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JOURNAL ARTICLE
Jingning Zhang, Jianan Zhan, Jin Jin, Cheng Ma, Ruzhang Zhao, Jared O'Connell, Yunxuan Jiang, Bertram L Koelsch, Haoyu Zhang, Nilanjan Chatterjee
Great efforts are being made to develop advanced polygenic risk scores (PRS) to improve the prediction of complex traits and diseases. However, most existing PRS are primarily trained on European ancestry populations, limiting their transferability to non-European populations. In this article, we propose a novel method for generating multi-ancestry Polygenic Risk scOres based on enSemble of PEnalized Regression models (PROSPER). PROSPER integrates genome-wide association studies (GWAS) summary statistics from diverse populations to develop ancestry-specific PRS with improved predictive power for minority populations...
April 15, 2024: Nature Communications
#2
JOURNAL ARTICLE
Rohit Mehra, Vikram Patra, Rishi Dhillan, Anuka Sharma, Sonal Kashyap, Garima Rastogi, Love Gupta, Reena Singh, Chirag Chopra, Varun Sharma
BACKGROUND: Varicose vein is a chronic condition that affects the lower extremities of the human body. Several factors have been implicated in the development of this disease, viz age, gender, weight, height and prolonged standing. Recently, genome-wide studies have identified genetic biomarkers that are associated with varicose veins in different ethnic groups. Such genetic studies are lacking in South Asians specifically in Indians where the prevalence of varicose veins is high, and it is important to replicate these variants in the stated population...
April 12, 2024: European Journal of Medical Research
#3
JOURNAL ARTICLE
Jin Jin, Jianan Zhan, Jingning Zhang, Ruzhang Zhao, Jared O'Connell, Yunxuan Jiang, Steven Buyske, Christopher Gignoux, Christopher Haiman, Eimear E Kenny, Charles Kooperberg, Kari North, Bertram L Koelsch, Genevieve Wojcik, Haoyu Zhang, Nilanjan Chatterjee
Polygenic risk scores (PRSs) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in summary statistics from genome-wide association studies (GWASs) across multiple ancestry groups via Bayesian hierarchical modeling and ensemble learning. In our simulation studies and data analyses across four distinct studies, totaling 5...
April 10, 2024: Cell Genom
#4
JOURNAL ARTICLE
Mariela V Jennings, José Jaime Martínez-Magaña, Natasia S Courchesne-Krak, Renata B Cupertino, Laura Vilar-Ribó, Sevim B Bianchi, Alexander S Hatoum, Elizabeth G Atkinson, Paola Giusti-Rodriguez, Janitza L Montalvo-Ortiz, Joel Gelernter, María Soler Artigas, Sarah L Elson, Howard J Edenberg, Pierre Fontanillas, Abraham A Palmer, Sandra Sanchez-Roige
BACKGROUND: Alcohol consumption is associated with numerous negative social and health outcomes. These associations may be direct consequences of drinking, or they may reflect common genetic factors that influence both alcohol consumption and other outcomes. METHODS: We performed exploratory phenome-wide association studies (PheWAS) of three of the best studied protective single nucleotide polymorphisms (SNPs) in genes encoding ethanol metabolising enzymes (ADH1B: rs1229984-T, rs2066702-A; ADH1C: rs698-T) using up to 1109 health outcomes across 28 phenotypic categories (e...
April 2, 2024: EBioMedicine
#5
Nora I Strom, Matthew W Halvorsen, Chao Tian, Christian Rück, Gerd Kvale, Bjarne Hansen, Jonas Bybjerg-Grauholm, Jakob Grove, Julia Boberg, Judith Becker Nissen, Thomas Damm Als, Thomas Werge, Elles de Schipper, Bengt Fundin, Christina Hultman, Kira D Höffler, Nancy Pedersen, Sven Sandin, Cynthia Bulik, Mikael Landén, Elinor Karlsson, Kristen Hagen, Kerstin Lindblad-Toh, David M Hougaard, Sandra M Meier, Stéphanie Le Hellard, Ole Mors, Anders D Børglum, Jan Haavik, David A Hinds, David Mataix-Cols, James J Crowley, Manuel Mattheisen
To date, four genome-wide association studies (GWAS) of obsessive-compulsive disorder (OCD) have been published, reporting a high single-nucleotide polymorphism (SNP)-heritability of 28% but finding only one significant SNP. A sub-stantial increase in sample size will likely lead to further identification of SNPs, genes, and biological pathways mediating the susceptibility to OCD. We conducted a GWAS meta-analysis with a 2-3-fold increase in case sample size (OCD cases: N = 37,015, controls: N = 948,616) compared to the last OCD GWAS, including six previously published cohorts (OCGAS, IOCDF-GC, IOCDF-GC-trio, NORDiC-nor, NORDiC-swe, and iPSYCH) and unpublished self-report data from 23andMe Inc...
