Article
Biology
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Summary: This study used nanopore sequencing data to map the imprinted intervals in the human genome. It successfully phased the human methylome and detected both known and novel imprinted DMRs. The study also found several conserved imprinted DMRs in mouse, rhesus monkey, and chimpanzee. These findings expand our understanding of imprinting and demonstrate the potential of nanopore sequencing in identifying imprinting regions.
Article
Biochemical Research Methods
Yingyu Chen, Chin Kiu Kwok, Hangjin Jiang, Xiaodan Fan
Summary: A novel Bayesian method called BSDMR was developed for detecting differentially methylated regions from paired bisulfite sequencing data, which provides a better modeling strategy for the spatial correlation between CpG sites and considers the relationship between methylation signals from normal and disease samples. Simulations showed that BSDMR performs well even under low read depth with smaller false discovery rates, and was validated in colon cancer data.
Article
Developmental Biology
Suzan N. Almomani, Abdulmonem A. Alsaleh, Robert J. Weeks, Aniruddha Chatterjee, Robert C. Day, Izumi Honda, Hidekazu Homma, Ryuji Fukuzawa, Tania L. Slatter, Noelyn A. Hung, Celia Devenish, Ian M. Morison, Erin C. Macaulay
Summary: This study identified consistent differential methylation in CMIP gene in pre-eclampsia, suggesting its potential as diagnostic biomarkers for this dangerous conditions of pregnancy. Targeted deep bisulfite sequencing confirmed two DMPs in CMIP gene, indicating its association with the pathogenesis of PE. Further studies are needed to explore the implications of these findings in understanding and managing pre-eclampsia.
Article
Multidisciplinary Sciences
Alexandra Noble, John Pearson, Joseph Boden, John Horwood, Neil Gemmell, Martin Kennedy, Amy Osborne
Summary: The study found that the bisulfite-based amplicon sequencing (BSAS) can effectively validate EPIC array data, but each locus must be compared on an individual basis. BSAS has advantages over the EPIC array in that it can discover novel CpG sites and differentially methylated regions that may not be present on the array.
Article
Obstetrics & Gynecology
Delna Irani, Vandana Bansal, Deepti Tandon, Anushree Patil, Dipty Singh
Summary: The objective of this study was to investigate the genome-wide alterations in sperm DNA methylation in male partners of idiopathic recurrent pregnancy loss (iRPL) cases and identify potential diagnostic markers. A case-control study and methylome analysis of human sperm were conducted. The control group consisted of apparently healthy fertile men (n = 39), while the case group consisted of male partners of iRPL cases (n = 47). Whole genome bisulfite sequencing was performed to analyze differentially methylated CpG sites and genes in iRPL cases compared to fertile controls. Pathway analysis revealed enrichment of development-related signaling pathways. Specific hypomethylated CpGs within genes PPARG, KCNQ1, SETD2, and MAP3K4 were identified in the iRPL study population. In conclusion, this study provides insights into the altered methylation landscape of iRPL sperm and suggests the potential use of specific hypomethylated CpG sites as predictive biomarkers.
FERTILITY AND STERILITY
(2023)
Article
Biochemistry & Molecular Biology
Naisi Zhao, Mengyuan Ruan, Devin C. Koestler, Jiayun Lu, Carmen J. Marsit, Karl T. Kelsey, Elizabeth A. Platz, Dominique S. Michaud
Summary: This study investigated the association between blood DNA methylation levels and lung cancer risk, identifying novel genomic regions and single CpG sites significantly associated with lung cancer risk. These findings serve as potential biomarkers for lung cancer risk stratification and may indicate causal relationships with lung cancer.
Article
Plant Sciences
Ivan Simko
Summary: This study provides the first insight into DNA methylation in cultivated lettuce and suggests a potential role of heritable variation in cytosine methylation in lettuce morphology. Differences in methylation profiles between different horticultural types are already detectable in seeds.
