Article
Oncology
Migle Gabrielaite, Mathias Husted Torp, Malthe Sebro Rasmussen, Sergio Andreu-Sanchez, Filipe Garrett Vieira, Christina Bligaard Pedersen, Savvas Kinalis, Majbritt Busk Madsen, Miyako Kodama, Guel Sude Demircan, Arman Simonyan, Christina Westmose Yde, Lars Ronn Olsen, Rasmus L. Marvig, Olga ostrup, Maria Rossing, Finn Cilius Nielsen, Ole Winther, Frederik Otzen Bagger
Summary: Copy-number variations (CNVs) have significant clinical implications for various diseases and cancers, but detecting relevant CNVs accurately remains challenging. Our study found diverse performance levels among different CNV calling tools, suggesting that combining the best tools could be a potential solution.
Article
Biochemical Research Methods
Brendan O'Fallon, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best
Summary: This study proposes two algorithmic adaptations to improve the accuracy of CNV detection in a Hidden Markov Model (HMM) context. First, it improves the accuracy by computing target- and copy number-specific emission distributions. Second, it enhances the sensitivity for small CNV calls using the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure. The prototype implementation, called Cobalt, shows similar sensitivity to other CNV detection tools but significantly reduces false positive detections.
BMC BIOINFORMATICS
(2022)
Article
Veterinary Sciences
Xiangwei Tang, Bo Zhu, Ruimin Ren, Bin Chen, Sheng Li, Jingjing Gu
Summary: Understanding the impact of genetic variants on phenotypes is crucial in genetic research. This study conducted whole-genome sequencing on 97 horses from 16 different populations, identifying numerous CNVs and candidate genes related to selection and adaptation. The findings provide valuable insights into horse genetics.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Biochemical Research Methods
Dayne L. Filer, Fengshen Kuo, Alicia T. Brandt, Christian R. Tilley, Piotr A. Mieczkowski, Jonathan S. Berg, Kimberly Robasky, Yun Li, Chris Bizon, Jeffery L. Tilson, Bradford C. Powell, Darius M. Bost, Clark D. Jeffries, Kirk C. Wilhelmsen
Summary: The introduction of multiplexed exome capture reduces variance and improves CNV detection through the novel mcCNV algorithm. This method, agnostic to prior information, demonstrates a favorable false discovery rate compared to ExomeDepth in simulation studies. The benefits of this approach include not requiring a database of reference samples and not needing prior information about variant prevalence or size.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Wan-Ping Lee, Albert A. Tucci, Mitchell Conery, Yuk Yee Leung, Amanda B. Kuzma, Otto Valladares, Yi-Fan Chou, Wenbin Lu, Li-San Wang, Gerard D. Schellenberg, Jung-Ying Tzeng
Summary: Alzheimer's Disease is a progressive neurologic disease, with genetics playing a key role in its etiology. The study found that Non-Hispanic-White cases on average have 16 more duplications than controls, and Hispanic cases have larger deletions compared to controls.
FRONTIERS IN GENETICS
(2021)
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
Genetics & Heredity
Fang Fu, Ru Li, Qiu-Xia Yu, Xiao Dang, Shu-Juan Yan, Hang Zhou, Ken Cheng, Rui-Bin Huang, You Wang, Yong-Ling Zhang, Xiang-Yi Jing, Li-Na Zhang, Dong-Zhi Li, Can Liao
Summary: This study aimed to demonstrate the value of comprehensive genomic evaluation in prenatal diagnosis and found that CNV sequencing and clinical exome sequencing can identify clinically significant CNVs and potentially pathogenic mutations in prenatal diagnosis. Additionally, CNV-seq is a reliable and cost-effective technique for detecting CNVs.
Article
Genetics & Heredity
Heming Wu, Qingyan Huang, Xia Zhang, Zhikang Yu, Zhixiong Zhong
Summary: This study identified a high rate of chromosomal abnormalities in fetuses with miscarriage during early and middle pregnancy, with a significantly higher numerical chromosomal abnormality rate in pregnant women aged >=35 compared to <35. The early fetal chromosomal abnormality rate was higher than the middle fetal rate, and there were 168 genes enriched in the VOUS + pCNV regions, associated with 41 functions and 12 pathways.
FRONTIERS IN GENETICS
(2021)
Article
Computer Science, Software Engineering
Emma Adolfsson, Jon Jonasson, Aniruddh Kashyap, Anna Nordenskold, Anna Green
Summary: We developed an efficient approach for copy number analysis in targeted gene panel or whole exome sequence data. Our new tool CNV-Z detects copy number variants with high specificity and sensitivity, ranging from single nucleotide to entire chromosome. Compared to other CNV callers, CNV-Z shows higher specificity and positive predictive value for detecting exonic CNVs.
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Oncology
Tomohiro Tanaka, Yasushi Goto, Masafumi Horie, Ken Masuda, Yuki Shinno, Yuji Matsumoto, Yusuke Okuma, Tatsuya Yoshida, Hidehito Horinouchi, Noriko Motoi, Yasushi Yatabe, Shunichi Watanabe, Noboru Yamamoto, Yuichiro Ohe
Summary: This study investigates somatic single-nucleotide variants or copy number variations in exceptional responders to pemetrexed treatment using whole-exome sequencing. The results suggest that exceptional responders may have a higher number of copy number variations. This study provides important insights into the mechanism of exceptional responses and contributes to genomic findings on thymomas and chemosensitivity.
