AbstractDecades of genetic association testing in human cohorts have provided important insights into the genetic architecture and biological underpinnings of complex traits and diseases. However, for certain traits, genome-wide association studies (GWAS) for common SNPs are approaching signal saturation, which underscores the need to explore other types of genetic variation to understand the genetic basis of traits and diseases.

摘要几十年来，人类队列中的遗传关联测试为复杂性状和疾病的遗传结构和生物学基础提供了重要见解。然而，对于某些性状，针对常见SNP的全基因组关联研究（GWAS）正在接近信号饱和，这强调需要探索其他类型的遗传变异，以了解性状和疾病的遗传基础。

Copy number variation (CNV) is an important source of heritability that is well known to functionally affect human traits. Recent technological and computational advances enable the large-scale, genome-wide evaluation of CNVs, with implications for downstream applications such as polygenic risk scoring and drug target identification.

拷贝数变异（CNV）是遗传力的重要来源，众所周知，它在功能上影响人类性状。最近的技术和计算进步使得能够对CNV进行大规模的全基因组评估，并对多基因风险评分和药物靶标鉴定等下游应用产生影响。

Here, we review the current state of CNV-GWAS, discuss current limitations in resource infrastructure that need to be overcome to enable the wider uptake of CNV-GWAS results, highlight emerging opportunities and suggest guidelines and standards for future GWAS for genetic variation beyond SNPs at scale..

在这里，我们回顾了CNV-GWAS的现状，讨论了目前需要克服的资源基础设施局限性，以便更广泛地吸收CNV-GWAS的结果，突出了新出现的机会，并为未来GWAS提出了大规模SNP以外的遗传变异的指南和标准。。

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Fig. 1: The cumulative total of association studies added to the GWAS Catalog between 2021 and 2023 for SNP- and CNV-based tests.Fig. 2: Biological and clinical impact of CNV.Fig. 3: Data flow depicting the key steps from cohort genetic data to CNV-GWAS results.Fig. 4: Differences between array-based and sequence-based genome resolution for CNV association testing.Fig.

图1:2021年至2023年间添加到GWAS目录中的基于SNP和CNV的测试的关联研究累积总数。图2:CNV的生物学和临床影响。图3：数据流描绘了从队列遗传数据到CNV-GWAS结果的关键步骤。图4:CNV关联测试的基于阵列和基于序列的基因组分辨率之间的差异。图。

5: Emerging opportunities..

5： 新兴机遇。。

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Download referencesAcknowledgementsThe authors thank all members of the CNV-GWAS Consortium for contributions and discussions and the EMBL-EBI for funding of the authors’ work.Author informationAuthor notesThese authors contributed equally: Laura Harris, Ellen M. McDonagh, Xiaolei Zhang.Authors and AffiliationsEuropean Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, UKLaura Harris, Ellen M.

下载参考文献致谢作者感谢CNV-GWAS联盟的所有成员的贡献和讨论，以及EMBL-EBI对作者工作的资助。作者信息作者注意到这些作者做出了同样的贡献：Laura Harris，Ellen M.McDonagh，Xiaolei Zhang。作者和附属机构欧洲分子生物学实验室（EMBL），欧洲生物信息学研究所（EBI），惠康基因组校园，辛克斯顿，UKLaura Harris，Ellen M。

McDonagh, Xiaolei Zhang, Katherine Fawcett, Amy Foreman, Panagiotis I. Sergouniotis, Helen Parkinson, Ewan Birney & Tomas FitzgeraldDepartment of Population Health Sciences, University of Leicester, Leicester, UKKatherine FawcettWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UKPetr DaneckDivision of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UKPanagiotis I.

麦克唐纳（McDonagh），张晓蕾（Xiaolei Zhang），凯瑟琳·福塞特（Katherine Fawcett），艾米·福尔曼（Amy Foreman），Panagiotis I.Sergouniotis，海伦·帕金森（Helen Parkinson），伊万·伯尼（Ewan Birney）和托马斯·菲茨杰拉德（Tomas FitzgeraldDepartment of Population Health Sciences），莱斯特大学（University of Leicester），英国凯瑟琳·福塞特（Katherine FawcettWellcome Sanger Institute），惠康基因组校园（Wellcome Genome Campus），辛克斯顿。

SergouniotisDepartment of Molecular and Translational Medicine, University of Brescia, Brescia, ItalyFrancesco MazzarottoNational Heart and Lung Institute, Imperial College London, London, UKFrancesco MazzarottoBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UKMichael InouyeCambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UKMichael InouyeCambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, AustraliaMichael InouyeDepartment of Genetics and Genome Biology, University of Leicester, Leicester, UKEdward J.

Sergouniotis布雷西亚大学分子与转化医学系，布雷西亚，意大利弗朗西斯科·马扎罗国家心肺研究所，伦敦帝国理工学院，英国弗朗西斯科·马扎罗托布里奇心脏基金会心血管流行病学组，剑桥大学公共卫生与初级保健系，剑桥大学，英国迈克尔·伊诺伊坎布里奇·贝克系统基因组学倡议，剑桥大学公共卫生与初级保健系，英国迈克尔·伊诺伊坎布里奇·贝克系统基因组学倡议，贝克心脏与糖尿病研究所，澳大利亚墨尔本莱斯特大学遗传学与基因组生物学系英国爱德华J。

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PubMed Google ScholarContributionsL.H., E.M.M., X.Z., K.F., P.I.S., F.M., M.I. and T.F. wrote the article. All authors researched the literature, provided substantial contributions to discussions of the content, and reviewed and/or edited the manuscript.Corresponding authorCorrespondence to.

