Article
Biotechnology & Applied Microbiology
Ahmad Farhadi, Andrew G. Jeffs, Shane D. Lavery
Summary: This study investigates the genetic divergence and potential secondary contact patterns among geographically distant populations of the spiny lobster species complex. The analysis reveals strong regional structure and a complex evolutionary history of these populations, including a hybrid origin of one population. The findings suggest that alternating periods of divergence and gene flow have shaped the current genetic patterns in this lobster species.
Review
Agronomy
Dinesh K. Saini, Yuvraj Chopra, Jagmohan Singh, Karansher S. Sandhu, Anand Kumar, Sumandeep Bazzer, Puja Srivastava
Summary: This review provides a comprehensive overview of the importance of GWAS in wheat, including population design, high-throughput genotyping and phenotyping platforms, statistical models, and the utilization of MTAs in breeding programs. Future breakthroughs in genomic selection, multi-omics-based approaches, and machine and deep learning models in wheat breeding are also discussed.
MOLECULAR BREEDING
(2022)
Article
Biotechnology & Applied Microbiology
Zsolt Banfai, Erzsebet Koevesdi, Katalin Suemegi, Gergely Bueki, Andras Szabo, Lili Magyari, Valerian adam, Ferenc Palos, Attila Miseta, Miklos Kasler, Bela Melegh
Summary: This study provides the first analysis of the genetic composition of the Danube Swabians based on genome-wide autosomal data. The results suggest that they have significant German and other West European ancestry, with a prominent Hungarian ancestry.
Article
Genetics & Heredity
Meng Lin, Danny S. Park, Noah A. Zaitlen, Brenna M. Henn, Christopher R. Gignoux
Summary: GWAS in admixed populations demonstrate higher statistical power in discovery and more accurate cross-population polygenic score estimates compared to single-ancestry cohorts. Common variant associations are more likely to replicate if first discovered in admixed populations and then transferred to ancestral populations.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Huma Asif, Ney Alliey-Rodriguez, Sarah Keedy, Carol A. Tamminga, John A. Sweeney, Godfrey Pearlson, Brett A. Clementz, Matcheri S. Keshavan, Peter Buckley, Chunyu Liu, Benjamin Neale, Elliot S. Gershon
Summary: An important issue in genome-wide association studies is determining the appropriate family-wise significance threshold. The effectiveness of different methods for adjusting for correlations, including permutation and spectral decomposition, varies depending on SNP minor allele frequency and the number of individuals tested. It may be necessary to establish separate permutation thresholds for different SNP frequency bins to achieve accurate family-wise significance levels.
MOLECULAR PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Xiaoyu Liang, Xuewei Cao, Qiuying Sha, Shuanglin Zhang
Summary: The article introduces a novel multivariate method for phenome-wide association studies (PheWAS) and demonstrates its superiority through extensive simulation studies and real-life application. The proposed method involves hierarchical clustering, clustering linear combination, and false discovery rate control steps.
Article
Computer Science, Interdisciplinary Applications
Xinyue Wang, Xiaoqian Jiang, Jaideep Vaidya
Summary: The paper proposes two algorithms for generating synthetic SNPs that are indistinguishable from real SNPs. Through game theoretic analysis, it demonstrates the possibility of incentivizing honest behavior by the server. Extensive experiments show that the proposed method can ensure efficient and trustworthy outsourcing of logistic regression for GWAS.
JOURNAL OF BIOMEDICAL INFORMATICS
(2021)
Article
Multidisciplinary Sciences
Abbas Saad Alatrany, Wasiq Khan, Abir Hussain, Dhiya Al-Jumeily
Summary: The increasing incidence of Alzheimer's disease (AD) poses socioeconomic challenges. In this study, a hybrid feature selection approach and neural network models are used to predict AD. The approach outperformed existing methods with 99% accuracy and f1-score, providing impactful outcomes for other chronic diseases.