Article
Biochemistry & Molecular Biology
Timothy J. Peters, Michael J. Buckley, Yunshun Chen, Gordon K. Smyth, Christopher C. Goodnow, Susan J. Clark
Summary: Whole genome bisulphite sequencing (WGBS) allows for genome-wide study of single molecule methylation patterns. The study aims to locate differential methylation patterns across the genome using statistical methods, data simulation, and benchmarking. DMRcate is found to be the fastest and the best predictor of DMRs among the methods compared in the study.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Bradley M. M. Downs, Sara-Jayne Thursby, Leslie Cope
Summary: The aim of this study was to determine probe-specific thresholds for identifying aberrant DNA methylation and provide guidance on using continuous or outlier methylation data. A reference database was constructed using Illumina Human 450K array data for over 2,000 normal samples, and probe-specific thresholds for identifying aberrations were derived. The utility of the outlier thresholds was explored in various analyses, and an R package called OutlierMeth containing these thresholds was developed.
Article
Statistics & Probability
Mohamed Milad, Gayla R. Olbricht
Summary: DNA methylation is an important epigenetic modification involved in biological processes and diseases. This study proposes a nonparametric approach based on functional principal component analysis to detect predefined differentially methylated regions (DMR). The performance of this approach is compared with two alternative methods using real and simulated data.
JOURNAL OF APPLIED STATISTICS
(2022)
Article
Biochemistry & Molecular Biology
Dorothea Seiler Vellame, Gemma Shireby, Ailsa MacCalman, Emma L. Dempster, Joe Burrage, Tyler Gorrie-Stone, Leonard S. Schalkwyk, Jonathan Mill, Eilis Hannon
Summary: Most epigenetic epidemiology studies have used bulk tissues for genome-wide profiling, but these can be confounded by variation in cellular composition. In this study, researchers developed a metric called CETYGO score to assess the accuracy of derived cellular heterogeneity variables. They found that the CETYGO score can distinguish inaccurate deconvolutions when applied to whole blood profiles. The study also revealed that estimating accurate cellular composition is influenced by technical and biological factors, such as gender, age, and smoking status.
Article
Biochemistry & Molecular Biology
Marina Laplana, Matthias Bieg, Christian Faltus, Svitlana Melnik, Olga Bogatyrova, Zuguang Gu, Thomas Muley, Michael Meister, Hendrik Dienemann, Esther Herpel, Christopher Amos, Matthias Schlesner, Roland Eils, Christoph Plass, Angela Risch
Summary: This study utilized a targeted sequencing approach to investigate DNA methylation changes in NSCLC patients, identifying differential methylation regions and confirming potential regulatory elements. The research contributes to understanding the mechanisms of lung cancer initiation and progression, and offers new potential targets for cancer treatment.
Article
Biology
Matteo Benelli, Gian Marco Franceschini, Alberto Magi, Dario Romagnoli, Chiara Biagioni, Ilenia Migliaccio, Luca Malorni, Francesca Demichelis
Summary: Researchers present a new computational method, Rocker-meth, which utilizes a heterogeneous hidden Markov model to detect differentially methylated regions (DMRs) in cancer. Through analysis of over 6,000 methylation profiles across 14 cancer types, Rocker-meth efficiently identifies tumor-specific and shared DMRs.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lei Zhang, Dapeng Li, Fenqi Du, Hao Huang, Chao Yuan, Jinming Fu, Simin Sun, Tian Tian, Xinyan Liu, Hongru Sun, Lin Zhu, Jing Xu, Yanlong Liu, Binbin Cui, Yashuang Zhao
Summary: The study aimed to identify differentially methylated regions (DMRs) for predicting survival outcomes in CRC patients, and validated the prediction potential of DMRs through targeted bisulfite sequencing. High prognostic index (high-PI) group demonstrated significantly unfavorable prognosis in both TCGA discovery cohort and independent validation cohort.
Article
Biochemical Research Methods
Zhenxing Guo, Andrew M. Shafik, Peng Jin, Zhijin Wu, Hao Wu
Summary: In this work, a novel statistical method is developed to identify mRNA epigenetic modification regions from MeRIP-seq data, based on an empirical Bayesian hierarchical model. This method accounts for various sources of variations in the data through rigorous modeling and applies shrinkage estimation by borrowing information from transcriptome-wide data to stabilize the parameter estimation, showing higher accuracy, robustness, and efficiency compared to existing peak calling methods in simulation and real data analyses.