Article
Immunology
Adiratna Mat Ripen, Mei Yee Chiow, Prakash Rao Rama Rao, Saharuddin Bin Mohamad
Summary: This study reports a rare case of a seven-year-old Murut girl with both Williams-Beuren syndrome and autosomal recessive chronic granulomatous disease. Whole exome sequencing revealed a chromosome deletion and a gene mutation in the patient, explaining the blended phenotypes observed.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Endocrinology & Metabolism
Wei Bai, Qi Zhang, Zhi Lin, Jin Ye, Xiaoqi Shen, Linshuang Zhou, Wenpin Cai
Summary: This study used CNV-seq technology to analyze copy number variations in 395 aborted fetal specimens from spontaneous abortion patients, and collected correlated data, including maternal age, gestational week, and BMI. The study found a potential correlation between chromosomal abnormalities and spontaneous abortion, and identified potential miscarriage candidate genes and functions.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Neurosciences
Tiejia Jiang, Jia Gao, Lihua Jiang, Lu Xu, Congying Zhao, Xiaojun Su, Yaping Shen, Weiyue Gu, Xiaohong Kong, Ying Yang, Feng Gao
Summary: The study found that trio-whole exome sequencing can identify potentially pathogenic or likely pathogenic gene variants in pediatric patients with epilepsy, leading to better management and treatment strategies. The research also discovered new genes not previously associated with epilepsy.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Article
Genetics & Heredity
Wan-Ping Lee, Qihui Zhu, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Charles Lee, Chengsheng Zhang
Summary: This study aimed to develop a CNV calling algorithm based on whole-genome sequencing that could replace the use of chromosomal microarray assay (CMA) in clinical diagnosis. The algorithm, called JAX-CNV, demonstrated excellent performance, with a false discovery rate of 4% and the ability to detect CNVs even at low coverage.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Tae-Joon Park, Lyong Heo, Sanghoon Moon, Young Jin Kim, Ji Hee Oh, Sohee Han, Bong-Jo Kim
INTERNATIONAL JOURNAL OF GENOMICS
(2015)
Letter
Biotechnology & Applied Microbiology
Min Jin Go, Joo-Yeon Hwang, Han Byul Jang, Lyong Heo, Tae-Joon Park, Hye-Ja Lee, Kyung-Hee Park, Jae Heon Kang, Juyoung Lee, Bok-Ghee Han, Jihyun Song, Bong-Jo Kim
Article
Genetics & Heredity
Ji-Young Lee, Bok-Soo Lee, Dong-Jik Shin, Kyung Woo Park, Young-Ah Shin, Kwang Joong Kim, Lyong Heo, Ji Young Lee, Yun Kyoung Kim, Young Jin Kim, Chang Bum Hong, Sang-Hak Lee, Dankyu Yoon, Hyo Jung Ku, Il-Young Oh, Bong-Jo Kim, Juyoung Lee, Seon-Joo Park, Jimin Kim, Hye-kyung Kawk, Jong-Eun Lee, Hye-kyung Park, Jae-Eun Lee, Hye-young Nam, Hyun-young Park, Chol Shin, Mitsuhiro Yokota, Hiroyuki Asano, Masahiro Nakatochi, Tatsuaki Matsubara, Hidetoshi Kitajima, Ken Yamamoto, Hyung-Lae Kim, Bok-Ghee Han, Myeong-Chan Cho, Yangsoo Jang, Hyo-Soo Kim, Jeong Euy Park, Jong-Young Lee
JOURNAL OF HUMAN GENETICS
(2013)
Article
Genetics & Heredity
Joo-Yeon Hwang, Duk-Hwan Kim, Yong-Ick Ji, Min Jin Go, Lyong Heo, Young Jin Kim, Tae Sung Sohn, Jae Hyung Noh, Sung Kim, Yeon-Su Lee, Sook-Young Kim, Young-Woo Kim, Keun Won Ryu, Il Ju Choi, Juyoung Lee, Bong-Jo Kim, Bok-Ghee Han, Joobae Park, Jong-Young Lee
JOURNAL OF HUMAN GENETICS
(2013)
Article
Medicine, Research & Experimental
Maggie H. Chasse, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E. Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary B. Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Summary: The study found that rhabdoid tumors are more sensitive to mithramycin and EC8042, with their sensitivity superior to traditional DNA damaging agents and linked to the causative mutation of SMARCB1 deletion in the tumor. Mithramycin can block the activity of SMARCB1-deficient SWI/SNF complex, leading to chromatin remodeling and restoration of cellular differentiation.
EMBO MOLECULAR MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Zutan Li, Bingbing Jin, Jingya Fang
Summary: In this study, we propose MetaAc4C, an advanced deep learning model for accurate identification of N4-acetylcytidine (ac4C) sites using pre-trained BERT and various optimization techniques. By adapting generative adversarial networks to address data imbalance and augmenting training RNA samples, our model outperforms existing methods in terms of ACC, MCC, and AUROC.