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Heterogeneous genetic architectures of prostate cancer susceptibility in sub-Saharan Africa 撒哈拉以南非洲地区前列腺癌易感性的异质遗传结构
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-02 DOI: 10.1038/s41588-024-01931-3
Rohini Janivara, Wenlong C. Chen, Ujani Hazra, Shakuntala Baichoo, Ilir Agalliu, Paidamoyo Kachambwa, Corrine N. Simonti, Lyda M. Brown, Saanika P. Tambe, Michelle S. Kim, Maxine Harlemon, Mohamed Jalloh, Dillon Muzondiwa, Daphne Naidoo, Olabode O. Ajayi, Nana Yaa Snyper, Lamine Niang, Halimatou Diop, Medina Ndoye, James E. Mensah, Afua O. D. Abrahams, Richard Biritwum, Andrew A. Adjei, Akindele O. Adebiyi, Olayiwola Shittu, Olufemi Ogunbiyi, Sikiru Adebayo, Maxwell M. Nwegbu, Hafees O. Ajibola, Olabode P. Oluwole, Mustapha A. Jamda, Audrey Pentz, Christopher A. Haiman, Petrus V. Spies, André van der Merwe, Michael B. Cook, Stephen J. Chanock, Sonja I. Berndt, Stephen Watya, Alexander Lubwama, Mazvita Muchengeti, Sean Doherty, Natalie Smyth, David Lounsbury, Brian Fortier, Thomas E. Rohan, Judith S. Jacobson, Alfred I. Neugut, Ann W. Hsing, Alexander Gusev, Oseremen I. Aisuodionoe-Shadrach, Maureen Joffe, Ben Adusei, Serigne M. Gueye, Pedro W. Fernandez, Jo McBride, Caroline Andrews, Lindsay N. Petersen, Joseph Lachance, Timothy R. Rebbeck
Men of African descent have the highest prostate cancer incidence and mortality rates, yet the genetic basis of prostate cancer in African men has been understudied. We used genomic data from 3,963 cases and 3,509 controls from Ghana, Nigeria, Senegal, South Africa and Uganda to infer ancestry-specific genetic architectures and fine-map disease associations. Fifteen independent associations at 8q24.21, 6q22.1 and 11q13.3 reached genome-wide significance, including four new associations. Intriguingly, multiple lead associations are private alleles, a pattern arising from recent mutations and the out-of-Africa bottleneck. These African-specific alleles contribute to haplotypes with odds ratios above 2.4. We found that the genetic architecture of prostate cancer differs across Africa, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that African prostate cancer associations are largely governed by neutral evolution. Collectively, our findings emphasize the utility of conducting genetic studies that use diverse populations. Genome-wide association analyses of prostate cancer in men from sub-Saharan Africa identify population-specific risk variants and regional differences in effect sizes. Founder effects contribute to continental differences in the genetic architecture of prostate cancer.
