Article
Agriculture, Dairy & Animal Science
Haoqiang Ye, Zhenqiang Xu, Semiu Folaniyi Bello, Qianghui Zhu, Shaofen Kong, Ming Zheng, Xiang Fang, Xinzheng Jia, Haiping Xu, Xiquan Zhang, Qinghua Nie
Summary: In this study, the performance of haplotype models for genomic prediction in a Chinese yellow-feathered chicken population was comprehensively evaluated. It was found that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.
Article
Evolutionary Biology
Hongwei Li, Zezhao Wang, Lei Xu, Qian Li, Han Gao, Haoran Ma, Wentao Cai, Yan Chen, Xue Gao, Lupei Zhang, Huijiang Gao, Bo Zhu, Lingyang Xu, Junya Li
Summary: In this study, haplotype blocks were constructed using LD-based and fixed-SNP methods in beef cattle. The predictive performance of different haplotype block partitioning methods was evaluated, and it was found that LD-based and fixed-SNP haplotype Bayesian methods outperform the Bayesian models. Filtering minor haplotype allele frequency can also improve the performance of genomic prediction.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Genetics & Heredity
Haoqiang Ye, Zipeng Zhang, Duanyang Ren, Xiaodian Cai, Qianghui Zhu, Xiangdong Ding, Hao Zhang, Zhe Zhang, Jiaqi Li
Summary: The size of reference population is important for genomic prediction. This study used WGS data to construct LD-based haplotypes and explored the impact of different SNP densities, variant representation, and reference population size on prediction accuracy. The results showed that GBLUP using WGS data improved prediction accuracy in multi-population and haplotype method had better performance in multi-population genomic evaluation.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Shan-Shan Dong, Wei-Ming He, Jing-Jing Ji, Chi Zhang, Yan Guo, Tie-Lin Yang
Summary: LDBlockShow is an open source software that visualizes LD and haplotype blocks, providing faster speed and lower memory consumption compared to other tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agronomy
Sang He, Shanshan Liang, Lijun Meng, Liyong Cao, Guoyou Ye
Summary: Multi-environment genomic selection is important in rice breeding for selecting resilient varieties. To achieve this, a robust training set with multi-environment phenotypic data is necessary. Optimizing genomic prediction methods and considering haplotype-based models can improve the accuracy of selection.
Article
Biochemistry & Molecular Biology
Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, A. Sorana Morrissy, Laura K. Sycuro, Guang Yang, Daniel C. Jeffares, Quan Long
Summary: DNA sequencing technologies offer unprecedented opportunities to study within-host evolution of microorganism populations, but current instruments struggle to directly distinguish long haplotypes. PoolHapX is a computational approach that integrates information from genetic sharing and genomic sequencing, outperforming other tools and capable of inferring whole-chromosome-scale haplotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Andre C. Araujo, Paulo L. S. Carneiro, Hinayah R. Oliveira, Flavio S. Schenkel, Renata Veroneze, Daniela A. L. Lourenco, Luiz F. Brito
Summary: Haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Jie Zheng, Yuan-yuan Wu, Wen-liang Fang, Xin-ying Cai, Zeng-yun-ou Zhang, Chong-xian Yu, Xiao-dong Zheng, Feng-li Xiao
Summary: This study confirmed the association between the TMEM232 gene and AD through haplotype analysis and targeted capture sequencing. The most strongly associated haplotype with AD was H15.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Reza Seyed Sharifi, Fatemeh Ala Noshahr, Jamal Seifdavati, Nemat Hedayat Evrigh, Moises Cipriano-Salazar, Maria A. Mariezcurrena-Berasain
Summary: The study found that when the length of haploblocks is properly characterized, covariates suitable for haplotype alleles instead of SNPs will improve the accuracy of the genome. Longer haploblocks are more negatively affected by increasing the frequency threshold, leading to a greater impact on accuracy and bias.
SMALL RUMINANT RESEARCH
(2021)
Article
Biochemical Research Methods
Brian M. Schilder, Jack Humphrey, Towfique Raj
Summary: echolocatoR integrates a diverse suite of statistical and functional fine-mapping tools to identify and verify high-confidence consensus variants in any phenotype quickly and accurately. It requires minimal input from users and utilizes a wide range of relevant datasets for comprehensive analysis.
Review
Agronomy
Theo Meuwissen, Ben Hayes, Iona MacLeod, Michael Goddard
Summary: This review discusses the possibility of identifying causal variants for complex traits, stressing the importance of large and diverse samples, accurate genotypes, multiple phenotypes, annotation of genomic sites, and other types of evidence required for this task.
