Article
Biochemistry & Molecular Biology
Wenwen Zhong, Dejuan Wang, Bing Yao, Xiaoxia Chen, Zhongyang Wang, Hu Qu, Bo Ma, Lei Ye, Jianguang Qiu
Summary: This study identified prognosis-related lncRNAs in bladder cancer by analyzing the expression profiles of lncRNAs and CNVs, and revealed a risk-score signature associated with overall survival in BLCA through multi-omics integration analysis. The enrichment analysis indicated that the imbalance in MAPK signaling pathway, focal adhesion pathway, and JAK-STAT signaling pathway is closely related to tumor development in BLCA.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2021)
Article
Genetics & Heredity
M. Muaaz Aslam, Peter John, Kang-Hsien Fan, Javaid Mehmood Malik, Eleanor Feingold, F. Yesim Demirci, M. Ilyas Kamboh
Summary: This study investigated the association of FCGR3B copy number variation with rheumatoid arthritis susceptibility and related serological traits. The results showed that FCGR3B copy number < 2 is associated with increased risk of rheumatoid arthritis and anti-CCP seropositivity.
Article
Genetics & Heredity
Wenwen Ren, Chun Huang, Xiaoming Ma, Yongfu La, Min Chu, Xian Guo, Xiaoyun Wu, Ping Yan, Chunnian Liang
Summary: This study found that HSF1-CNV is significantly associated with body length and withers height in Ashidan yaks. Additionally, HSF1 expression is higher in the heart and muscle.
Article
Biotechnology & Applied Microbiology
Rongrong Ding, Zhanwei Zhuang, Yibin Qiu, Xingwang Wang, Jie Wu, Shenping Zhou, Donglin Ruan, Cineng Xu, Linjun Hong, Ting Gu, Enqin Zheng, Gengyuan Cai, Wen Huang, Zhenfang Wu, Jie Yang
Summary: This study integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to identify genetic variations and genes associated with loin muscle area, loin muscle depth, and lean meat percentage in Duroc pigs. By determining the CNV detection accuracy and constructing a genomic CNV map, valuable genetic variation resources for pig genome research were provided. The utilization of a composite genetic strategy for complex traits in pigs will contribute to elucidating the genetic architecture influenced by multiple forms of variations.
Article
Clinical Neurology
Aurelien Perrin, Raul Juntas Morales, Francoise Chapon, Corinne Theze, Delphine Lacourt, Henri Pegeot, Emmanuelle Uro-Coste, Diane Giovannini, Nicolas Leboucq, Martial Mallaret, Emmeline Lagrange, Valerie Rigau, Karen Gaudon, Pascale Richard, Michel Koenig, Corinne Metay, Mireille Cossee
Summary: This study analyzed patients from two distinct families with a novel distal titinopathy phenotype associated with the same CNV in the TTN gene. The CNV reported in this study is the most proximal out-of-frame TTN variant and leads to aberrant splicing transcripts, resulting in frameshift and possibly dominant effects. This data represents a novel phenotype-genotype association and provides hypotheses for its dominant effects.
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Agriculture, Dairy & Animal Science
Yifan Wen, Hua He, Hongbing Liu, Qingming An, Dahui Wang, Xiaoting Ding, Qiaoting Shi, Yajie Feng, Eryao Wang, Chuzhao Lei, Zijing Zhang, Yongzhen Huang
Summary: Researchers found that copy number variations (CNVs) of the USP16 gene play an important role in milk traits of Chinese Holstein. The gain type CNV is advantageous for daily milk yield, while the loss type CNV is advantageous for fat percentage. This finding provides a theoretical basis for the genetic improvement of cow breeds in China.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Zijing Zhang, Peng Yang, Pan He, Jiawei Xu, Shijie Lyu, Xian Liu, Cuicui Cai, Huimin Li, Zhiming Li, Baorui Ru, Jianliang Xie, Chuzhao Lei, Hong Chen, Eryao Wang, Yongzhen Huang
Summary: Copy number variation of the PLAG1 gene significantly affects the growth traits of XN cattle, JA cattle, and JX cattle. This may provide the basic material for molecular marker-assisted selection breeding of Chinese cattle breeds.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Jia-Lu Qiao, Rebecca T. Levinson, Bowang Chen, Stefan T. Engelter, Philipp Erhart, Brady J. Gaynor, Patrick F. McArdle, Kristina Schlicht, Michael Krawczak, Martin Stenman, Arne G. Lindgren, John W. Cole, Caspar Grond-Ginsbach
Summary: In this study, a novel scatterplot-based method was explored for detecting copy number variation (CNV) in microarray samples. Compared to standard methods, this method showed higher detection accuracy.