Article
Biotechnology & Applied Microbiology
Jiawen Wang, Jun Wu, Qiuxia Sun, Qian Wu, Youjing Li, Shuhan Duan, Lin Yang, Wenxin Wu, Zheng Wang, Yan Liu, Renkuan Tang, Junbao Yang, Chuanchao Wang, Chao Liu, Jianwei Xu, Mengge Wang, Guanglin He
Summary: This study comprehensively investigated the genetic characteristics of Tai-Kadai-speaking Zhuang and Dong populations in the Yungui Plateau of Southwest China. It revealed close genetic affinity between these populations and geographically close Tai-Kadai and Han populations, as well as genetic evidence supporting a common origin hypothesis between Tai-Kadai and Austronesian populations. The study also identified specific selection candidate signatures associated with human immune systems and neurological disorders, providing evolutionary evidence for the frequency distribution pattern of genetic risk loci.
Article
Biochemistry & Molecular Biology
Wibhu Kutanan, Dang Liu, Jatupol Kampuansai, Metawee Srikummool, Suparat Srithawong, Rasmi Shoocongdej, Sukrit Sangkhano, Sukhum Ruangchai, Pittayawat Pittayaporn, Leonardo Arias, Mark Stoneking
Summary: The study revealed genetic structure among different ethnolinguistic groups in Thailand and Laos, with heterogeneity in certain language families and populations reflecting population interactions and genetic drift. Some Thai groups show admixture from South Asia, likely associated with intensive international trade networks around 600-1000 years ago.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Ruidong Xiang, Iona M. MacLeod, Hans D. Daetwyler, Gerben de Jong, Erin O'Connor, Chris Schrooten, Amanda J. Chamberlain, Michael E. Goddard
Summary: This study presents a method for fine-mapping potentially causal mutations by integrating functional, evolutionary, and pleiotropic information and developing a custom genotyping array. The custom array, containing variants with biological functions, outperformed the standard array in predicting genetic values for multiple traits in dairy cattle populations across different countries. This highlights the potential improvement in genomic prediction by utilizing mutations with functional, evolutionary, and pleiotropic consequences.
NATURE COMMUNICATIONS
(2021)
Article
Evolutionary Biology
Tram Vi, Yves Vigouroux, Philippe Cubry, Pierre Marraccini, Ha Viet Phan, Giang Ngan Khong, Valerie Poncet
Summary: Humans have played a significant role in spreading crops beyond their native range, creating new opportunities for hybridization. Analyzing admixed genomes can provide valuable information about the adaptive history of crops and their impact on current varietal diversity.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Narayana Bhat Devate, Hari Krishna, Sunil Kumar V. Parmeshwarappa, Karthik Kumar Manjunath, Divya Chauhan, Shweta Singh, Jang Bahadur Singh, Monu Kumar, Ravindra Patil, Hanif Khan, Neelu Jain, Gyanendra Pratap Singh, Pradeep Kumar Singh
Summary: This study conducted a genome-wide association study to identify markers associated with traits under heat and drought stress in bread wheat. The results provide valuable markers that can be used for marker-assisted breeding to develop climate-resilient cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Karansher S. Sandhu, Paul D. Mihalyov, Megan J. Lewien, Michael O. Pumphrey, Arron H. Carter
Summary: Grain protein content (GPC) is controlled by complex genetic systems and their interactions and is an important quality determinant for hard spring wheat. Understanding the genetic control of wheat GPC and identifying genotypes with improved stability is an important breeding goal. Through a genome-wide association study, eighteen significant QTLs for GPC stability were identified, demonstrating the potential of genomic selection to improve genetic gain for GPC.