March 8, 2024: medRxiv
#6
JOURNAL ARTICLE
Xiao-Bin Zhang, He-He Jiang, Lin-Lin Zhang, Chun-Jing Li, Chen Chen, Meng-Zhen Xing, Yu-Ning Ma, Yu-Xia Ma
BACKGROUND: Myopia is the most prevalent refractive error and a growing global health concern that significantly affects visual function. Researchers have recently emphasized considerably on the influence of lifestyle on myopia incidence and development. This study investigates the relationship between leisure sedentary behaviors (LSB)/physical activity (PA)/sleep traits and myopia. METHODS: LSB, PA, and sleep trait-associated genetic variants were used as instrument variables in a Mendelian randomization (MR) study to examine their causal effects on myopia...
March 5, 2024: BMC Ophthalmology
#7
JOURNAL ARTICLE
Yixin Liu, Yimin Gu, Jianfeng Zhou, Hanlu Zhang, Qixin Shang, Yushang Yang, Longqi Chen
BACKGROUND: Emerging observational studies showed an association between atopic dermatitis (AD) and gastrointestinal cancers. However, it remains unclear whether this association is causal, particularly in the case of cancers like esophageal cancer, which exhibit ancestral genetic traits. METHODS: To assess the potential causal relationship between AD and esophageal cancer across diverse ancestral backgrounds, we conducted a 2-sample Mendelian randomization study...
February 2024: World Allergy Organization Journal
#8
S C Kanjira, M J Adams, Yunxuan Jiang, Chao Tian, C M Lewis, K Kuchenbaecker, A M McIntosh
INTRODUCTION: Genome-Wide Association Studies (GWAS) over-represent European ancestries compared to the global population, neglecting all other ancestry groups and low-income nations. Consequently, polygenic risk scores (PRS) more accurately predict complex traits in Europeans than African Ancestries groups. Very few studies have looked at the transferability of European-derived PRS for behavioural and mental health phenotypes to non-Europeans. We assessed the comparative accuracy of PRS for Major Depressive Disorder (MDD) trained on European and African Ancestries GWAS studies to predict MDD and related traits in African Ancestries participants from the UK Biobank...
December 28, 2023: medRxiv
#9
JOURNAL ARTICLE
Vanessa Pitz, Mary B Makarious, Sara Bandres-Ciga, Hirotaka Iwaki, Andrew B Singleton, Mike Nalls, Karl Heilbron, Cornelis Blauwendraat
Although many rare variants have been reportedly associated with Parkinson's disease (PD), many have not been replicated or have failed to replicate. Here, we conduct a large-scale replication of rare PD variants. We assessed a total of 27,590 PD cases, 6701 PD proxies, and 3,106,080 controls from three data sets: 23andMe, Inc., UK Biobank, and AMP-PD. Based on well-known PD genes, 834 variants of interest were selected from the ClinVar annotated 23andMe dataset. We performed a meta-analysis using summary statistics of all three studies...
January 8, 2024: NPJ Parkinson's Disease
#10
JOURNAL ARTICLE
Hélène Choquet, Chen Jiang, Jie Yin, Yuhree Kim, Thomas J Hoffmann, Eric Jorgenson, Maryam M Asgari
Basal cell carcinoma (BCC) is one of the most common malignancies worldwide, yet its genetic determinants are incompletely defined. We perform a European ancestry genome-wide association (GWA) meta-analysis and a Hispanic/Latino ancestry GWA meta-analysis and meta-analyze both in a multi-ancestry GWAS meta-analysis of BCC, totaling 50,531 BCC cases and 762,234 controls from four cohorts (GERA, Mass-General Brigham Biobank, UK Biobank, and 23andMe research cohort). Here we identify 122 BCC-associated loci, of which 36 were novel, and subsequently fine-mapped these associations...
