Coleman, Ben; Dalgleish, Raymond; Freeman, Peter J.; Graefe, Adam S. L.; Groza, Tudor; Hansen, Peter; Jacobsen, Julius O. B.; Klocperk, Adam; Kusters, Maaike; Ladewig, Markus S.; Marcello, Allison J.; Mattina, Teresa; Mungall, Christopher J.; Munoz-Torres, Monica C.; Reese, Justin T.; Rehburg, Filip; Reis, Bárbara C. S.; Schuetz, Catharina; Smedley, Damian; Strauss, Timmy; Sundaramurthi, Jagadish Chandrabose; Thun, Sylvia; Wissink, Kyran; Wagstaff, John F.; Zocche, David; Haendel, Melissa A.; Robinson, Peter N.

doi:10.1016/j.xhgg.2024.100371

Title: A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

Journal Article · 01 January 2025 · Human Genetics and Genomics Advances

DOI: https://doi.org/10.1016/j.xhgg.2024.100371 · OSTI ID:2476067

Danis, Daniel;

;

; Caballero-Oteyza, Andrés;

;

; Chimirri, Leonardo;

;

; Hansen, Peter;

;

; Marcello, Allison J.;

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Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2476067

Journal Information:: Human Genetics and Genomics Advances, Journal Name: Human Genetics and Genomics Advances Journal Issue: 1 Vol. 6; ISSN 2666-2477

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (23)

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How many rare diseases are there? Haendel, Melissa; Vasilevsky, Nicole; Unni, Deepak Nature Reviews Drug Discovery, Vol. 19, Issue 2 https://doi.org/10.1038/d41573-019-00180-y	journal	November 2019
Next-generation diagnostics and disease-gene discovery with the Exomiser Smedley, Damian; Jacobsen, Julius O. B.; Jäger, Marten Nature Protocols, Vol. 10, Issue 12 https://doi.org/10.1038/nprot.2015.124	journal	November 2015
RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases Lochmüller, Hanns; Badowska, Dorota M.; Thompson, Rachel European Journal of Human Genetics, Vol. 26, Issue 6 https://doi.org/10.1038/s41431-018-0115-5	journal	February 2018
Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database Nguengang Wakap, Stéphanie; Lambert, Deborah M.; Olry, Annie European Journal of Human Genetics, Vol. 28, Issue 2 https://doi.org/10.1038/s41431-019-0508-0	journal	September 2019
Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases Zurek, Birte; Ellwanger, Kornelia; Vissers, Lisenka E. L. M. European Journal of Human Genetics, Vol. 29, Issue 9 https://doi.org/10.1038/s41431-021-00859-0	journal	June 2021
The GA4GH Phenopacket schema defines a computable representation of clinical data Jacobsen, Julius O. B.; Baudis, Michael; Baynam, Gareth S. Nature Biotechnology, Vol. 40, Issue 6 https://doi.org/10.1038/s41587-022-01357-4	journal	June 2022
Classification, Ontology, and Precision Medicine Haendel, Melissa A.; Chute, Christopher G.; Robinson, Peter N. New England Journal of Medicine, Vol. 379, Issue 15 https://doi.org/10.1056/NEJMra1615014	journal	October 2018
Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea Janecke, Andreas R.; Heinz-Erian, Peter; Yin, Jianyi Human Molecular Genetics, Vol. 24, Issue 23 https://doi.org/10.1093/hmg/ddv367	journal	September 2015
The case for open science: rare diseases Rubinstein, Yaffa R.; Robinson, Peter N.; Gahl, William A. JAMIA Open, Vol. 3, Issue 3 https://doi.org/10.1093/jamiaopen/ooaa030	journal	September 2020
The Human Phenotype Ontology in 2024: phenotypes around the world Gargano, Michael A.; Matentzoglu, Nicolas; Coleman, Ben Nucleic Acids Research, Vol. 52, Issue D1 https://doi.org/10.1093/nar/gkad1005	journal	November 2023
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species Putman, Tim E.; Schaper, Kevin; Matentzoglu, Nicolas Nucleic Acids Research, Vol. 52, Issue D1 https://doi.org/10.1093/nar/gkad1082	journal	November 2023
OMIM.org: leveraging knowledge across phenotype–gene relationships Amberger, Joanna S.; Bocchini, Carol A.; Scott, Alan F. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1151	journal	November 2018
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species Shefchek, Kent A.; Harris, Nomi L.; Gargano, Michael Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz997	journal	November 2019
Improved exome prioritization of disease genes through cross-species phenotype comparison Robinson, P. N.; Kohler, S.; Oellrich, A. Genome Research, Vol. 24, Issue 2 https://doi.org/10.1101/gr.160325.113	journal	October 2013
PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care Havrilla, James M.; Singaravelu, Anbumalar; Driscoll, Dennis M. BMC Medical Informatics and Decision Making, Vol. 22, Issue S2 https://doi.org/10.1186/s12911-022-01927-1	journal	July 2022
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing Danis, Daniel; Jacobsen, Julius O. B.; Balachandran, Parithi Genome Medicine, Vol. 14, Issue 1 https://doi.org/10.1186/s13073-022-01046-6	journal	April 2022
Phenopacket-tools: Building and validating GA4GH Phenopackets Danis, Daniel; Jacobsen, Julius O. B.; Wagner, Alex H. PLOS ONE, Vol. 18, Issue 5 https://doi.org/10.1371/journal.pone.0285433	journal	May 2023
Initiative on Rare and Undiagnosed Disease in Japan Takahashi, Yuji; Mizusawa, Hidehiro JMA Journal, Vol. 4, Issue 2, p. 112-118 https://doi.org/10.31662/jmaj.2021-0003	journal	January 2021

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