非洲裔男性的前列腺癌发病率和死亡率都是最高的,但对非洲男性前列腺癌的遗传基础却研究不足。我们利用来自加纳、尼日利亚、塞内加尔、南非和乌干达的 3,963 例病例和 3,509 例对照的基因组数据,推断了特定祖先的基因结构,并绘制了疾病相关的精细图谱。8q24.21、6q22.1和11q13.3的15个独立关联达到了全基因组意义,其中包括4个新关联。耐人寻味的是,多个主要关联是私有等位基因,这种模式产生于最近的突变和非洲以外的瓶颈。这些非洲特异性等位基因导致单倍型的几率比超过 2.4。我们发现,前列腺癌的遗传结构在非洲各地有所不同,效应大小差异比等位基因频率差异对这种异质性的影响更大。人群遗传分析表明,非洲前列腺癌的关联在很大程度上受中性进化的影响。总之,我们的研究结果强调了利用不同人群进行遗传研究的实用性。
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引用次数: 0
Aneuploidy as a driver of human cancer 非整倍体是人类癌症的驱动因素
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-02 DOI: 10.1038/s41588-024-01916-2
Eran Sdeor, Hajime Okada, Ron Saad, Tal Ben-Yishay, Uri Ben-David
Aneuploidy, an abnormal chromosome composition, is a major contributor to cancer development and progression and an important determinant of cancer therapeutic responses and clinical outcomes. Despite being recognized as a hallmark of human cancer, the exact role of aneuploidy as a ‘driver’ of cancer is still largely unknown. Identifying the specific genetic elements that underlie the recurrence of common aneuploidies remains a major challenge of cancer genetics. In this Review, we discuss recurrent aneuploidies and their function as drivers of tumor development. We then delve into the context-dependent identification and functional characterization of the driver genes underlying driver aneuploidies and examine emerging strategies to uncover these driver genes using cancer genomics data and cancer models. Lastly, we explore opportunities for targeting driver aneuploidies in cancer by leveraging the functional consequences of these common genetic alterations. This Review discusses recurrent aneuploidies driving human cancer, methods to identify them and strategies to uncover underlying driver genes. It highlights genomic and experimental approaches to study and ultimately target driver aneuploidies.
非整倍体(染色体组成异常)是癌症发生和发展的主要因素,也是癌症治疗反应和临床结果的重要决定因素。尽管非整倍体被认为是人类癌症的标志,但其作为癌症 "驱动因素 "的确切作用在很大程度上仍不为人所知。确定导致常见非整倍体复发的特定遗传因素仍是癌症遗传学的一大挑战。在本综述中,我们将讨论复发性非整倍体及其作为肿瘤发生驱动因素的功能。然后,我们深入探讨了驱动非整倍体的驱动基因的识别和功能特征,并研究了利用癌症基因组学数据和癌症模型发现这些驱动基因的新策略。最后,我们探讨了利用这些常见基因改变的功能性后果来靶向治疗癌症驱动非整倍体的机会。
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引用次数: 0
Genetic and non-genetic HLA disruption is widespread in lung and breast tumors 遗传性和非遗传性 HLA 干扰广泛存在于肺癌和乳腺癌中
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-02 DOI: 10.1038/s41588-024-01886-5
Immune recognition of cancers can be inhibited if the molecules that present cancer cell-specific antigens are disrupted. We have developed a tool that can detect four different types of disruption. Overall, we find that both genetic and non-genetic disruption of these molecules is common in lung and breast tumors.
如果呈现癌细胞特异性抗原的分子受到破坏,癌症的免疫识别就会受到抑制。我们开发了一种工具,可以检测四种不同类型的破坏。总体而言,我们发现这些分子的基因和非基因干扰在肺癌和乳腺癌中都很常见。
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引用次数: 0
Multivariate genomic analysis of 5 million people elucidates the genetic architecture of shared components of the metabolic syndrome 对 500 万人进行的多变量基因组分析阐明了代谢综合征共有成分的基因结构
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-30 DOI: 10.1038/s41588-024-01933-1
Sanghyeon Park, Soyeon Kim, Beomsu Kim, Dan Say Kim, Jaeyoung Kim, Yeeun Ahn, Hyejin Kim, Minku Song, Injeong Shim, Sang-Hyuk Jung, Chamlee Cho, Soohyun Lim, Sanghoon Hong, Hyeonbin Jo, Akl C. Fahed, Pradeep Natarajan, Patrick T. Ellinor, Ali Torkamani, Woong-Yang Park, Tae Yang Yu, Woojae Myung, Hong-Hee Won

Metabolic syndrome (MetS) is a complex hereditary condition comprising various metabolic traits as risk factors. Although the genetics of individual MetS components have been investigated actively through large-scale genome-wide association studies, the conjoint genetic architecture has not been fully elucidated. Here, we performed the largest multivariate genome-wide association study of MetS in Europe (nobserved = 4,947,860) by leveraging genetic correlation between MetS components. We identified 1,307 genetic loci associated with MetS that were enriched primarily in brain tissues. Using transcriptomic data, we identified 11 genes associated strongly with MetS. Our phenome-wide association and Mendelian randomization analyses highlighted associations of MetS with diverse diseases beyond cardiometabolic diseases. Polygenic risk score analysis demonstrated better discrimination of MetS and predictive power in European and East Asian populations. Altogether, our findings will guide future studies aimed at elucidating the genetic architecture of MetS.

