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AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

Lees, William D. ; Christley, Scott ; Peres, Ayelet ; Kos, Justin T. ; Corrie, Brian ; Ralph, Duncan ; Breden, Felix ; Cowell, Lindsay G. ; Yaari, Gur and Corcoran, Martin , et al. (2023) In Immunoinformatics 10.
Abstract
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.... (More)
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. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Immunoinformatics
volume
10
article number
100025
publisher
Elsevier
external identifiers
  • pmid:37388275
ISSN
2667-1190
DOI
10.1016/j.immuno.2023.100025
language
English
LU publication?
yes
id
6d57c4c2-6b75-427f-ae47-6e2871f4258b
date added to LUP
2023-07-31 14:29:58
date last changed
2023-11-07 10:03:09
@article{6d57c4c2-6b75-427f-ae47-6e2871f4258b,
  abstract     = {{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.}},
  author       = {{Lees, William D. and Christley, Scott and Peres, Ayelet and Kos, Justin T. and Corrie, Brian and Ralph, Duncan and Breden, Felix and Cowell, Lindsay G. and Yaari, Gur and Corcoran, Martin and Karlsson Hedestam, Gunilla B. and Ohlin, Mats and Collins, Andrew M. and Watson, Corey T. and Busse, Christian E.}},
  issn         = {{2667-1190}},
  language     = {{eng}},
  publisher    = {{Elsevier}},
  series       = {{Immunoinformatics}},
  title        = {{AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets}},
  url          = {{http://dx.doi.org/10.1016/j.immuno.2023.100025}},
  doi          = {{10.1016/j.immuno.2023.100025}},
  volume       = {{10}},
  year         = {{2023}},
}