PubMed谷歌学术贡献l。H、 ，E.M.M.，X.Z.，K.F.，P.I.S.，F.M.，M.I.和T.F.撰写了这篇文章。所有作者都研究了文献，为内容的讨论做出了重大贡献，并审查和/或编辑了手稿。对应作者对应。

Tomas Fitzgerald.Ethics declarations

托马斯·菲茨杰拉德。道德宣言

Competing interests

相互竞争的利益

The authors declare no competing interests.

作者声明没有利益冲突。

Peer review

同行评审

Peer review information

同行评审信息

Nature Reviews Genetics thanks Bjarni V. Halldórsson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

《自然评论》遗传学感谢Bjarni V.Halldórsson和另一位匿名审稿人对这项工作的同行评审做出的贡献。

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Related linksAll of Us: https://allofus.nih.gov/ClinGen: https://clinicalgenome.org/Finngen: https://www.finngen.fi/enGenomics England: https://www.genomicsengland.co.uk/gnomAD: https://gnomad.broadinstitute.org/GWAS Catalog: https://www.ebi.ac.uk/gwas/Linkage disequilibrium: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gene-linkage-disequilibriumOpen Targets Platform: https://platform.opentargets.org/PGS Catalog: https://www.pgscatalog.org/PharmGKB: https://www.pharmgkb.org/gene/PA128/labelAnnotationPRECISE: https://npm.sg/UK Biobank: https://www.ukbiobank.ac.uk/Supplementary informationSupplementary Information 1Supplementary Information 2GlossaryCryptic relatedness.

Additional informationPublisher的注释Springer Nature在已发布的地图和机构隶属关系中的管辖权主张方面保持中立。相关链接我们所有人：https://allofus.nih.gov/ClinGen:（笑声）https://clinicalgenome.org/Finngen:（笑声）https://www.finngen.fi/enGenomics英格兰：https://www.genomicsengland.co.uk/gnomAD:（笑声）https://gnomad.broadinstitute.org/GWAS目录：https://www.ebi.ac.uk/gwas/Linkage不平衡：https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gene-linkage-disequilibriumOpen目标平台：https://platform.opentargets.org/PGS目录：https://www.pgscatalog.org/PharmGKB:（笑声）https://www.pharmgkb.org/gene/PA128/labelAnnotationPRECISE:（笑声）https://npm.sg/UK生物库：https://www.ukbiobank.ac.uk/Supplementary信息补充信息1补充信息2损失与cryptic的相关性。

Confounding relatedness within a population, which can occur when individuals in the study cohort are more closely related to one another than assumed by the investigators.

当研究队列中的个体彼此之间的关系比研究人员假设的更密切时，可能会发生人群内的混淆相关性。

Diplotype

外交官

The combination of two alleles for a gene, one inherited from each of the individual’s parents.

一个基因的两个等位基因的组合，一个遗传自个体的父母。

Dosage sensitivity

剂量敏感性

When a variation in the number of copies of a gene or genetic element leads to a change in phenotype.

当基因或遗传元件拷贝数的变化导致表型改变时。

Epistasis

上位性

A phenomenon whereby nonlinear interactions between different genes or variants affect the same trait.

不同基因或变体之间的非线性相互作用影响同一性状的现象。

FAIR recommendations

公平的建议

A set of guidelines to increase the value of data by making it findable, accessible, interoperable and reusable.

通过使数据可查找、可访问、可互操作和可重用来提高数据价值的一组准则。

Imputation

插补

A method for inferring genotypes (or genetic variants) at locations that were not included in the assay.

在测定中未包括的位置推断基因型（或遗传变异）的方法。

Lead associations

领导协会

A lead association is the genetic variant that has the strongest association signals (lowest P value) from the association test. This variant may or may not be causal.

铅关联是关联测试中具有最强关联信号（最低P值）的遗传变异。这种变异可能是也可能不是因果关系。

LOEUF score

LOEUF评分

A continuous metric designed to assess how intolerant a gene is to loss-of-function variation.

旨在评估基因对功能丧失变异的不耐受程度的连续指标。

Mendelian randomization

孟德尔随机化

An epidemiological method used to study the causal effect of a risk factor (such as genetic variation) on health, social or economic outcomes.

一种流行病学方法，用于研究风险因素（如遗传变异）对健康、社会或经济结果的因果影响。

Optical mapping

光学测绘

An imaging method that analyses fluorescently labelled DNA molecules to provide a high-resolution map of structural variation.

一种成像方法，分析荧光标记的DNA分子以提供结构变异的高分辨率图谱。

Polygenic score

多基因评分

(PGS). A weighted estimate of how genetic variants affect a phenotype, often used to estimate a person’s risk of developing a disease or complex trait.

（第页）。对遗传变异如何影响表型的加权估计，通常用于估计一个人患疾病或复杂性状的风险。

Single-nucleotide polymorphism

单核苷酸多态性

(SNP). A germline genetic variant that is present in more than 1% of the population, in which a single nucleotide base differs from the reference genome.

（SNP）。存在于超过1%的人群中的种系遗传变异，其中单个核苷酸碱基与参考基因组不同。

Rights and permissionsSpringer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.Reprints and permissionsAbout this articleCite this articleHarris, L., McDonagh, E.M., Zhang, X.

权利和许可Pringer Nature或其许可人（例如协会或其他合作伙伴）根据与作者或其他权利持有人的出版协议对本文拥有专有权；本文接受稿件版本的作者自行存档仅受此类出版协议和适用法律的条款管辖。转载和许可本文引用本文Harris，L.，McDonagh，E.M.，Zhang，X。

et al. Genome-wide association testing beyond SNPs..

等。超越SNP的全基因组关联测试。。

Nat Rev Genet (2024). https://doi.org/10.1038/s41576-024-00778-yDownload citationAccepted: 03 September 2024Published: 07 October 2024DOI: https://doi.org/10.1038/s41576-024-00778-yShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

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