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Assessment of ability of AlphaMissense to identify variants affecting susceptibility to common disease 评估 AlphaMissense 识别影响常见疾病易感性变异的能力。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-03 DOI: 10.1038/s41431-024-01675-y
David Curtis
An important issue in the analysis of rare variant association studies is the ability to annotate nonsynonymous variants in terms of their likely importance as affecting protein function. To address this, AlphaMissense was recently released and was shown to have good performance using benchmarks based on variants causing severe disease and on functional assays. Here, we assess the performance of AlphaMissense across 18 genes which had previously demonstrated association between rare coding variants and hyperlipidaemia, hypertension or type 2 diabetes. The strength of evidence in favour of association, expressed as the signed log p value (SLP), was compared between AlphaMissense and 43 other annotation methods. The results demonstrated marked variability between genes regarding the extent to which nonsynonymous variants contributed to evidence for association and also between the performance of different methods of annotating the nonsynonymous variants. Although AlphaMissense produced the highest SLP on average across genes, it produced the maximum SLP for only 4 genes. For some genes, other methods produced a considerably higher SLP and there were examples of genes where AlphaMissense produced no evidence for association while another method performed well. The marked inconsistency across genes means that it is difficult to decide on an optimal method of analysis of sequence data. The fact that different methods perform well for different genes suggests that if one wished to use sequence data for individual risk prediction then gene-specific annotation methods should be used.
罕见变异关联研究分析中的一个重要问题是,能否根据非同义变异影响蛋白质功能的重要性对其进行注释。为了解决这个问题,AlphaMissense 最近发布了,根据导致严重疾病的变异和功能测试的基准,它被证明具有良好的性能。在这里,我们评估了 AlphaMissense 在 18 个基因中的表现,这些基因以前曾被证明与罕见编码变异和高脂血症、高血压或 2 型糖尿病有关。我们比较了 AlphaMissense 和其他 43 种注释方法之间以符号对数值(SLP)表示的支持关联的证据强度。结果表明,在非同义变异对关联证据的贡献程度方面,不同基因之间存在明显差异,不同非同义变异注释方法的性能之间也存在明显差异。虽然 AlphaMissense 在各基因中平均产生了最高的 SLP,但它只对 4 个基因产生了最大的 SLP。对于某些基因,其他方法产生的 SLP 要高得多,还有一些基因,AlphaMissense 没有产生关联的证据,而另一种方法却有很好的表现。不同基因之间存在明显的不一致性,这意味着很难确定分析序列数据的最佳方法。不同的方法对不同的基因都有很好的效果,这一事实表明,如果希望使用序列数据进行个体风险预测,就应该使用特定基因的注释方法。
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引用次数: 0
Correction: EMQN best practice guidelines for genetic testing in hereditary breast and ovarian cancer. 更正:EMQN 遗传性乳腺癌和卵巢癌基因检测最佳实践指南。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-02 DOI: 10.1038/s41431-024-01670-3
Trudi McDevitt, Miranda Durkie, Norbert Arnold, George J Burghel, Samantha Butler, Kathleen B M Claes, Peter Logan, Rachel Robinson, Katie Sheils, Nicola Wolstenholme, Helen Hanson, Clare Turnbull, Stacey Hume
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引用次数: 0
Colorectal cancer risk stratification using a polygenic risk score in symptomatic primary care patients—a UK Biobank retrospective cohort study 使用多基因风险评分对有症状的初级保健患者进行结直肠癌风险分层--英国生物库回顾性队列研究。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-01 DOI: 10.1038/s41431-024-01654-3
Bethan Mallabar-Rimmer, Samuel W. D. Merriel, Amy P. Webster, Leigh Jackson, Andrew R. Wood, Matthew Barclay, Jessica Tyrrell, Katherine S. Ruth, Christina Thirlwell, Richard Oram, Michael N. Weedon, Sarah E. R. Bailey, Harry D. Green
Colorectal cancer (CRC) is a leading cause of cancer mortality worldwide. Accurate cancer risk assessment approaches could increase rates of early CRC diagnosis, improve health outcomes for patients and reduce pressure on diagnostic services. The faecal immunochemical test (FIT) for blood in stool is widely used in primary care to identify symptomatic patients with likely CRC. However, there is a 6–16% noncompliance rate with FIT in clinic and ~90% of patients over the symptomatic 10 µg/g test threshold do not have CRC. A polygenic risk score (PRS) quantifies an individual’s genetic risk of a condition based on many common variants. Existing PRS for CRC have so far been used to stratify asymptomatic populations. We conducted a retrospective cohort study of 50,387 UK Biobank participants with a CRC symptom in their primary care record at age 40+. A PRS based on 201 variants, 5 genetic principal components and 22 other risk factors and markers for CRC were assessed for association with CRC diagnosis within 2 years of first symptom presentation using logistic regression. Associated variables were included in an integrated risk model and trained in 80% of the cohort to predict CRC diagnosis within 2 years. An integrated risk model combining PRS, age, sex, and patient-reported symptoms was predictive of CRC development in a testing cohort (receiver operating characteristic area under the curve, ROCAUC: 0.76, 95% confidence interval: 0.71–0.81). This model has the potential to improve early diagnosis of CRC, particularly in cases of patient noncompliance with FIT.