代谢综合征(MetS)是一种复杂的遗传病,由各种代谢特征作为风险因素组成。虽然通过大规模的全基因组关联研究,对 MetS 单个成分的遗传学进行了积极的调查,但联合遗传结构尚未完全阐明。在这里,我们利用 MetS 成分之间的遗传相关性,在欧洲开展了最大规模的 MetS 多变量全基因组关联研究(nobserved = 4,947,860)。我们确定了 1,307 个与 MetS 相关的基因位点,这些位点主要富集在脑组织中。利用转录组数据,我们确定了 11 个与 MetS 密切相关的基因。我们的全表型关联分析和孟德尔随机分析强调了 MetS 与心脏代谢疾病以外的多种疾病的关联。多基因风险评分分析表明,在欧洲和东亚人群中,MetS 的分辨能力和预测能力更强。总之,我们的研究结果将指导未来旨在阐明 MetS 遗传结构的研究。
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引用次数: 0
Valid inference for machine learning-assisted genome-wide association studies 机器学习辅助全基因组关联研究的有效推断
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-30 DOI: 10.1038/s41588-024-01934-0
Jiacheng Miao, Yixuan Wu, Zhongxuan Sun, Xinran Miao, Tianyuan Lu, Jiwei Zhao, Qiongshi Lu

Machine learning (ML) has become increasingly popular in almost all scientific disciplines, including human genetics. Owing to challenges related to sample collection and precise phenotyping, ML-assisted genome-wide association study (GWAS), which uses sophisticated ML techniques to impute phenotypes and then performs GWAS on the imputed outcomes, have become increasingly common in complex trait genetics research. However, the validity of ML-assisted GWAS associations has not been carefully evaluated. Here, we report pervasive risks for false-positive associations in ML-assisted GWAS and introduce Post-Prediction GWAS (POP-GWAS), a statistical framework that redesigns GWAS on ML-imputed outcomes. POP-GWAS ensures valid and powerful statistical inference irrespective of imputation quality and choice of algorithm, requiring only GWAS summary statistics as input. We employed POP-GWAS to perform a GWAS of bone mineral density derived from dual-energy X-ray absorptiometry imaging at 14 skeletal sites, identifying 89 new loci and revealing skeletal site-specific genetic architecture. Our framework offers a robust analytic solution for future ML-assisted GWAS.

机器学习(ML)在包括人类遗传学在内的几乎所有科学学科中都越来越受欢迎。由于样本收集和精确表型方面的挑战,ML 辅助全基因组关联研究(GWAS)在复杂性状遗传学研究中越来越常见,该研究使用复杂的 ML 技术来推算表型,然后对推算结果进行 GWAS。然而,ML 辅助 GWAS 关联的有效性尚未得到仔细评估。在此,我们报告了 ML 辅助 GWAS 中普遍存在的假阳性关联风险,并介绍了预测后 GWAS(POP-GWAS)--一种在 ML 估算结果上重新设计 GWAS 的统计框架。POP-GWAS 不考虑估算质量和算法选择,只需将 GWAS 摘要统计作为输入,就能确保有效且强大的统计推断。我们利用 POP-GWAS 对 14 个骨骼部位的双能 X 射线吸收仪成像得出的骨矿物质密度进行了 GWAS 分析,发现了 89 个新的基因位点,并揭示了骨骼部位特异性遗传结构。我们的框架为未来的 ML 辅助 GWAS 提供了强大的分析解决方案。
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引用次数: 0
Structural remodeling of the inactive X chromosome during early mouse development 小鼠早期发育过程中无活性 X 染色体的结构重塑
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-27 DOI: 10.1038/s41588-024-01936-y
Edda G. Schulz, Alexandra Martitz
The mammalian inactive X chromosome shows unusual folding dominated by large-scale structures. A study finds a megadomain structure with a boundary at the Xist locus, preceding the well-known Dxz4-separated megadomains in somatic cells.