Article
Immunology
Wei-You Li, Szu-Wei Huang, Sheng-Fan Wang, Hsin-Fu Liu, Chih-Hung Chou, Shang-Jung Wu, Hsien-Da Huang, Po-Liang Lu, Cathy S. J. Fann, Marcelo Chen, Yen-Hsu Chen, Yi-Ming Arthur Chen
Summary: This study introduced phylogenetic tree results as forensic evidence in HIV-1 transmission cases in Taiwan. The analysis helped identify transmission sources in lawsuits, but limitations such as delayed sampling time and data interpretation were observed.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2021)
Article
Immunology
Ming-Ling Chang, Yu-Sheng Lin, Ming-Yu Chang, Chia-Lin Hsu, Rong-Nan Chien, Cathy S. J. Fann
Summary: This study found that eNAMPT levels and certain genotypes are associated with incident cardiovascular events in CHC patients with sustained virological responses, indicating a potential risk factor for cardiovascular events in these patients.
Article
Virology
Ming-Ling Chang, Su-Wei Chang, Shiang-Chi Chen, Rong-Nan Chien, Chia-Lin Hsu, Ming-Yu Chang, Cathy S. J. Fann
Summary: This study revealed that HCV RNA, IFNL3-rs12979860 and ARNTL-rs6486122 were associated with baseline mixed cryoglobulinemia (MC), while RETN-rs1423096 and SERPINE1-rs6976053 were associated with short-term and long-term post-therapy MC in sustained virological response (SVR) patients, respectively. The links with HCV RNA and immune-associated single nucleotide polymorphisms suggest MC as an immune reaction to expel HCV.
Article
Cardiac & Cardiovascular Systems
Chih-Min Liu, Chien-Liang Liu, Kai-Wen Hu, Vincent S. Tseng, Shih-Lin Chang, Yenn-Jiang Lin, Li-Wei Lo, Fa-Po Chung, Tze-Fan Chao, Ta-Chuan Tuan, Jo-Nan Liao, Chin-Yu Lin, Ting-Yung Chang, Cathy Shen-Jang Fann, Satoshi Higa, Nobumori Yagi, Yu-Feng Hu, Shih-Ann Chen
Summary: In this study, a deep learning ECG model was developed for automatic screening of Brugada syndrome, showing higher consistency and better diagnostic performance compared to cardiologists. The deep learning model also demonstrated satisfactory diagnostic performance in an independent validation ECG dataset.
CANADIAN JOURNAL OF CARDIOLOGY
(2022)
Article
Clinical Neurology
Yu-Chien Tsao, Shuu-Jiun Wang, Chia-Lin Hsu, Yen-Feng Wang, Jong-Ling Fuh, Shih-Pin Chen, Cathy Shen-Jang Fann
Summary: This study identified two novel loci, rs10493859 in TGFBR3 and rs13312779 in FGF23, associated with self-reported headache in Asian populations. Gene enrichment analysis indicated that these genes were significantly enriched in artery and adipose tissue. These results suggest that vascular dysfunction may play a role in the pathogenesis of self-reported headache in Asians.
Article
Psychiatry
Lawrence Shih-Hsin Wu, Ming-Chyi Huang, Cathy Shen-Jang Fann, Hsien-Yuan Lane, Chian-Jue Kuo, Wei-Che Chiu, Pui-Yan Kwok, Andrew Tai-Ann Cheng
Summary: The study conducted a genome-wide association study for early-onset bipolar I disorder in patients of Han Chinese descent, revealing an association between the SNP rs11127876 in the intron of CADM2 gene and early-onset BPI.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Gastroenterology & Hepatology
Ai-Ru Hsieh, Cathy S. J. Fann, Hung-Chun Lin, Jennifer Tai, Sen-Yung Hsieh, Dar-In Tai
Summary: Genome-wide association studies have shown the importance of HLA-DP and HLA-DQ loci in persistent hepatitis B virus infections. In a study on families with hepatocellular carcinoma, non-genetic factors were found to play a major role in persistent HBV infection, while genetic factors affected viral load equally in the HCC family cohort. Sex, relationship to the index case, and certain genetic polymorphisms were associated with viral load in HBsAg carriers.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Health Care Sciences & Services
Lawrence Shih-Hsin Wu, Ming-Chyi Huang, Chih-Ken Chen, Chen-Yang Shen, Cathy Shen-Jang Fann, Chun-Yuan Lin, Chih-Chien Lin, Andrew Tai-Ann Cheng
Summary: Dry mouth is a common adverse drug reaction to lithium treatment in patients with bipolar I disorder, with a specific SNP located in the immunoglobulin heavy chain locus showing the strongest association with dry mouth. This genetic variant could potentially be used for early identification and management of dry mouth in individuals undergoing lithium therapy, ultimately improving medication adherence.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Clinical Neurology
Yun-Jin Jiang, Cathy Shen-Jang Fann, Jong-Ling Fuh, Ming-Yi Chung, Hui-Ying Huang, Kuo-Chang Chu, Yen-Feng Wang, Chia-Lin Hsu, Lung-Sen Kao, Shih-Pin Chen, Shuu-Jiun Wang
Summary: Through a genome-wide association study, we identified VSTM2L and CCDC141 as genes associated with restless legs syndrome in migraineurs. Functional analysis in zebrafish confirmed the role of these genes in the pathogenesis of restless legs syndrome.