结直肠癌(CRC)是全球癌症死亡的主要原因。准确的癌症风险评估方法可以提高 CRC 的早期诊断率,改善患者的健康状况,减轻诊断服务的压力。针对便血的粪便免疫化学检验(FIT)被广泛用于初级保健,以识别可能患有 CRC 的无症状患者。然而,临床上对 FIT 的不符合率为 6-16%,超过 10 µg/g 检测阈值的无症状患者中约有 90% 没有患上 CRC。多基因风险评分(PRS)根据许多常见变异量化个人的遗传风险。迄今为止,现有的 CRC 风险评分系统都是用于对无症状人群进行分层。我们对 50,387 名 40 岁以上、初级保健记录中有 CRC 症状的英国生物库参与者进行了一项回顾性队列研究。利用逻辑回归评估了基于 201 个变异、5 个遗传主成分和 22 个其他 CRC 风险因素和标记物的 PRS 与首次出现症状后 2 年内 CRC 诊断的关联性。相关变量被纳入综合风险模型,并对 80% 的队列进行了训练,以预测 2 年内的 CRC 诊断。结合了 PRS、年龄、性别和患者报告症状的综合风险模型在测试队列中可预测 CRC 的发展(曲线下接收器操作特征面积,ROCAUC:0.76,95% 置信区间:0.71-0.81)。该模型有望改善对 CRC 的早期诊断,尤其是在患者不遵守 FIT 的情况下。
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引用次数: 0
Summer reading in EJHG EJHG 的暑期阅读。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-31 DOI: 10.1038/s41431-024-01672-1
Alisdair McNeill
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引用次数: 0
Bardet-Biedl syndrome improved diagnosis criteria and management: Inter European Reference Networks consensus statement and recommendations 巴尔德-比德尔综合征的改进诊断标准和管理:欧洲参考网络共识声明和建议。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-31 DOI: 10.1038/s41431-024-01634-7
Hélène Dollfus, Marc R. Lilien, Pietro Maffei, Alain Verloes, Jean Muller, Giacomo M. Bacci, Metin Cetiner, Erica L. T. van den Akker, Monika Grudzinska Pechhacker, Francesco Testa, Didier Lacombe, Marijn F. Stokman, Francesca Simonelli, Aurélie Gouronc, Amélie Gavard, Mieke M. van Haelst, Jens Koenig, Sylvie Rossignol, Carsten Bergmann, Miriam Zacchia, Bart P. Leroy, Héléna Mosbah, Albertien M. Van Eerde, Djalila Mekahli, Aude Servais, Christine Poitou, Diana Valverde
Four European Reference Networks (ERN-EYE, ERKNet, Endo-ERN, ERN-ITHACA) have teamed up to establish a consensus statement and recommendations for Bardet-Biedl syndrome (BBS). BBS is an autosomal recessive ciliopathy with at least 26 genes identified to date. The clinical manifestations are pleiotropic, can be observed in utero and will progress with age. Genetic testing has progressively improved in the last years prompting for a revision of the diagnostic criteria taking into account clinical Primary and Secondary features, as well as positive or negative molecular diagnosis. This consensus statement also emphasizes on initial diagnosis, monitoring and lifelong follow-up, and symptomatic care that can be provided to patients and family members according to the involved care professionals. For paediatricians, developmental anomalies can be at the forefront for diagnosis (such as polydactyly) but can require specific care, such as for associated neuro developmental disorders. For ophthalmology, the early onset retinal degeneration requires ad hoc functional and imaging technologies and specific care for severe visual impairment. For endocrinology, among other manifestations, early onset obesity and its complications has benefited from better evaluation of eating behaviour problems, improved lifestyle programs, and from novel pharmacological therapies. Kidney and urinary track involvements warrants lifespan attention, as chronic kidney failure can occur and early management might improve outcome. This consensus recommends revised diagnostic criteria for BBS that will ensure certainty of diagnosis, giving robust grounds for genetic counselling as well as in the perspective of future trials for innovative therapies.
