A fully adjusted two-stage procedure for rank-normalization in genetic association studies.
Tamar Sofer,Tamar Sofer,Xiuwen Zheng,Stephanie M. Gogarten,Cecelia A. Laurie,Kelsey Grinde,John R. Shaffer,Dmitry Shungin,Dmitry Shungin,Jeffrey R. O'Connell,Ramon A. Durazo-Arvizo,Laura M. Raffield,Leslie A. Lange,Solomon K. Musani,Ramachandran S. Vasan,L. Adrienne Cupples,Alex P. Reiner,Cathy C. Laurie,Kenneth Rice +18 more
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TL;DR: It is shown that a widely used two‐stage approach to genotype–phenotype associations can lead to tests with undesirable statistical properties, due to both combination of a mis‐specified mean–variance relationship and remaining covariate associations between the rank‐normalized residuals and genotypes.
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Abstract: When testing genotype–phenotype associations using linear regression, departure of the trait distribution from normality can impact both Type I error rate control and statistical power, with worse ...
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Citations
Operating characteristics of the rank-based inverse normal transformation for quantitative trait analysis in genome-wide association studies.
TL;DR: The results demonstrate that, for nonnormally distributed traits, INT‐based tests outperform the standard untransformed association test, both in terms of power and type I error rate control.
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Daniel H. Katz,Jeremy M. Robbins,Shuliang Deng,Usman A. Tahir,Alexander G. Bick,Akhil Pampana,Zhi Yu,Debby Ngo,Mark D. Benson,Zsu Zsu Chen,Daniel E. Cruz,Dongxiao Shen,Yan Gao,Claude Bouchard,Mark A. Sarzynski,Adolfo Correa,Pradeep Natarajan,James F. Wilson,Robert E. Gerszten +18 more
TL;DR: Evidence is shown supporting more reliable protein target specificity and a higher number of phenotypic associations for the Olink platform, while the Soma platforms benefit from greater measurement precision and analytic breadth across the proteome.
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Clinical laboratory test-wide association scan of polygenic scores identifies biomarkers of complex disease
Jessica Dennis,Jessica Dennis,Julia M. Sealock,Peter Straub,Younga H Lee,Younga H Lee,Donald Hucks,Ky’Era Actkins,Ky’Era Actkins,Annika Faucon,Yen-Chen Anne Feng,Yen-Chen Anne Feng,Tian Ge,Tian Ge,Slavina B. Goleva,Maria Niarchou,Kritika Singh,Theodore Morley,Jordan W. Smoller,Jordan W. Smoller,Douglas M. Ruderfer,Jonathan D. Mosley,Guanhua Chen,Lea K. Davis +23 more
TL;DR: In this paper, the authors cleaned lab traits extracted from the EHR performed lab-wide association scans (LabWAS) of the lipids and CAD polygenic risk scores across 315 heritable lab tests then replicated the pipeline and analyses in the Massachusetts General Brigham Biobank.
A Genome-wide Association Study Discovers 46 Loci of the Human Metabolome in the Hispanic Community Health Study/Study of Latinos.
Elena V. Feofanova,Han Chen,Yulin Dai,Peilin Jia,Megan L. Grove,Alanna C. Morrison,Qibin Qi,Martha L. Daviglus,Jianwen Cai,Kari E. North,Cathy C. Laurie,Robert C. Kaplan,Eric Boerwinkle,Bing Yu +13 more
TL;DR: The findings document the genetic architecture of circulating metabolites in an underrepresented Hispanic/Latino community, shedding light on disease etiology.
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Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations
Michael Elgart,Genevieve Lyons,Santiago Romero-Brufau,Nuzulul Kurniansyah,Jennifer A. Brody,Xiuqing Guo,Henry J. Lin,Laura M. Raffield,Yan Gao,Han Chen,Paul S. de Vries,Donald M. Lloyd-Jones,Leslie A. Lange,Gina M. Peloso,Myriam Fornage,Jerome I. Rotter,Stephen S. Rich,Alanna C. Morrison,Bruce M. Psaty,Daniel Levy,Susan Redline,Tamar Sofer +21 more
TL;DR: In this article , the authors used an ensemble method of SNP selection followed by gradient boosted trees (XGBoost) to allow for non-linearities and interaction effects between single nucleotide polymorphisms (SNPs).
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Meta-analysis identifies common variants associated with body mass index in east Asians
Wanqing Wen,Yoon Shin Cho,Wei Zheng,Rajkumar Dorajoo,Rajkumar Dorajoo,Norihiro Kato,Lu Qi,Chien Hsiun Chen,Chien Hsiun Chen,Ryan J. Delahanty,Yukinori Okada,Yasuharu Tabara,Dongfeng Gu,Dingliang Zhu,Christopher A. Haiman,Zengnan Mo,Yu Tang Gao,Seang-Mei Saw,Min Jin Go,Fumihiko Takeuchi,Li Ching Chang,Yoshihiro Kokubo,Jun Liang,Mei Hao,Loic Le Marchand,Yi Zhang,Yanling Hu,Tien Yin Wong,Tien Yin Wong,Jirong Long,Bok Ghee Han,Michiaki Kubo,Ken Yamamoto,Mei Hsin Su,Tetsuro Miki,Brian E. Henderson,Huai-Dong Song,Aihua Tan,Jiang He,Daniel P.K. Ng,Qiuyin Cai,Tatsuhiko Tsunoda,Fuu Jen Tsai,Naoharu Iwai,Gary K. Chen,Jiajun Shi,Jianfeng Xu,Xueling Sim,Yong-Bing Xiang,Shiro Maeda,Rick Twee-Hee Ong,Rick Twee-Hee Ong,Chun Li,Yusuke Nakamura,Tin Aung,Tin Aung,Naoyuki Kamatani,Jianjun Liu,Wei Lu,Mitsuhiro Yokota,Mitsuhiro Yokota,Mark Seielstad,Mark Seielstad,Cathy S.J. Fann,Cathy S.J. Fann,Jer-Yuarn Wu,Jer-Yuarn Wu,Jong-Young Lee,Frank B. Hu,Toshihiro Tanaka,E. Shyong Tai,Xiao-Ou Shu +71 more
TL;DR: A meta-analysis of associations between BMI and approximately 2.4 million SNPs in 27,715 east Asians and three additional loci nearly reached the genome-wide significance threshold may shed light on new pathways involved in obesity and demonstrate the value of conducting genetic studies in non-European populations.
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