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ITGA2B/ITGB3变异评估指南规范:临床基因组资源血小板疾病变异评估小组

Specifications of the variant curation guidelines for ITGA2B/ITGB3: ClinGen Platelet Disorder Variant Curation Panel.

作者信息

Ross Justyne E, Zhang Bing M, Lee Kristy, Mohan Shruthi, Branchford Brian R, Bray Paul, Dugan Stefanie N, Freson Kathleen, Heller Paula G, Kahr Walter H A, Lambert Michele P, Luchtman-Jones Lori, Luo Minjie, Perez Botero Juliana, Rondina Matthew T, Ryan Gabriella, Westbury Sarah, Bergmeier Wolfgang, Di Paola Jorge

机构信息

Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.

Department of Pathology, Stanford University School of Medicine, Stanford, CA.

出版信息

Blood Adv. 2021 Jan 26;5(2):414-431. doi: 10.1182/bloodadvances.2020003712.


DOI:10.1182/bloodadvances.2020003712
PMID:33496739
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7839359/
Abstract

Accurate and consistent sequence variant interpretation is critical to the correct diagnosis and appropriate clinical management and counseling of patients with inherited genetic disorders. To minimize discrepancies in variant curation and classification among different clinical laboratories, the American College of Medical Genetics and Genomics (ACMG), along with the Association for Molecular Pathology (AMP), published standards and guidelines for the interpretation of sequence variants in 2015. Because the rules are not universally applicable to different genes or disorders, the Clinical Genome Resource (ClinGen) Platelet Disorder Expert Panel (PD-EP) has been tasked to make ACMG/AMP rule specifications for inherited platelet disorders. ITGA2B and ITGB3, the genes underlying autosomal recessive Glanzmann thrombasthenia (GT), were selected as the pilot genes for specification. Eight types of evidence covering clinical phenotype, functional data, and computational/population data were evaluated in the context of GT by the ClinGen PD-EP. The preliminary specifications were validated with 70 pilot ITGA2B/ITGB3 variants and further refined. In the final adapted criteria, gene- or disease-based specifications were made to 16 rules, including 7 with adjustable strength; no modification was made to 5 rules; and 7 rules were deemed not applicable to GT. Employing the GT-specific ACMG/AMP criteria to the pilot variants resulted in a reduction of variants classified with unknown significance from 29% to 20%. The overall concordance with the initial expert assertions was 71%. These adapted criteria will serve as guidelines for GT-related variant interpretation to increase specificity and consistency across laboratories and allow for better clinical integration of genetic knowledge into patient care.

摘要

准确且一致的序列变异解读对于遗传性疾病患者的正确诊断、适当的临床管理及咨询至关重要。为尽量减少不同临床实验室在变异整理和分类方面的差异,美国医学遗传学与基因组学学会(ACMG)与分子病理学协会(AMP)于2015年发布了序列变异解读的标准和指南。由于这些规则并非普遍适用于不同基因或疾病,临床基因组资源(ClinGen)血小板疾病专家小组(PD-EP)受命制定针对遗传性血小板疾病的ACMG/AMP规则规范。ITGA2B和ITGB3这两个常染色体隐性遗传性血小板无力症(GT)的致病基因被选为规范制定的试点基因。ClinGen PD-EP在GT背景下评估了涵盖临床表型、功能数据及计算/群体数据的八种证据类型。初步规范通过70个试点ITGA2B/ITGB3变异进行了验证并进一步完善。在最终的适配标准中,针对16条规则制定了基于基因或疾病的规范,其中7条强度可调;5条规则未作修改;7条规则被认为不适用于GT。将GT特异性的ACMG/AMP标准应用于试点变异,使意义不明的变异分类比例从29%降至20%。与最初专家判断的总体一致性为71%。这些适配标准将作为GT相关变异解读的指南,以提高各实验室间的特异性和一致性,并使遗传知识能更好地临床整合到患者护理中。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0fb9/7839359/77eb987acc72/advancesADV2020003712absf1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0fb9/7839359/77eb987acc72/advancesADV2020003712absf1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0fb9/7839359/77eb987acc72/advancesADV2020003712absf1.jpg

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[6]
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引用本文的文献

[1]
Is genetic testing for heritable thrombocytopenia coming of age?

Res Pract Thromb Haemost. 2025-7-22

[2]
Diagnosis of Inherited Platelet Disorders: Clinical Evaluation and Functional and Molecular Assays.

Biomolecules. 2025-6-10

[3]
REVEL Is Better at Predicting Pathogenicity of Loss-of-Function than Gain-of-Function Variants.

Hum Mutat. 2023-12-4

[4]
Discordance between a deep learning model and clinical-grade variant pathogenicity classification in a rare disease cohort.

NPJ Genom Med. 2025-2-28

[5]
Canadian College of Medical Geneticists: clinical practice advisory document - responsibility to recontact for reinterpretation of clinical genetic testing.

J Med Genet. 2024-11-25

[6]
Catheter Intervention in a Patient with Intracranial Aneurysms and Glanzmann Thrombasthenia Caused by a Novel Homozygous Likely Pathogenic Variant in the Gene.

Diseases. 2024-6-27

[7]
Discordance between a deep learning model and clinical-grade variant pathogenicity classification in a rare disease cohort.

medRxiv. 2024-5-23

[8]
How human genetic context can inform pathogenicity classification: FGFR1 variation in idiopathic hypogonadotropic hypogonadism.

Hum Genet. 2023-11

[9]
The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants.

Blood. 2023-12-14

[10]
A single F153Sβ3 mutation causes constitutive integrin αIIbβ3 activation in a variant form of Glanzmann thrombasthenia.

Blood Adv. 2023-7-11

本文引用的文献

[1]
Glanzmann thrombasthenia: genetic basis and clinical correlates.

Haematologica. 2020-4

[2]
ClinGen Myeloid Malignancy Variant Curation Expert Panel recommendations for germline RUNX1 variants.

Blood Adv. 2019-10-22

[3]
Challenges and Considerations in Sequence Variant Interpretation for Mendelian Disorders.

Ann Lab Med. 2019-9

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J Hematol Oncol. 2019-3-7

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Transfus Apher Sci. 2019-2

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Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss.

Hum Mutat. 2018-11

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Hum Mutat. 2018-11

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Genet Med. 2018-12

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ClinGen's RASopathy Expert Panel consensus methods for variant interpretation.

Genet Med. 2018-3-1

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