四个欧洲参考网络(ERN-EYE、ERKNet、Endo-ERN、ERN-ITHACA)联手为巴尔德-比德综合征(BBS)制定了一份共识声明和建议。BBS 是一种常染色体隐性纤毛症,迄今已发现至少 26 个基因。其临床表现具有多向性,可在子宫内观察到,并随着年龄的增长而发展。近些年来,基因检测技术不断进步,促使诊断标准的修订考虑到了临床原发性和继发性特征,以及分子诊断的阳性或阴性。这份共识声明还强调了初步诊断、监测和终生随访,以及根据相关专业护理人员为患者和家属提供的对症护理。对于儿科医生来说,发育异常可能是诊断的首要因素(如多指畸形),但也可能需要特殊护理,如相关的神经发育障碍。对于眼科来说,早期视网膜变性需要特殊的功能和成像技术,以及对严重视力障碍的特殊护理。在内分泌学方面,除其他表现外,早发性肥胖症及其并发症得益于对饮食行为问题的更好评估、生活方式计划的改进以及新型药物疗法。肾脏和泌尿系统受累也值得引起重视,因为可能会出现慢性肾衰竭,而早期治疗可能会改善预后。本共识建议修订 BBS 诊断标准,以确保诊断的确定性,为遗传咨询和未来创新疗法试验提供有力依据。
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引用次数: 0
ERN GENTURIS clinical practice guidelines for the diagnosis, surveillance and management of people with Birt-Hogg-Dubé syndrome. ERN GENTURIS 诊断、监测和管理 Birt-Hogg-Dubé 综合征患者的临床实践指南。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-31 DOI: 10.1038/s41431-024-01671-2
Marianne Geilswijk, Maurizio Genuardi, Emma R Woodward, Katie Nightingale, Jazzmin Huber, Mia Gebauer Madsen, Dieke Liekelema-van der Heij, Ian Lisseman, Jenny Marlé-Ballangé, Cormac McCarthy, Fred H Menko, R Jeroen A van Moorselaar, Elzbieta Radzikowska, Stéphane Richard, Neil Rajan, Mette Sommerlund, Maria T A Wetscherek, Nataliya Di Donato, Eamonn R Maher, Joan Brunet

Birt-Hogg-Dubé syndrome (BHD syndrome) is an autosomal dominant multisystem disorder with variable expression due to pathogenic constitutional variants in the FLCN gene. Patients with BHD syndrome are predisposed to benign cutaneous fibrofolliculomas/trichodischomas, pulmonary cysts with an associated risk of spontaneous pneumothorax, and renal cell carcinoma. A requirement for updated International consensus recommendations for the diagnosis and management of BHD syndrome was identified. Based on a comprehensive literature review and expert consensus within the fields of respiratory medicine, urology, radiology, dermatology, clinical oncology and clinical genetics, updated recommendations for diagnosis, surveillance and management in BHD syndrome were developed. With the widespread availability of FLCN genetic testing, clinical scenarios in which a diagnosis should be considered and criteria for genetic testing were defined. Following a clinical and/or molecular diagnosis of BHD syndrome, a multidisciplinary approach to disease management is required. Regular renal cancer surveillance is recommended in adulthood and life-long, but the evidence base for additional tumour surveillance is limited and further research warranted. Recommendations for the treatment of cutaneous, pulmonary and renal manifestations are provided. Awareness of BHD syndrome needs to be raised and better knowledge of the clinical settings in which the diagnosis should be considered should enable earlier diagnosis. Further details, including areas for future research topics are available at: https://www.genturis.eu/l=eng/Guidelines-and-pathways/Clinical-practice-guidelines.html .