Article
Multidisciplinary Sciences
Noorliza Mohamad Noordin, Joon Liang Tan, Chee Kheong Chong, Yu Kie Chem, Norazimah Tajudin, Rehan Shuhada Abu Bakar, Selvanesan Sengol, Hannah Yik Phing Phoon, Nurul Aina Murni Che Azid, W. Nur Afiza W. Mohd Arifin, Zirwatul Adilah Aziz, Hani Hussin, Nurul Syahida Ibrahim, Aziyati Omar, Ushananthiny Ravi, Kamal Hisham Kamarul Zaman, Mohd Asri Yamin, Yun Fong Ngeow
Summary: A study on 277 SARS-CoV-2 genomes sequenced in Malaysia between January and December 2020 revealed 22 sub-lineages, 13 clonal complexes, 178 sequence types, and identified key mutations in the virus. The most frequent mutations were found in ORF1ab, S, and N genes, with a mean genomic diversity value of 3.26 x 10(-4) over 12 months. Continuous genomic surveillance is crucial to understand viral diversity and its impact on human health.
Article
Biochemistry & Molecular Biology
Ben A. Flanagan, Stacy A. Krueger-Hadfield, Courtney J. Murren, Chris C. Nice, Allan E. Strand, Erik E. Sotka
Summary: The genomic variation of an invasive species is influenced by complex demographic histories, with founder effects playing a key role. Bottlenecks, clonality, and population expansion all impact the genomic variability of the red macroalga Agarophyton vermiculophyllum. The study suggests that a severe population bottleneck, shift towards clonal reproduction, and genetic source diversity contribute to the observed patterns of genomic variability in invasive populations.
Article
Biochemistry & Molecular Biology
Krystyna Nadachowska-Brzyska, Ludovic Dutoit, Linnea Smeds, Martin Kardos, Lars Gustafsson, Hans Ellegren
Summary: Long-term effective population size (N-e) is crucial in evolutionary biology and population genetics, with numerous estimates available for various species and populations. However, estimating contemporary N-e remains challenging, especially with LD-based methods. Whole-genome sequencing data offers new possibilities in estimating high contemporary N-e.
Article
Agriculture, Dairy & Animal Science
Njabulo M. Dlamini, Edgar F. Dzomba, Mpumelelo Magawana, Sphamandla Ngcamu, Farai C. Muchadeyi
Summary: This study investigated the genetic diversity and similarities and differences within and between two conservation herds of the South African Nguni Cattle. The results showed reduced genetic diversity in the two herds, calling for measures to protect the diversity of the South African Nguni cattle.
Article
Urology & Nephrology
Wan-Chuan Tsai, Hon-Yen Wu, Yen-Ling Chiu, Ju-Yeh Yang, Mei-Fen Pai, Yong-Ru Wu, Wan-Yu Lin, Kuan-Yu Hung, Kuo-Liong Chien, Shih-Ping Hsu, Yu-Sen Peng
Summary: The study found that increased dietary phosphorus intake rapidly increases serum phosphate, iPTH, and iFGF23 levels, and decreases serum calcium levels, highlighting the important role of daily fluctuations in dietary habits in disturbed mineral homeostasis in hemodialysis patients.
Article
Environmental Studies
Tzong-Gang Wu, Jung-Chi Chang, Sheng-Hsiu Huang, Wan-Yu Lin, Chang-Chuan Chan, Chang-Fu Wu
Summary: Cyclists and motorcyclists in Taipei were found to have different exposure levels to benzene, toluene, ethylbenzene, xylenes (BTEXs), and PM2.5, with suggestions to reduce the number of scooters to decrease air pollution.
TRANSPORTATION RESEARCH PART D-TRANSPORT AND ENVIRONMENT
(2021)
Article
Nutrition & Dietetics
Wan-Yu Lin
Summary: Regular jogging is associated with decreased levels of triglyceride and TG/HDL-C ratio, as well as increased levels of HDL-C. Swimming, dancing, and cycling are also significantly associated with increased levels of HDL-C. Individuals seeking to improve their lipoprotein-lipid profiles have multiple exercise options to choose from.
JOURNAL OF THE INTERNATIONAL SOCIETY OF SPORTS NUTRITION
(2021)
Article
Endocrinology & Metabolism
Ching-Chu Lu, Ruoh-Fang Yen, Kang-Yung Peng, Jei-Yie Huang, Kwan-Dun Wu, Jeff S. Chueh, Wan-Yu Lin
Summary: Somatic KCNJ5 mutation in primary aldosteronism (PA) patients is associated with higher NP-59 uptake in adrenal scintigraphy. Preoperative NP-59 adrenal scintigraphy may help predict the occurrence of KCNJ5 mutation in PA patients undergoing adrenalectomy.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Genetics & Heredity
Sheue-Jane Hou, Shih-Jen Tsai, Po-Hsiu Kuo, Wan-Yu Lin, Yu-Li Liu, Albert C. Yang, Eugene Lin, Tsuo-Hung Lan
Summary: Through a study involving 10,127 Taiwanese subjects, it was found that the GABRB3-GABRA5-GABRG3 gene cluster is associated with sleep duration, especially a variant in the GABRA5 gene.
