Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity.
Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity.
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DOI：
10.1016/j.jaci.2021.04.033
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发表时间：
2022-01
影响因子：
14.2
通讯作者：
Boztug, Kaan
中科院分区：
文献类型：
--
作者：
Haimel, Matthias;Pazmandi, Julia;Heredia, Raul Jimenez;Dmytrus, Jasmin;Bal, Sevgi Koestel;Zoghi, Samaneh;van Daele, Paul;Briggs, Tracy A.;Wouters, Carine;Bader-Meunier, Brigitte;Aeschlimann, Florence A.;Caorsi, Roberta;Eleftheriou, Despina;Hoppenreijs, Esther;Salzer, Elisabeth;Bakhtiar, Shahrzad;Derfalvi, Beata;Saettini, Francesco;Kusters, Maaike A. A.;Elfeky, Reem;Truck, Johannes;Riviere, Jacques G.;van der Burg, Mirjam;Gattorno, Marco;Seidel, Markus G.;Burns, Siobhan;Warnatz, Klaus;Hauck, Fabian;Brogan, Paul;Gilmour, Kimberly C.;Schuetz, Catharina;Simon, Anna;Bock, Christoph;Hambleton, Sophie;de Vries, Esther;Robinson, Peter N.;van Gijn, Marielle;Boztug, Kaan
关键词：
准确、详尽且标准化的表型描述对于支持遗传变异的诊断解读以及发现新疾病至关重要。人类表型本体（HPO）在罕见病研究中应用广泛，它以层次结构提供了丰富的标准化表型描述词汇集。然而，截至目前，HPO在原发性免疫缺陷病（IEIs）领域尚未得到广泛应用，这主要是由于缺乏全面的与IEIs相关的术语。
我们试图系统回顾HPO中用于描述IEIs的现有术语，对HPO进行扩展以生成更全面的术语集，并使用HPO术语对IEIs进行重新注释，从而提供准确、标准化的表型描述。
我们发起了一项合作，参与者包括临床专家、遗传学家、从事IEIs研究的科研人员以及生物信息学家。在专家评审的基础上，对HPO树形结构的多个分支进行了重构和扩展。我们将基于本体的机器学习与两级专家评审相结合，应用于对IEIs特定亚组的重新注释。
我们修订并扩展了HPO树形结构的4个主要分支。在此，我们使用HPO术语对国际免疫学会联盟定义的4个IEI疾病亚组中的73种疾病进行了重新注释。每种疾病的表型术语数量增加了4.7倍。鉴于新的HPO注释，我们证明了在计算上将选定的IEI病例与其已知诊断进行匹配的能力得到提升，并且表型驱动的疾病分类也有所改进。
我们有针对性的扩展和重新注释提高了疾病注释的精确性，将实现更出色的基于HPO的IEI特征描述，从而使IEI的诊断和研究工作均受益。
Accurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms. We sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions. We initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs. We revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies–defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification. Our targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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影响因子：
14.9
作者：
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 HJ;DeMare LE;Devereau AD;de Vries BB;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 MW;Vulliamy T;Yu J;von Ziegenweidt J;Zankl A;Züchner S;Zemojtel T;Jacobsen JO;Groza T;Smedley D;Mungall CJ;Haendel M;Robinson PN
通讯作者：
Robinson PN
影响因子：
14.9
作者：
Shefchek, Kent A.;Harris, Nomi L.;Osumi-Sutherland, David
通讯作者：
Osumi-Sutherland, David
影响因子：
3.9
作者：
Amberger, Joanna;Bocchini, Carol;Hamosh, Ada
通讯作者：
Hamosh, Ada
影响因子：
3.5
作者：
Rae, W.;Ward, D.;Williams, A. P.
通讯作者：
Williams, A. P.
影响因子：
9.1
作者：
Bousfiha A;Jeddane L;Picard C;Ailal F;Bobby Gaspar H;Al-Herz W;Chatila T;Crow YJ;Cunningham-Rundles C;Etzioni A;Franco JL;Holland SM;Klein C;Morio T;Ochs HD;Oksenhendler E;Puck J;Tang MLK;Tangye SG;Torgerson TR;Casanova JL;Sullivan KE
通讯作者：
Sullivan KE