JOURNAL OF HEADACHE AND PAIN
(2022)
Article
Biology
Chia-Jung Lee, Ting-Huei Chen, Aylwin Ming Wee Lim, Chien-Ching Chang, Jia-Jyun Sie, Pei-Lung Chen, Su-Wei Chang, Shang-Jung Wu, Chia-Lin Hsu, Ai-Ru Hsieh, Wei-Shiung Yang, Cathy S. J. Fann
Summary: This study conducted a comprehensive PheWAS to identify genetic loci associated with specific diseases and traits in the Taiwanese population, contributing to a better understanding of complex diseases and genetic pleiotropy. The findings were further supported by transcriptomics data, enhancing the relevance to metabolic disorders. Additionally, genetic risk scores were developed for predicting the absolute risk of type 2 diabetes in the Taiwanese population.
COMMUNICATIONS BIOLOGY
(2022)
Article
Clinical Neurology
Shih-Pin Chen, Chia-Lin Hsu, Yen-Feng Wang, Fu-Chi Yang, Ting-Huei Chen, Jia-Hsin Huang, Li-Ling Hope Pan, Jong-Ling Fuh, Hsueh-Chen Chang, Yi-Lun Lee, Hung-Ching Chang, Ko-Han Lee, Yu-Chuan Chang, Cathy Shen-Jang Fann, Shuu-Jiun Wang
Summary: This study investigates the genetic architecture and susceptibility loci of cluster headache in Han Chinese residing in Taiwan, revealing novel susceptible loci and providing mechanistic insights into the pathogenesis of cluster headache.
JOURNAL OF HEADACHE AND PAIN
(2022)
Article
Oncology
Tsung-Hsing Chen, Hung-Chih Hsu, Jeng-Fu You, Cheng-Chou Lai, Yung-Kuan Tsou, Chia-Lin Hsu, Cathy S. J. Fann, Rong-Nan Chien, Ming-Ling Chang
Summary: This 2-year prospective cohort study found a correlation between extracellular nicotinamide phosphoribosyltransferase (eNAMPT) and malignant potential in colonic polyps. Higher eNAMPT levels were observed in polyps with prominent malignant potential, and eNAMPT levels were associated with polyp pathology, total cholesterol, neutrophil-to-lymphocyte ratio, age, and polyp size. Additionally, eNAMPT levels decreased after polypectomy and could serve as a surrogate marker of malignant potential in colonic polyps.
Article
Biochemistry & Molecular Biology
Peng Peng Ip, Qiongyu Li, Wei-Han Lin, Chien-Ching Chang, Cathy Shen-Jang Fann, Huan-Yuan Chen, Fu-Tong Liu, Carlito B. Lebrilla, Chih-Chao Yang, Fang Liao
Summary: Glycosylation plays a key role in protein biological functions and can be used to understand disease etiology, differentiate diseases, and develop therapeutics. Differences in glycosylation profiles of serum proteins between patients with remitting multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD) were observed. Site-specific N-glycans on certain proteins were identified as potential markers to differentiate between MS and NMOSD. Monitoring serum protein glycan profiles using high-throughput analysis may provide additional diagnostic criteria for differentiating diseases and assessing treatment effects.
Meeting Abstract
Clinical Neurology
S. P. Chen, Y. F. Wang, C. L. Hsu, J. L. Fuh, Y. H. Ling, L. L. Pan, C. S. Fann, S. J. Wang
JOURNAL OF HEADACHE AND PAIN
(2021)
Meeting Abstract
Clinical Neurology
S. P. Chen, Y. F. Wang, C. L. Hsu, J. L. Fuh, Y. H. Ling, L. L. Pan, C. S. Fann, S. J. Wang