BMC MEDICAL GENOMICS
(2021)
Article
Environmental Sciences
Sheng-Han Lee, Wei-Chen Tseng, Zhi-Yi Du, Wan-Yu Lin, Mei-Huei Chen, Ching-Chun Lin, Guang-Wen Lien, Hao-Jan Liang, Hui-Ju Wen, Yue-Leon Guo, Pau-Chung Chen, Ching-Yu Lin
Summary: This study evaluated the impact of PFASs exposure on lipid changes in children, finding that children exposed to different levels of specific PFASs exhibited different lipid patterns, potentially related to hepatic lipid metabolism, metabolic disorders, and PFASs-membrane interactions.
ENVIRONMENTAL POLLUTION
(2021)
Article
Geriatrics & Gerontology
Wan-Yu Lin
Summary: This study investigated the biological age and associated lifestyle factors and genetic variants in Taiwan Biobank participants. The results showed that increased body mass index, smoking, and drinking were associated with accelerated biological aging.
JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES
(2022)
Article
Endocrinology & Metabolism
Wan-Yu Lin, Yu-Cyuan Wang, I-Hsuan Teng, Chi Liu, Xiang-Yang Lou
Summary: Abdominal obesity and general obesity are significantly associated with male and female EAA, respectively. The prevention of abdominal obesity and general obesity is associated with a lower risk of EAA in men and women, respectively.
Article
Health Care Sciences & Services
Eugene Lin, Po-Hsiu Kuo, Wan-Yu Lin, Yu-Li Liu, Albert C. Yang, Shih-Jen Tsai
Summary: The study integrated machine learning and genome-wide analysis to predict probable major depressive disorder (MDD), identifying genes and SNPs associated with MDD and establishing prediction models, with random forests performing the best among the predictive algorithms.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Wan-Yu Lin
Summary: The study identified genetic loci associated with epigenetic aging and its surrogate markers, with a specific focus on individuals of Asian ancestry. By conducting a GWAS and prioritized subset analysis on a Taiwan Biobank cohort, the researchers replicated previously reported aging-associated loci and identified novel loci. One of the newly discovered loci, rs117530284 in the IBA57 gene, was associated with epigenetic age acceleration. This study contributes to our understanding of the genetic architecture underlying epigenetic aging in individuals of Asian ancestry.
HUMAN MOLECULAR GENETICS
(2022)
Article
Oncology
Yun-Hsiang Lo, Wan-Yu Lin
Summary: This study comprehensively investigates the associations between cardiovascular health and four epigenetic clocks. The findings suggest that ideal cardiovascular health is associated with lower levels of biological aging, reducing the risk of aging-related disorders.
CLINICAL EPIGENETICS
(2022)
Article
Environmental Sciences
Sheng-Han Lee, Zhi-Yi Du, Wei-Chen Tseng, Wan-Yu Lin, Mei-Huei Chen, Ching-Chun Lin, Hao-Jan Liang, Hui-Ju Wen, Yue-Leon Guo, Pau-Chung Chen, Ching-Yu Lin
Summary: This study used a metabolomic approach to reveal associations between phthalate exposure and the serum metabolome in Taiwanese children. Unique phthalate exposures were associated with distinct serum metabolite profiles, potentially affecting energy mechanisms, oxidative stress, and lipid metabolism in children.
ENVIRONMENTAL POLLUTION
(2023)
Article
Geriatrics & Gerontology
Wan-Yu Lin
Summary: Obesity is associated with the central nervous system and cognitive functions, but the relationship between obesity indicators and cognitive performance remains unclear. This study found that waist-hip ratio is significantly associated with cognitive impairment, while hip circumference and general obesity are not significantly associated.
Article
Oncology
Xue-Yong Chang, Wan-Yu Lin
Summary: This study comprehensively investigates the role of five measures of epigenetic age acceleration (EAA) in mediating the associations of smoking with health outcomes in an Asian population. The results show that the second-generation epigenetic clocks (GrimEAA, DunedinPACE, and PhenoEAA) significantly mediate smoking associations with diabetes-related outcomes. In contrast, the first-generation epigenetic clocks (HannumEAA and IEAA) do not significantly mediate any associations of smoking variables with the four health outcomes. Cigarette smoking can directly and indirectly deteriorate human health through DNA methylation changes in aging-related CpG sites.
CLINICAL EPIGENETICS
(2023)
Article
Cell Biology
Eugene Lin, Po-Hsiu Kuo, Wan-Yu Lin, Yu-Li Liu, Albert C. Yang, Shih-Jen Tsai
Summary: The study suggests that genetic variants in dopamine receptor-related loci may influence cognitive aging individually and through gene-physical activity interactions. Three novel genes associated with cognitive aging were identified: ZBTB20, NCAM1, and TTC12. Additionally, interplays between physical activity and these three novel genes were found.