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Akademický článek

DNA methylation correlates of chronological age in diverse human tissue types

Autor: Niyati Jain, James L. Li, Lin Tong, Farzana Jasmine, Muhammad G. Kibriya, Kathryn Demanelis, Meritxell Oliva, Lin S. Chen, Brandon L. Pierce

Publikováno v: Epigenetics & Chromatin, Vol 17, Iss 1, Pp 1-14 (2024)

Abstract Background While the association of chronological age with DNA methylation (DNAm) in whole blood has been extensively studied, the tissue-specificity of age-related DNAm changes remains an active area of research. Studies investigating the a

Externí odkaz: https://doaj.org/article/3769ff580e254d24bd05ac83d2daf568

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Akademický článek

Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits

Autor: Yihao Lu, Meritxell Oliva, Brandon L. Pierce, Jin Liu, Lin S. Chen

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)

Abstract Genetic effects on functionally related ‘omic’ traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propo

Externí odkaz: https://doaj.org/article/41e2b8339a3045c7ba98d487b26cd84f

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Akademický článek

Mendelian randomization accounting for complex correlated horizontal pleiotropy while elucidating shared genetic etiology

Autor: Qing Cheng, Xiao Zhang, Lin S. Chen, Jin Liu

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-13 (2022)

Mendelian randomization uses genetic variation to study the causal effect of exposure on outcome, but results can be biased by confounders, such as horizontal pleiotropy. Here, the authors present MR-CUE, a method to determine causal effects by accou

Externí odkaz: https://doaj.org/article/d9030a743e2745929938007afa0b13a6

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Akademický článek

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits

Autor: Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He, Lin S. Chen

Publikováno v: Genome Biology, Vol 21, Iss 1, Pp 1-24 (2020)

Abstract To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistic

Externí odkaz: https://doaj.org/article/2dec3656a2734bdd8395c727ad44a4e5

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Akademický článek

Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Autor: Jason J. Pitt, Markus Riester, Yonglan Zheng, Toshio F. Yoshimatsu, Ayodele Sanni, Olayiwola Oluwasola, Artur Veloso, Emma Labrot, Shengfeng Wang, Abayomi Odetunde, Adeyinka Ademola, Babajide Okedere, Scott Mahan, Rebecca Leary, Maura Macomber, Mustapha Ajani, Ryan S. Johnson, Dominic Fitzgerald, A. Jason Grundstad, Jigyasa H. Tuteja, Galina Khramtsova, Jing Zhang, Elisabeth Sveen, Bryce Hwang, Wendy Clayton, Chibuzor Nkwodimmah, Bisola Famooto, Esther Obasi, Victor Aderoju, Mobolaji Oludara, Folusho Omodele, Odunayo Akinyele, Adewunmi Adeoye, Temidayo Ogundiran, Chinedum Babalola, Kenzie MacIsaac, Abiodun Popoola, Michael P. Morrissey, Lin S. Chen, Jiebiao Wang, Christopher O. Olopade, Adeyinka G. Falusi, Wendy Winckler, Kerstin Haase, Peter Van Loo, John Obafunwa, Dimitris Papoutsakis, Oladosu Ojengbede, Barbara Weber, Nasiru Ibrahim, Kevin P. White, Dezheng Huo, Olufunmilayo I. Olopade, Jordi Barretina

Publikováno v: Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)

Research on racial and ethnic influence on breast cancer mortality is stymied by a lack of genomic studies in diverse populations. Here, the authors genomically interrogate 194 Nigerian breast cancers, unveiling molecular features that could explain

Externí odkaz: https://doaj.org/article/b7a3f3164f4543798d357434bd2c072e

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Akademický článek

Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

Autor: Brandon L. Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md. Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md. Yunus, Muhammad G. Kibriya, Lin S. Chen, Habibul Ahsan

Publikováno v: Nature Communications, Vol 9, Iss 1, Pp 1-12 (2018)

Most expression QTLs (eQTLs) co-occur with a DNA methylation QTL (meQTL), suggesting a common causal variant. Here the authors analyse DNA and RNA from blood and identify eQTL-meQTL pairs likely to share a causal variant, finding that expression and

Externí odkaz: https://doaj.org/article/0e237f531ba64865aebc696a3861462b

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