FRONTIERS IN GENETICS
(2023)
Article
Food Science & Technology
Jiayuan Wu, Tianyi Wu, Xueyuan Xie, Qunhao Niu, Zhida Zhao, Bo Zhu, Yan Chen, Lupei Zhang, Xue Gao, Xiaoyan Niu, Huijiang Gao, Junya Li, Lingyang Xu
Summary: In this study, CNV analysis was used to investigate the genetic mechanism of meat quality traits. Significant CNV segments and candidate genes related to meat quality were identified. These findings will enhance the selection process in breeding programs.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Agriculture, Dairy & Animal Science
Xingya Song, Xinmiao Li, Xian Liu, Zijing Zhang, Xiaoting Ding, Yanan Chai, Zhiming Li, Hongli Wang, Jungang Li, Huifeng Liang, Xiaoyan Sun, Guojie Yang, Zengfang Qi, Fuying Chen, Qiaoting Shi, Eryao Wang, Baorui Ru, Chuzhao Lei, Hong Chen, Wujun Liu, Yongzhen Huang
Summary: This study found that copy number variations (CNVs) of the ZNF679 gene are correlated with growth traits in Chinese cattle, suggesting that ZNF679-CNVs could be used as molecular genetic markers for assisted selection breeding to improve Chinese cattle.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Juliana Carron, Caroline Torricelli, Janet Keller Silva, Yichuan Liu, Renata Pellegrino, Carmen Silvia Passos Lima, Gustavo Jacob Lourenco
Summary: Research has found that inherited copy number variations (CNVs) in ADAM3A and ADAM5 pseudogenes could modulate the occurrence and prognosis of oropharynx squamous cell carcinoma (OPSCC) through the interaction of ADAM5 pseudogene transcript, miR-122b-5p, and ADAM9.
Article
Dermatology
Rachel L. Fulton, David J. Margolis, Patrick G. Sockler, Nandita Mitra, Xuan Fei Colin Cornelius Wong, John E. Common
Summary: Atopic dermatitis is a chronic inflammatory skin condition with a multifactorial pathophysiology. Research has shown that filaggrin gene (FLG) plays a significant role in skin barrier dysfunction and can increase the risk of developing AD. However, a study evaluating FLG CNV in Whites and Blacks found that while racial differences exist, they do not seem to explain the risk of developing AD.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiao Chang, Yan Zhao, Cuiping Hou, Joseph Glessner, Lee McDaniel, Maura A. Diamond, Kelly Thomas, Jin Li, Zhi Wei, Yichuan Liu, Yiran Guo, Frank D. Mentch, Haijun Qiu, Cecilia Kim, Perry Evans, Zalman Vaksman, Sharon J. Diskin, Edward F. Attiyeh, Patrick Sleiman, John M. Maris, Hakon Hakonarson
NATURE COMMUNICATIONS
(2017)
Article
Genetics & Heredity
Joseph T. Glessner, Jin Li, Dai Wang, Michael March, Leandro Lima, Akshatha Desai, Dexter Hadley, Charlly Kao, Raquel E. Gur, Nadine Cohen, Patrick M. A. Sleiman, Qingqin Li, Hakon Hakonarson, Zhiliang Wu, Cecilia Kim, Kelly Thomas, Janssen, Reyna Favis, Dong-Jing Fu, Hedy Chung, Adam Savitz, Srihari Gopal
Article
Genetics & Heredity