Article
Biochemistry & Molecular Biology
Kwondo Kim, Donghee Kim, Olivier Hanotte, Charles Lee, Heebal Kim, Choongwon Jeong
Summary: Present-day African cattle have a unique genetic profile resulting from a mixture of Bos taurus and Bos indicus populations. Research suggests that the earliest domestic cattle in Africa likely had a significant contribution from an extinct African aurochs lineage, and the indicine ancestry of African cattle is closely related to both North Indian and Southeast Asian indicine breeds.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Heming Wang, Brian E. Cade, Tamar Sofer, Scott A. Sands, Han Chen, Sharon R. Browning, Adrienne M. Stilp, Tin L. Louie, Timothy A. Thornton, W. Craig Johnson, Jennifer E. Below, Matthew P. Conomos, Daniel S. Evans, Sina A. Gharib, Xiuqing Guo, Alexis C. Wood, Hao Mei, Kristine Yaffe, Jose S. Loredo, Alberto R. Ramos, Elizabeth Barrett-Connor, Sonia Ancoli-Israel, Phyllis C. Zee, Raanan Arens, Neomi A. Shah, Kent D. Taylor, Gregory J. Tranah, Katie L. Stone, Craig L. Hanis, James G. Wilson, Daniel J. Gottlieb, Sanjay R. Patel, Ken Rice, Wendy S. Post, Jerome I. Rotter, Shamil R. Sunyaev, Jianwen Cai, Xihong Lin, Shaun M. Purcell, Cathy C. Laurie, Richa Saxena, Susan Redline, Xiaofeng Zhu
HUMAN MOLECULAR GENETICS
(2019)
Article
Genetics & Heredity
Xiaowen Tian, Brian L. Browning, Sharon R. Browning
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Hematology
Laura M. Raffield, Ake T. Lu, Mindy D. Szeto, Amarise Little, Kelsey E. Grinde, Jessica Shaw, Paul L. Auer, Mary Cushman, Steve Horvath, Marguerite R. Irvin, Ethan M. Lange, Leslie A. Lange, Deborah A. Nickerson, Timothy A. Thornton, James G. Wilson, Marsha M. Wheeler, Neil A. Zakai, Alex P. Reiner
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2020)
Article
Multidisciplinary Sciences
Michael D. Kessler, Douglas P. Loesch, James A. Perry, Nancy L. Heard-Costa, Daniel Taliun, Brian E. Cade, Heming Wang, Michelle Daya, John Ziniti, Soma Datta, Juan C. Celedon, Manuel E. Soto-Quiros, Lydiana Avila, Scott T. Weiss, Kathleen Barnes, Susan S. Redline, Ramachandran S. Vasan, Andrew D. Johnson, Rasika A. Mathias, Ryan Hernandez, James G. Wilson, Deborah A. Nickerson, Goncalo Abecasis, Sharon R. Browning, Sebastian Zollner, Jeffrey R. O'Connell, Braxton D. Mitchell, Timothy D. O'Connora
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Genetics & Heredity
Ying Zhou, Sharon R. Browning, Brian L. Browning
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Multidisciplinary Sciences
Daniel N. Harris, Michael D. Kessler, Amol C. Shetty, Daniel E. Weeks, Ryan L. Minster, Sharon Browning, Ethan E. Cochrane, Ranjan Deka, Nicola L. Hawley, Muagututi'a Sefuiva Reupena, Take Naseri, Stephen T. McGarvey, Timothy D. O'Connor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Genetics & Heredity
Ying Zhou, Brian L. Browning, Sharon R. Browning
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Genetics & Heredity
Sharon R. Browning, Brian L. Browning
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Medicine, General & Internal