January 5, 2024: Communications Biology
#11
JOURNAL ARTICLE
Xiangrui Meng, Georgina Navoly, Olga Giannakopoulou, Daniel F Levey, Dora Koller, Gita A Pathak, Nastassja Koen, Kuang Lin, Mark J Adams, Miguel E Rentería, Yanzhe Feng, J Michael Gaziano, Dan J Stein, Heather J Zar, Megan L Campbell, David A van Heel, Bhavi Trivedi, Sarah Finer, Andrew McQuillin, Nick Bass, V Kartik Chundru, Hilary C Martin, Qin Qin Huang, Maria Valkovskaya, Chia-Yi Chu, Susan Kanjira, Po-Hsiu Kuo, Hsi-Chung Chen, Shih-Jen Tsai, Yu-Li Liu, Kenneth S Kendler, Roseann E Peterson, Na Cai, Yu Fang, Srijan Sen, Laura J Scott, Margit Burmeister, Ruth J F Loos, Michael H Preuss, Ky'Era V Actkins, Lea K Davis, Monica Uddin, Agaz H Wani, Derek E Wildman, Allison E Aiello, Robert J Ursano, Ronald C Kessler, Masahiro Kanai, Yukinori Okada, Saori Sakaue, Jill A Rabinowitz, Brion S Maher, George Uhl, William Eaton, Carlos S Cruz-Fuentes, Gabriela A Martinez-Levy, Adrian I Campos, Iona Y Millwood, Zhengming Chen, Liming Li, Sylvia Wassertheil-Smoller, Yunxuan Jiang, Chao Tian, Nicholas G Martin, Brittany L Mitchell, Enda M Byrne, Swapnil Awasthi, Jonathan R I Coleman, Stephan Ripke, Tamar Sofer, Robin G Walters, Andrew M McIntosh, Renato Polimanti, Erin C Dunn, Murray B Stein, Joel Gelernter, Cathryn M Lewis, Karoline Kuchenbaecker
Most genome-wide association studies (GWAS) of major depression (MD) have been conducted in samples of European ancestry. Here we report a multi-ancestry GWAS of MD, adding data from 21 cohorts with 88,316 MD cases and 902,757 controls to previously reported data. This analysis used a range of measures to define MD and included samples of African (36% of effective sample size), East Asian (26%) and South Asian (6%) ancestry and Hispanic/Latin American participants (32%). The multi-ancestry GWAS identified 53 significantly associated novel loci...
January 4, 2024: Nature Genetics
#12
JOURNAL ARTICLE
Jonggeol Jeffrey Kim, Dan Vitale, Diego Véliz Otani, Michelle Mulan Lian, Karl Heilbron, Hirotaka Iwaki, Julie Lake, Caroline Warly Solsberg, Hampton Leonard, Mary B Makarious, Eng-King Tan, Andrew B Singleton, Sara Bandres-Ciga, Alastair J Noyce, Cornelis Blauwendraat, Mike A Nalls, Jia Nee Foo, Ignacio Mata
Although over 90 independent risk variants have been identified for Parkinson's disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson's disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci...
December 28, 2023: Nature Genetics
#13
JOURNAL ARTICLE
Alexandra Reynoso, Roberta Torricelli, Benjamin Meir Jacobs, Jingchunzi Shi, Stella Aslibekyan, Lucy Norcliffe-Kaufmann, Alastair J Noyce, Karl Heilbron
OBJECTIVE: Parkinson's disease (PD) is a neurodegenerative disorder with complex aetiology. Multiple genetic and environmental factors have been associated with PD, but most PD risk remains unexplained. The aim of this study was to test for statistical interactions between PD-related genetic and environmental exposures in the 23andMe, Inc. research dataset. METHODS: Using a validated PD polygenic risk score (PRS) and common PD-associated variants in the GBA gene, we explored interactions between genetic susceptibility factors and seven life-style and environmental factors: body mass index (BMI), type 2 diabetes (T2D), tobacco use, caffeine consumption, pesticide exposure, head injury, and physical activity (PA)...
December 19, 2023: Annals of Neurology
#14
Paula Saffie-Awad, Inas Elsayed, Arinola O Sanyaolu, Peter Wild Crea, Artur F Schumacher Schuh, Kristin S Levine, Dan Vitale, Mathew J Korestky, Jeffrey Kim, Thiago Peixoto Leal, María Teresa Periñan, Sumit Dey, Alastair J Noyce, Armando Reyes-Palomares, Noela Rodriguez-Losada, Jia Nee Foo, Wael Mohamed, Karl Heilbron, Lucy Norcliffe-Kaufmann, Mie Rizig, Njideka Okubadejo, Mike Nalls, Cornelis Blauwendraat, Andrew Singleton, Hampton Leonard, Mary B Makarious, Ignacio F Mata, Sara Bandres-Ciga
OBJECTIVE: This study aims to address disparities in risk prediction by evaluating the performance of polygenic risk score (PRS) models using the 90 risk variants across 78 independent loci previously linked to Parkinson's disease (PD) risk across seven diverse ancestry populations. METHODS: We conducted a multi-stage study, testing PRS models in predicting PD status across seven different ancestries applying three approaches: 1) PRS adjusted by gender and age; 2) PRS adjusted by gender, age and principal components (PCs); and 3) PRS adjusted by gender, age and percentage of population admixture...