Donna M. Werling, Harrison Brand, Joon-Yong An, Matthew R. Stone, Lingxue Zhu, Joseph T. Glessner, Ryan L. Collins, Shan Dong, Ryan M. Layer, Eirene Markenscoff-Papadimitriou, Andrew Farrell, Grace B. Schwartz, Harold Z. Wang, Benjamin B. Currall, Xuefang Zhao, Jeanselle Dea, Clif Duhn, Carolyn A. Erdman, Michael C. Gilson, Rachita Yadav, Robert E. Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D. Mandell, Tomasz J. Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F. Walker, Matthew J. Waterman, Xin He, Arnold R. Kriegstein, John L. Rubenstein, Nenad Sestan, Steven A. McCarroll, Benjamin M. Neale, Hilary Coon, A. Jeremy Willsey, Joseph D. Buxbaum, Mark J. Daly, Matthew W. State, Aaron R. Quinlan, Gabor T. Marth, Kathryn Roeder, Bernie Devlin, Michael E. Talkowski, Stephan J. Sanders
Article
Psychiatry
Xiao Chang, Huiqi Qi, Yichuan Liu, Joseph Glessner, Cuiping Hou, Fengxiang Wang, Jin Li, Patrick Sleiman, Hakon Hakonarson
JOURNAL OF PSYCHIATRIC RESEARCH
(2019)
Article
Biochemical Research Methods
Joseph T. Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick M. A. Sleiman, Hakon Hakonarson, Zhi Wei
Summary: Copy number variations (CNVs) are important in disease pathogenesis, but detection and validation remain challenging. DeepCNV, a deep learning-based tool, improves CNV call accuracy and reduces false positives and failures in CNV-disease association results.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Psychiatry
Xueming Yao, Joseph T. Glessner, Junyi Li, Xiaohui Qi, Xiaoyuan Hou, Chonggui Zhu, Xiaoge Li, Michael E. March, Liu Yang, Frank D. Mentch, Heather S. Hain, Xinyi Meng, Qianghua Xia, Hakon Hakonarson, Jin Li
Summary: This study identified novel genetic loci associated with ADHD, BIP, and MDD through large-scale data analysis, with partial replication of results in a pediatric cohort. Through an integrative multi-omics approach, the study identified new genetic loci for these neuropsychiatric disorders, aiding in a better understanding of their underlying molecular mechanisms.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Biotechnology & Applied Microbiology
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: The study developed a tool called Montage to enhance the accuracy of detecting mosaic copy number variants, identified numerous mosaic CNVs associated with phenotypes, and presented a novel algorithm for efficient detection of mosaic CNVs.
Article
Biology
Hui-Qi Qu, Jingchun Qu, Jonathan Bradfield, Luc Marchand, Joseph Glessner, Xiao Chang, Michael March, Jin Li, John J. Connolly, Jeffrey D. Roizen, Patrick Sleiman, Constantin Polychronakos, Hakon Hakonarson
Summary: This study conducted a case-control association study on European patients with type 1 diabetes (T1D) of low genetic risk score, identifying 41 loci associated with T1D of low genetic risk score, including regions previously linked to viral infection and autism spectrum disorder, altogether providing further insight into the pathogenesis of T1D.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yichuan Liu, Hui-Qi Qu, Frank D. Mentch, Jingchun Qu, Xiao Chang, Kenny Nguyen, Lifeng Tian, Joseph Glessner, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: Diagnosing mental disorders, especially for patients with multiple disorders, can be challenging. However, deep learning algorithms combined with genomic sequencing data show promise in accurately diagnosing mental disorders and identifying potential drug targets. Non-coding genomic variants may serve as alternative markers for mental disorders.
