Article
Biochemical Research Methods
Yongwen Zhuang, Brooke N. Wolford, Kisung Nam, Wenjian Bi, Wei Zhou, Cristen J. Willer, Bhramar Mukherjee, Seunggeun Lee
Summary: A new method for genetic association test with family disease history is proposed, which can control the problems caused by increased phenotype correlation and case-control imbalance, and has better performance in detecting variant-phenotype associations.
Review
Endocrinology & Metabolism
Kan Wang, Fei Ye, Yong Chen, Jianxin Xu, Yufang Zhao, Yeping Wang, Tian Lan
Summary: This meta-analysis suggests that there is an association between enterovirus infection and type 1 diabetes (T1D). The association was observed in various populations and sample types, with blood and tissue samples showing a correlation while stool samples did not.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Nutrition & Dietetics
Carlotta Franchi, Ilaria Ardoino, Cristina Bosetti, Eva Negri, Diego Serraino, Anna Crispo, Attilio Giacosa, Elena Fattore, Alberto Dolci, Francesca Bravi, Federica Turati, Carlo La Vecchia, Barbara D'Avanzo
Summary: Canned fish consumption is inversely associated with colorectal cancer risk, with significant risk reduction observed for consuming one to two times per week and two or more times per week.
Article
Biotechnology & Applied Microbiology
Shuai Wang, James B. Meigs, Josee Dupuis
Summary: Advancements in statistical methods and sequencing technology have led to numerous novel discoveries in human genetics in the past two decades. We propose an efficient score test to analyze a multinomial trait in family samples, in the context of genome-wide association/sequencing studies. Both proposed tests have correct type-I error rate and similar power.
Article
Biochemistry & Molecular Biology
Aurina Arnatkeviciute, Mathieu Lemire, Claire Morrison, Michael Mooney, Peter Ryabinin, Nicole M. Roslin, Molly Nikolas, James Coxon, Jeggan Tiego, Ziarih Hawi, Alex Fornito, Walter Henrik, Jean-Luc Martinot, Marie-Laure Paillere Martinot, Eric Artiges, Hugh Garavan, Joel Nigg, Naomi P. Friedman, Christie Burton, Russell Schachar, Jennifer Crosbie, Mark A. Bellgrove
Summary: Deficits in effective executive function are associated with psychiatric disorders and impact everyday functioning. The genetic architecture of these traits is not well understood. This study identified genetic influences on inhibitory control using a genome wide association study, but larger sample sizes are needed for more robust associations. The results also support the use of executive function measures as endophenotypes for neuropsychiatric disorders.
MOLECULAR PSYCHIATRY
(2023)
Review
Nutrition & Dietetics
Ting Zhang, Sang Shin Song, Meiling Liu, Sunmin Park
Summary: This comprehensive meta-analysis study found a significant positive association between fried food intake and gastric cancer risk, which was present in both non-Asians and Asians. Reducing fried food consumption is recommended as a measure to reduce gastric cancer risk.
Article
Medicine, General & Internal
Shilin Xue, Wenya Shen, Jianning Cai, Jinhai Jia, Dan Zhao, Shan Zhang, Xiujun Zhao, Ning Ma, Wenjuan Wang, Bingshuang Wang, Xiaolin Zhang, Xuehui Liu
Summary: This meta-analysis aimed to examine the association between rs735482 polymorphism and cancer risk. The results showed that there is no significant association between rs735482 polymorphism and susceptibility to various cancers overall. However, stratified analysis by ethnicity indicated that rs735482 is associated with an increased risk of cancer in the Chinese population and a decreased risk in the Italian population.
Article
Biology
Han Zhang, Lu Deng, William Wheeler, Jing Qin, Kai Yu
Summary: This paper introduces a flexible inference procedure that integrates individual-level data collected from internal studies with summary data borrowed from external studies, addressing the challenges of sharing individual data among studies. The procedure is built on a retrospective empirical likelihood framework, able to be applied to external studies in different populations and showing efficiency advantages over other methods both theoretically and numerically.