November 29, 2023: medRxiv
#15
JOURNAL ARTICLE
Weilong Guo, Yixin Zhao, Jin Liu, Jiansong Zhou, Xiaoping Wang
BACKGROUND: Risk preference is often defined as the tendency to engage in risky activities. Increasing evidence shows that risk preference is associated with mood disorders. However, the causality and direction of this association are not clear. METHODS: Genome-wide association study summary data of risk preference in 939,908 participants from UK Biobank and 23andMe were used to identify general risk preference. Data for 413,466 individuals taken from The Psychiatric Genomics Consortium were used to identify bipolar disorder (BP)...
December 7, 2023: Journal of Affective Disorders
#16
JOURNAL ARTICLE
Haihao Yan, Chenghua Zhu, Xiao Jin, Ganzhu Feng
BACKGROUND: Previous studies have found that the persistence of herpesvirus significantly increases the risk of idiopathic pulmonary fibrosis (IPF), but it is unclear whether this effect is causal. We conducted a two-sample Mendelian randomization (MR) study to evaluate the causal relationship between three herpesvirus infections and IPF. METHODS: We used genome-wide association studies (GWAS) data from three independent datasets, including FinnGen cohort, Milieu Intérieur cohort, and 23andMe cohort, to screen for instrumental variables (IVs) of herpesvirus infection or herpesvirus-related immunoglobulin G (IgG) levels...
2023: PloS One
#17
Gökberk Alagöz, Else Eising, Yasmina Mekki, Giacomo Bignardi, Pierre Fontanillas, Michel G Nivard, Michelle Luciano, Nancy J Cox, Simon E Fisher, Reyna L Gordon
Rhythm and language-related traits are phenotypically correlated, but their genetic overlap is largely unknown. Here, we leveraged two large-scale genome-wide association studies performed to shed light on the shared genetics of rhythm (N=606,825) and dyslexia (N=1,138,870). Our results reveal an intricate shared genetic and neurobiological architecture, and lay groundwork for resolving longstanding debates about the potential co-evolution of human language and musical traits.
November 2, 2023: bioRxiv
#18
JOURNAL ARTICLE
Rebecca C Richmond, Laurence J Howe, Karl Heilbron, Samuel Jones, Junxi Liu, Xin Wang, Michael N Weedon, Martin K Rutter, Deborah A Lawlor, George Davey Smith, Céline Vetter
Spouses may affect each other's sleeping behaviour. In 47,420 spouse-pairs from the UK Biobank, we found a weak positive phenotypic correlation between spouses for self-reported sleep duration (r = 0.11; 95% CI = 0.10, 0.12) and a weak inverse correlation for chronotype (diurnal preference) (r = -0.11; -0.12, -0.10), which replicated in up to 127,035 23andMe spouse-pairs. Using accelerometer data on 3454 UK Biobank spouse-pairs, the correlation for derived sleep duration was similar to self-report (r = 0...
November 13, 2023: Communications Biology
#19
JOURNAL ARTICLE
Andreas Katsimpris, Sebastian-Edgar Baumeister, Hansjörg Baurecht, Andrew J Tatham, Michael Nolde
Several observational studies have investigated the association between cannabis use and intraocular pressure, but its association with primary open-angle glaucoma (POAG) remains unclear. In this study, we leveraged human genetic data to assess through Mendelian randomization (MR) whether cannabis use affects POAG. We used five single-nucleotide polymorphisms (SNPs) associated with lifetime cannabis use (P-value < 5 × 10-8 ) from a genome-wide association study (GWAS) (N = 184,765) by the International Cannabis Consortium, 23andMe, and UK Biobank and eleven SNPs associated with cannabis use disorder (P-value < 5 × 10-7 ) from a GWAS meta-analysis of (17,068 cases and 357,219 controls of European descent) from Psychiatric Genomics Consortium Substance Use Disorders working group, Lundbeck Foundation Initiative for Integrative Psychiatric Research, and deCode...
November 10, 2023: Scientific Reports
#20
JOURNAL ARTICLE
Lin Li, Lixin Fu, Liwen Zhang, Yanyan Feng
Primary membranous nephropathy (MN) is a rare autoimmune cause of kidney failure. Observational studies have suggested some relationship between virus infection and primary MN, but the association remains unclear. The current study performed a two‑sample Mendelian randomization (MR) analysis to explore the causal association between varicella-zoster virus (VZV) infection (chickenpox and shingles) and primary MN using genome‑wide association studies (GWASs) summary statistics. The exposure datasets containing chickenpox and shingles were obtained from the GWASs conducted by the 23andMe cohort...
November 6, 2023: Scientific Reports
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