MOLECULAR PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Ryan L. Collins, Joseph T. Glessner, Eleonora Porcu, Maarja Lepamets, Rhonda Brandon, Christopher Lauricella, Lide Han, Theodore Morley, Lisa-Marie Niestroj, Jacob Ulirsch, Selin Everett, Daniel P. Howrigan, Philip M. Boone, Jack Fu, Konrad J. Karczewski, Georgios Kellaris, Chelsea Lowther, Diane Lucente, Kiana Mohajeri, Margit Noukas, Xander Nuttle, Kaitlin E. Samocha, Mi Trinh, Farid Ullah, Urmo Vosa, Matthew E. Hurles, Swaroop Aradhya, Erica E. Davis, Hilary Finucane, James F. Gusella, Aura Janze, Nicholas Katsanis, Ludmila Matyakhina, Benjamin M. Neale, David Sanders, Stephanie Warren, Jennelle C. Hodge, Dennis Lal, Douglas M. Ruderfer, Jeanne Meck, Reedik Magi, Tonu Esko, Alexandre Reymond, Zoltan Kutalik, Hakon Hakonarson, Shamil Sunyaev, Harrison Brand, Michael E. Talkowski
Summary: This study aims to quantify the properties of haploinsufficiency and triplosensitivity throughout the human genome and construct a genome-wide catalog of dosage sensitivity for 54 disorders. The study identified dosage sensitive segments and developed a machine-learning model to predict probabilities of dosage sensitivity for all autosomal genes.
Article
Clinical Neurology
Isabella Slaby, Heather S. Hain, Debra Abrams, Frank D. Mentch, Joseph T. Glessner, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: This study established a new algorithm and demonstrated the feasibility of using an electronic algorithm approach to accurately diagnose ADHD and comorbid conditions, verifying the efficiency of the large biorepository for further genetic discovery-based analyses.
JOURNAL OF NEURODEVELOPMENTAL DISORDERS
(2022)
Article
Biochemistry & Molecular Biology
Joseph T. Glessner, Jin Li, Yichuan Liu, Munir Khan, Xiao Chang, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: This study proposes a next-generation approach to CNV association, which supports VCF specification and PennCNV format, allowing for fast and efficient analysis of large cohorts. The study also emphasizes the importance of CNV curation and clinical applications.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Hui-Qi Qu, Charlly Kao, James Garifallou, Fengxiang Wang, James Snyder, Diana J. Slater, Cuiping Hou, Michael March, John J. Connolly, Joseph T. Glessner, Hakon Hakonarson
Summary: This study investigated the impact of varying time periods from blood draw to PBMC isolation on the subsequent transcriptome profiling of different cell types in PBMCs using single cell RNA-seq. The results showed significant changes in the transcriptome expression of various cell types over time, highlighting the importance of considering this factor in interpreting experimental results.
Article
Clinical Neurology
Joseph T. Glessner, Munir E. Khan, Xiao Chang, Yichuan Liu, F. George Otieno, Maria Lemma, Isabella Slaby, Heather Hain, Frank Mentch, Jin Li, Charlly Kao, Patrick M. A. Sleiman, Michael E. March, John Connolly, Hakon Hakonarson
Summary: Neurodevelopmental disorders (NDDs), such as ADHD and ASD, have complex genetic associations implicated by rare recurrent CNVs. Investigating shared biological pathways and genes can help understand the underlying biology of these disorders and identify potential risk factors.
JOURNAL OF NEURODEVELOPMENTAL DISORDERS
(2023)
Article
Psychiatry
Xiao Chang, Yichuan Liu, Frank Mentch, Joseph Glessner, Huiqi Qu, Kenny Nguyen, Patrick M. A. Sleiman, Hakon Hakonarson
TRANSLATIONAL PSYCHIATRY
(2020)