AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known...
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Elsevier
2023-06-01
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| Series: | ImmunoInformatics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667119023000058 |
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| author | William D. Lees Scott Christley Ayelet Peres Justin T. Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G. Cowell Gur Yaari Martin Corcoran Gunilla B. Karlsson Hedestam Mats Ohlin Andrew M. Collins Corey T. Watson Christian E. Busse |
| author_facet | William D. Lees Scott Christley Ayelet Peres Justin T. Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G. Cowell Gur Yaari Martin Corcoran Gunilla B. Karlsson Hedestam Mats Ohlin Andrew M. Collins Corey T. Watson Christian E. Busse |
| author_sort | William D. Lees |
| collection | DOAJ |
| description | Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability. |
| format | Article |
| id | doaj-art-9bc6b57d823043ca8d936aafe8d2afc6 |
| institution | OA Journals |
| issn | 2667-1190 |
| language | English |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | ImmunoInformatics |
| spelling | doaj-art-9bc6b57d823043ca8d936aafe8d2afc62025-08-20T02:27:39ZengElsevierImmunoInformatics2667-11902023-06-011010002510.1016/j.immuno.2023.100025AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline setsWilliam D. Lees0Scott Christley1Ayelet Peres2Justin T. Kos3Brian Corrie4Duncan Ralph5Felix Breden6Lindsay G. Cowell7Gur Yaari8Martin Corcoran9Gunilla B. Karlsson Hedestam10Mats Ohlin11Andrew M. Collins12Corey T. Watson13Christian E. Busse14Institute of Structural and Molecular Biology, Birkbeck College, London, England; Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering Technology and Science, Porto, Portugal; Corresponding author at: Institutie of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England.Peter O’Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USABioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, IsraelDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USADepartment of Biological Sciences, Simon Fraser University, Burnaby, BC, CanadaFred Hutchinson Cancer Research Center, Seattle, WA, USADepartment of Biological Sciences, Simon Fraser University, Burnaby, BC, CanadaPeter O’Donnell Jr. School of Public Health, Department of Immunology, School of Biomedical Sciences, UT Southwestern Medical Center, Dallas, TX, USABioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, IsraelDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SwedenDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SwedenDepartment of Immunotechnology and SciLifeLab, Lund University, Lund, SwedenSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, AustraliaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, KY, USADivision of B Cell Immunology, German Cancer Research Center, Heidelberg, GermanyAnalysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.http://www.sciencedirect.com/science/article/pii/S2667119023000058Immune receptorImmune receptor repertoireAIRR-seqRep-seqImmune receptor germline |
| spellingShingle | William D. Lees Scott Christley Ayelet Peres Justin T. Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G. Cowell Gur Yaari Martin Corcoran Gunilla B. Karlsson Hedestam Mats Ohlin Andrew M. Collins Corey T. Watson Christian E. Busse AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets ImmunoInformatics Immune receptor Immune receptor repertoire AIRR-seq Rep-seq Immune receptor germline |
| title | AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets |
| title_full | AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets |
| title_fullStr | AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets |
| title_full_unstemmed | AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets |
| title_short | AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets |
| title_sort | airr community curation and standardised representation for immunoglobulin and t cell receptor germline sets |
| topic | Immune receptor Immune receptor repertoire AIRR-seq Rep-seq Immune receptor germline |
| url | http://www.sciencedirect.com/science/article/pii/S2667119023000058 |
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