哺乳动物的非活性 X 染色体显示出以大规模结构为主的不寻常折叠。一项研究发现,在体细胞中众所周知的Dxz4分隔的巨型结构之前,Xist基因座上有一个具有边界的巨型结构。
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引用次数: 0
Methylated GCC repeat expansion in AFF3 associates with intellectual disability AFF3 中甲基化的 GCC 重复扩增与智力残疾有关
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-27 DOI: 10.1038/s41588-024-01918-0
We identified methylated tandem repeat expansions that resemble the FMR1 CGG repeat that causes fragile X syndrome and investigated their association with traits in the UK Biobank. AFF3 expansion carriers had a 2.4-fold reduced probability of completing secondary education and were enriched in a cohort of individuals with intellectual disability.
我们发现了与导致脆性X综合征的FMR1 CGG重复相似的甲基化串联重复扩增,并调查了它们与英国生物库中特征的关联。AFF3 扩增携带者完成中等教育的概率降低了 2.4 倍,并且富集在智障人群中。
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引用次数: 0
Long-term 3D primary epithelioid cultures reveal genes that regulate esophageal cell fitness 长期三维原代上皮细胞培养揭示调控食管细胞健康的基因
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-27 DOI: 10.1038/s41588-024-01887-4
Primary cell cultures need to be frequently passaged, which limits the study of long-term biological processes, such as how mutant clones colonize aging epithelia. Esophageal epithelioids self-maintain for months, recapitulating progenitor cell behavior in vivo. Epithelioid CRISPR–Cas9 screens reveal genes encoding molecules that control cell fitness.
原代细胞培养物需要频繁传代,这限制了对长期生物过程的研究,例如突变克隆如何定植于老化上皮。食管上皮细胞可自我维持数月之久,再现了体内祖细胞的行为。上皮细胞 CRISPR-Cas9 筛选揭示了编码控制细胞适应性分子的基因。
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引用次数: 0
Publisher Correction: Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance 出版商更正:来自1405名人类的血液eQTL和pQTL的统计和功能精细映射揭示了不同的调控模式和疾病相关性
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-27 DOI: 10.1038/s41588-024-01959-5
Qingbo S. Wang, Takanori Hasegawa, Ho Namkoong, Ryunosuke Saiki, Ryuya Edahiro, Kyuto Sonehara, Hiromu Tanaka, Shuhei Azekawa, Shotaro Chubachi, Yugo Takahashi, Saori Sakaue, Shinichi Namba, Kenichi Yamamoto, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Hideki Makishima, Yasuhito Nannya, Zicong Zhang, Rika Tsujikawa, Ryuji Koike, Tomomi Takano, Makoto Ishii, Akinori Kimura, Fumitaka Inoue, Takanori Kanai, Koichi Fukunaga, Seishi Ogawa, Seiya Imoto, Satoru Miyano, Yukinori Okada, Japan COVID-19 Task Force
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引用次数: 0
Context-specific targeting of the androgen receptor in prostate cancer 前列腺癌中雄激素受体的特异性靶向作用
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-27 DOI: 10.1038/s41588-024-01935-z
Cory Abate-Shen
A co-factor for the androgen receptor, NSD2, provides insights into context-specific functions of the androgen receptor and is a new target for intervention.
雄激素受体的辅助因子 NSD2 可帮助人们深入了解雄激素受体在特定环境下的功能,是一个新的干预目标。
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引用次数: 0
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Nature genetics
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