比尔-霍格-杜贝综合征(Birt-Hogg-Dubé Syndrome,BHD 综合征)是一种常染色体显性多系统疾病,由于 FLCN 基因中的致病基因变异而表现各异。BHD 综合征患者易患良性皮肤纤维组织瘤/三叉神经瘤、肺囊肿并伴有自发性气胸和肾细胞癌的风险。国际上需要就 BHD 综合征的诊断和管理提出最新的共识建议。根据全面的文献综述以及呼吸内科、泌尿科、放射科、皮肤科、临床肿瘤学和临床遗传学领域的专家共识,制定了有关 BHD 综合征诊断、监测和管理的最新建议。随着 FLCN 基因检测的普及,确定了应考虑诊断的临床情况和基因检测的标准。在对 BHD 综合征进行临床和/或分子诊断后,需要采用多学科方法进行疾病管理。建议在成年期和终身定期进行肾癌监测,但额外肿瘤监测的证据基础有限,需要进一步研究。对皮肤、肺部和肾脏表现的治疗提出了建议。需要提高人们对 BHD 综合征的认识,并更好地了解应考虑诊断的临床环境,以便更早地做出诊断。更多详细信息,包括未来研究课题的领域,请访问:https://www.genturis.eu/l=eng/Guidelines-and-pathways/Clinical-practice-guidelines.html 。
{"title":"ERN GENTURIS clinical practice guidelines for the diagnosis, surveillance and management of people with Birt-Hogg-Dubé syndrome.","authors":"Marianne Geilswijk, Maurizio Genuardi, Emma R Woodward, Katie Nightingale, Jazzmin Huber, Mia Gebauer Madsen, Dieke Liekelema-van der Heij, Ian Lisseman, Jenny Marlé-Ballangé, Cormac McCarthy, Fred H Menko, R Jeroen A van Moorselaar, Elzbieta Radzikowska, Stéphane Richard, Neil Rajan, Mette Sommerlund, Maria T A Wetscherek, Nataliya Di Donato, Eamonn R Maher, Joan Brunet","doi":"10.1038/s41431-024-01671-2","DOIUrl":"10.1038/s41431-024-01671-2","url":null,"abstract":"<p><p>Birt-Hogg-Dubé syndrome (BHD syndrome) is an autosomal dominant multisystem disorder with variable expression due to pathogenic constitutional variants in the FLCN gene. Patients with BHD syndrome are predisposed to benign cutaneous fibrofolliculomas/trichodischomas, pulmonary cysts with an associated risk of spontaneous pneumothorax, and renal cell carcinoma. A requirement for updated International consensus recommendations for the diagnosis and management of BHD syndrome was identified. Based on a comprehensive literature review and expert consensus within the fields of respiratory medicine, urology, radiology, dermatology, clinical oncology and clinical genetics, updated recommendations for diagnosis, surveillance and management in BHD syndrome were developed. With the widespread availability of FLCN genetic testing, clinical scenarios in which a diagnosis should be considered and criteria for genetic testing were defined. Following a clinical and/or molecular diagnosis of BHD syndrome, a multidisciplinary approach to disease management is required. Regular renal cancer surveillance is recommended in adulthood and life-long, but the evidence base for additional tumour surveillance is limited and further research warranted. Recommendations for the treatment of cutaneous, pulmonary and renal manifestations are provided. Awareness of BHD syndrome needs to be raised and better knowledge of the clinical settings in which the diagnosis should be considered should enable earlier diagnosis. Further details, including areas for future research topics are available at: https://www.genturis.eu/l=eng/Guidelines-and-pathways/Clinical-practice-guidelines.html .</p>","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: STAC3 disorder: a common cause of congenital hypotonia in Southern African patients. 更正:STAC3紊乱:导致南部非洲患者先天性肌张力低下的常见原因。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-30 DOI: 10.1038/s41431-024-01669-w
Fahmida Essop, Bronwyn Dillon, Felicity Mhlongo, Louisa Bhengu, Thirona Naicker, Lindsay Lambie, Liani Smit, Karen Fieggen, Anneline Lochan, Jessica Dawson, Phelelani Mpangase, Marc Hauptfleisch, Gail Scher, Odirile Tabane, Marelize Immelman, Michael Urban, Amanda Krause
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引用次数: 0
Correction: Expanded phenotypic spectrum of neurodevelopmental and neurodegenerative disorder Bryant-Li-Bhoj syndrome with 38 additional individuals 更正:扩大神经发育和神经退行性疾病布赖恩特-李-博伊综合征的表型谱,新增 38 例患者。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-26 DOI: 10.1038/s41431-024-01659-y