Article
Nutrition & Dietetics
Giulia Collatuzzo, Federica Teglia, Claudio Pelucchi, Eva Negri, Charles S. Rabkin, Linda M. Liao, Rashmi Sinha, Lizbeth Lopez-Carrillo, Nuno Lunet, Samantha Morais, Nuria Aragones, Victor Moreno, Jesus Vioque, Manoli Garcia de la Hera, Mary H. Ward, Reza Malekzadeh, Mohammadreza Pakseresht, Raul Ulises Hernandez-Ramirez, Malaquias Lopez-Cervantes, Rossella Bonzi, Michela Dalmartello, Shoichiro Tsugane, Akihisa Hidaka, M. Constanza Camargo, Maria Paula Curado, Zuo-Feng Zhang, Nadia Zubair, Carlo La Vecchia, Shailja Shah, Paolo Boffetta
Summary: This study analyzed data from 11 case-control studies and found an inverse relationship between dietary iron intake and the risk of gastric cancer. The protective effect of dietary iron was consistent across different types of gastric cancer and was independent of smoking and salt intake. Additional adjustment for meat and fruit/vegetable intake did not change the results.
Article
Biochemistry & Molecular Biology
Xuewei Cao, Xiaoyu Liang, Shuanglin Zhang, Qiuying Sha
Summary: This paper proposes a gene selection approach that incorporates genetic networks into case-control association studies for DNA sequence or DNA methylation data. By using linear combination approaches and regularizing the signals at the gene level, the proposed methods have higher true positive rates compared to traditional dimension reduction techniques.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Public, Environmental & Occupational Health
Fei Wan, Graham A. Colditz, Siobhan Sutcliffe
Summary: This study compared different analytical methods in matched case-control studies and found that CLR is unbiased in exact matching, while unadjusted CLR tends to be biased in nonexact matching, but bias can be alleviated by spline smoothing of matching variables. Adjusted ULR generally has biases and is sensitive to model specification errors, highlighting the importance of using CLR as the primary analytical approach.
AMERICAN JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Multidisciplinary Sciences
Han-Ming Liu, Jin-Ping Zheng, Dan Yang, Zhao-Fa Liu, Zi Li, Zhen-Zhen Hu, Ze-Nan Li
Summary: The study indicates that a recessive/dominant model may be more effective than the additive model in case-control-based genome-wide association studies. Through experiments, it was shown that the recessive model has better accuracy and area under the curve compared to the additive model, suggesting a new direction for research.
Review
Medicine, General & Internal
Qiang Xiao, Jian Chen, Jia Zhu, Shukun Zeng, Hu Cai, Guomin Zhu
Summary: This study analyzed the correlation between SMAD7 polymorphisms and colorectal cancer (CRC) based on 34 studies. The results showed that the C allele of rs4939827 can decrease the risk of CRC, while the T allele of rs12953717 and the C allele of rs4464148 were associated with an increased risk of CRC.
Article
Genetics & Heredity
Hongjing Xie, Xuewei Cao, Shuanglin Zhang, Qiuying Sha
Summary: This research presents a method to address the issue of inflated type I error rates in joint analysis of multiple unbalanced case-control phenotypes in genome-wide association studies. The method involves grouping the phenotypes into clusters, merging them into single phenotypes, and estimating p-values using the saddlepoint approximation. The proposed approach demonstrates good control of type I error rate and higher power compared to other available methods. Application of the method to the UK Biobank dataset identified more significant SNPs than other viable methods.
GENETIC EPIDEMIOLOGY
(2023)
Article
Medicine, Research & Experimental
Zia Ul Islam, Umul Baneen, Taqdees Khaliq, Syed Muhammad Nurulain, Zahid Muneer, Sabir Hussain
Summary: This study investigated the association of miRNA-146a and miRNA-499 polymorphisms with rheumatoid arthritis (RA) in Pakistani patients. The results showed significant associations between miRNA-146a and miRNA-499 genotypes and RA, suggesting a genetic link. These findings contribute to a better understanding of the pathogenesis and genetic factors of RA.