Bridget M. Lin, Kelsey E. Grinde, Jennifer A. Brody, Charles E. Breeze, Laura M. Raffield, Josyf C. Mychaleckyj, Timothy A. Thornton, James A. Perry, Leslie J. Baier, Lisa de las Fuentes, Xiuqing Guo, Benjamin D. Heavner, Robert L. Hanson, Yi-Jen Hung, Huijun Qian, Chao A. Hsiung, Shih-Jen Hwang, Margaret R. Irvin, Deepti Jain, Tanika N. Kelly, Sayuko Kobes, Leslie Lange, James P. Lash, Yun Li, Xiaoming Liu, Xuenan Mi, Solomon K. Musani, George J. Papanicolaou, Afshin Parsa, Alex P. Reiner, Shabnam Salimi, Wayne H-H Sheu, Alan R. Shuldiner, Kent D. Taylor, Albert Smith, Jennifer A. Smith, Adrienne Tin, Dhananjay Vaidya, Robert B. Wallace, Kenichi Yamamoto, Saori Sakaue, Koichi Matsuda, Yoichiro Kamatani, Yukihide Momozawa, Lisa R. Yanek, Betsi A. Young, Wei Zhao, Yukinori Okada, Gonzalo Abecasis, Bruce M. Psaty, Donna K. Arnett, Eric Boerwinkle, Jianwen Cai, Ida Yii-Der Chen, Adolfo Correa, L. Adrienne Cupples, Jiang He, Sharon Lr Kardia, Charles Kooperberg, Rasika A. Mathias, Braxton D. Mitchell, Deborah A. Nickerson, Steve T. Turner, Ramachandran S. Vasan, Jerome Rotter, Daniel Levy, Holly J. Kramer, Anna Kottgen, Stephen S. Rich, Dan-Yu Lin, Sharon R. Browning, Nora Franceschini
Summary: This study utilized WGS data from multi-ethnic studies to identify novel loci influencing kidney traits, with some driven by low frequency variants more commonly observed in non-European ancestries. Additionally, the study replicated two known loci, and applied statistical approaches to detect aggregated variants and ancestry-specific variants.
Article
Virology
Dora Zucko, Abdullgadir Hayir, Kelsey Grinde, Kathleen Boris-Lawrie
Summary: Since the onset of the HIV-1/AIDS epidemic in 1981, 75 million people have been infected with the virus, and the disease remains a public health crisis worldwide. This study used a bioinformatic pipeline to analyze RNA sequencing data from 19 HIV-1-positive patients and identified circRNAs that became undetectable after antiretroviral therapy. These circRNAs shared common miRNA response elements with their parent mRNAs, some of which were also present in HIV-1 mRNAs. These findings may provide a novel targeting strategy for the treatment of HIV-1 and other diseases.
Article
Oncology
Freddy A. Barragan, Lauren J. Mills, Andrew R. Raduski, Erin L. Marcotte, Kelsey E. Grinde, Logan G. Spector, Lindsay A. Williams
Summary: Black children have lower incidence yet worse survival in B-cell acute lymphoblastic leukemia (B-ALL). Genetic ancestry and differentially expressed genes associated with ancestry play a role in death risk. The impact of reported race/ethnicity on death risk varies after adjusting for genetic ancestry genes. Other factors also contribute to B-ALL survival.
Article
Genetics & Heredity
Sharon R. Browning, Ryan K. Waples, Brian L. Browning
Summary: FLARE is a method for inferring local ancestry in admixed individuals, achieving high accuracy and exceptional computational performance through an extended model and computational techniques. It can handle large-scale datasets and provides superior accuracy.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Xiaowen Tian, Ruoyi Cai, Sharon R. Browning
Summary: This study presents an IBD-based method for estimating the genome-wide mutation rate from sequence data of unrelated individuals. The method does not require family data and can be applied to different populations, with the results showing similar genome-wide mutation rates among these three populations.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Meeting Abstract
Genetics & Heredity
Kelsey E. Grinde, Brian L. Browning, Sharon R. Browning
GENETIC EPIDEMIOLOGY
(2021)
Article
Biochemical Research Methods
Ying Zhou, Sharon R. Browning
Summary: The SPrime program is designed to detect variants in current populations that originated from ancient sources. It is specifically optimized for identifying introgression from Neanderthals and Denisovans in modern humans, with a focus on the Han Chinese population in the 1000 Genomes Project data.