Dana E. Layo-Carris, Emily E. Lubin, Annabel K. Sangree, Kelly J. Clark, Emily L. Durham, Elizabeth M. Gonzalez, Sarina Smith, Rajesh Angireddy, Xiao Min Wang, Erin Weiss, Annick Toutain, Roberto Mendoza-Londono, Lucie Dupuis, Nadirah Damseh, Danita Velasco, Irene Valenzuela, Marta Codina-Solà, Catherine Ziats, Jaclyn Have, Katie Clarkson, Dora Steel, Manju Kurian, Katy Barwick, Diana Carrasco, Aditi I. Dagli, M. J. M. Nowaczyk, Miroslava Hančárová, Šárka Bendová, Darina Prchalova, Zdeněk Sedláček, Alica Baxová, Catherine Bearce Nowak, Jessica Douglas, Wendy K. Chung, Nicola Longo, Konrad Platzer, Chiara Klöckner, Luisa Averdunk, Dagmar Wieczorek, Ilona Krey, Christiane Zweier, Andre Reis, Tugce Balci, Marleen Simon, Hester Y. Kroes, Antje Wiesener, Georgia Vasileiou, Nikolaos M. Marinakis, Danai Veltra, Christalena Sofocleous, Konstantina Kosma, Joanne Traeger Synodinos, Konstantinos A. Voudris, Marie-Laure Vuillaume, Paul Gueguen, Nicolas Derive, Estelle Colin, Clarisse Battault, Billie Au, Martin Delatycki, Mathew Wallis, Lyndon Gallacher, Fatma Majdoub, Noor Smal, Sarah Weckhuysen, An-Sofie Schoonjans, R. Frank Kooy, Marije Meuwissen, Benjamin T. Cocanougher, Kathryn Taylor, Carolyn E. Pizoli, Marie T. McDonald, Philip James, Elizabeth R. Roeder, Rebecca Littlejohn, Nicholas A. Borja, Willa Thorson, Kristine King, Radka Stoeva, Manon Suerink, Esther Nibbeling, Stephanie Baskin, Gwenaël L. E. Guyader, Julie Kaplan, Candace Muss, Deanna Alexis Carere, Elizabeth J. K. Bhoj, Laura M. Bryant
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引用次数: 0
Are employees ready to engage in genetic cancer risk assessment in the workplace setting? 员工是否准备好参与工作场所的遗传性癌症风险评估?
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-23 DOI: 10.1038/s41431-024-01655-2
Isabelle R Chandler, Jesse T Brewer, Muhammad Danyal Ahsan, Tamar Nicole Soussana, Emily M Webster, Michelle Primiano, Ravi N Sharaf, Melissa K Frey
{"title":"Are employees ready to engage in genetic cancer risk assessment in the workplace setting?","authors":"Isabelle R Chandler, Jesse T Brewer, Muhammad Danyal Ahsan, Tamar Nicole Soussana, Emily M Webster, Michelle Primiano, Ravi N Sharaf, Melissa K Frey","doi":"10.1038/s41431-024-01655-2","DOIUrl":"https://doi.org/10.1038/s41431-024-01655-2","url":null,"abstract":"","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction: Diagnosis of tuberous sclerosis in the prenatal period: a retrospective study of 240 cases and review of the literature. 更正:产前诊断结节性硬化症:240 个病例的回顾性研究和文献综述。
IF 3.7 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-22 DOI: 10.1038/s41431-024-01658-z
Vincent Milon, Marie-Claire Malinge, Maud Blanluet, Marine Tessarech, Clarisse Battault, Sarah Prestwich, Béatrice Vary, Pierre Gueracher, Louis Legoff, Magalie Barth, Clara Houdayer, Agnès Guichet, Audrey Rousseau, Dominique Bonneau, Vincent Procaccio, Céline Bris, Estelle Colin
{"title":"Correction: Diagnosis of tuberous sclerosis in the prenatal period: a retrospective study of 240 cases and review of the literature.","authors":"Vincent Milon, Marie-Claire Malinge, Maud Blanluet, Marine Tessarech, Clarisse Battault, Sarah Prestwich, Béatrice Vary, Pierre Gueracher, Louis Legoff, Magalie Barth, Clara Houdayer, Agnès Guichet, Audrey Rousseau, Dominique Bonneau, Vincent Procaccio, Céline Bris, Estelle Colin","doi":"10.1038/s41431-024-01658-z","DOIUrl":"10.1038/s41431-024-01658-z","url":null,"abstract":"","PeriodicalId":12016,"journal":{"name":"European Journal of Human Genetics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
European Journal of Human Genetics
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