CLINICAL AND EXPERIMENTAL MEDICINE
(2023)
Correction
Oncology
Chongjuan Wei, Bo Peng, Younghun Han, Wei V. Chen, Joshua Rother, Gail E. Tomlinson, C. Richard Boland, Damien Chaussabel, Marsha L. Frazier, Christopher I. Amos
Article
Oncology
Chongjuan Wei, Bo Peng, Younghun Han, Wei V. Chen, Joshua Rother, Gail E. Tomlinson, C. Richard Boland, Marc Chaussabel, Marsha L. Frazier, Christopher I. Amos
Article
Genetics & Heredity
Xiaoming Liu, Simon White, Bo Peng, Andrew D. Johnson, Jennifer A. Brody, Alexander H. Li, Zhuoyi Huang, Andrew Carroll, Peng Wei, Richard Gibbs, Robert J. Klein, Eric Boerwinkle
JOURNAL OF MEDICAL GENETICS
(2016)
Article
Genetics & Heredity
Gao T. Wang, Bo Peng, Suzanne M. Leal
AMERICAN JOURNAL OF HUMAN GENETICS
(2014)
Article
Biochemical Research Methods
Tao Yang, Hong-Wen Deng, Tianhua Niu
BMC BIOINFORMATICS
(2014)
Article
Genetics & Heredity
Bo Peng, Huann-Sheng Chen, Leah E. Mechanic, Ben Racine, John Clarke, Elizabeth Gillanders, Eric J. Feuer
GENETIC EPIDEMIOLOGY
(2015)
Article
Genetics & Heredity
Huann-Sheng Chen, Carolyn M. Hutter, Leah E. Mechanic, Christopher I. Amos, Vineet Bafna, Elizabeth R. Hauser, Ryan D. Hernandez, Chun Li, David A. Liberles, Kimberly McAllister, Jason H. Moore, Dina N. Paltoo, George J. Papanicolaou, Bo Peng, Marylyn D. Ritchie, Gabriel Rosenfeld, John S. Witte, Elizabeth M. Gillanders, Eric J. Feuer
GENETIC EPIDEMIOLOGY
(2015)
Article
Genetics & Heredity
Ivan P. Gorlov, Jason H. Moore, Bo Peng, Jennifer L. Jin, Olga Y. Gorlova, Christopher I. Amos
Review
Biochemistry & Molecular Biology
Sean Hoban
Article
Biochemistry & Molecular Biology
Danielle Welter, Jacqueline MacArthur, Joannella Morales, Tony Burdett, Peggy Hall, Heather Junkins, Alan Klemm, Paul Flicek, Teri Manolio, Lucia Hindorff, Helen Parkinson
NUCLEIC ACIDS RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Benjamin A. Keen, Stanislaw K. Jozwiakowski, Laura J. Bailey, Julie Bianchi, Aidan J. Doherty
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura L. Elnitski, Peggy J. Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, Thomas R. Gingeras, Eric D. Green, Roderic Guigo, Tim Hubbard, Jim Kent, Jason D. Lieb, Richard M. Myers, Michael J. Pazin, Bing Ren, John A. Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Biochemical Research Methods
Gao Wang, Bo Peng
PLOS COMPUTATIONAL BIOLOGY
(2019)
Review
Genetics & Heredity
Kaleigh Riggs, Huann-Sheng Chen, Melissa Rotunno, Bing Li, Naoko I. Simonds, Leah E. Mechanic, Bo Peng
Summary: Simulation studies play a crucial role in genetic research, but there is a lack of sharing of simulation software and datasets, highlighting the need for more information and encouragement towards sharing and reuse.
GENETIC EPIDEMIOLOGY
(2021)
Article
Health Care Sciences & Services
Bo Peng, Rowland W. Pettit, Christopher Amos
Summary: The study developed a COVID-19 outbreak simulator to quantitatively estimate the effectiveness of preventative measures for specific populations, aiding in policy development and emergency planning. Successful application of the simulator requires realistic parameter estimation and robustness analysis.