Article
Biochemical Research Methods
Jianteng Zhou, Jianing Gao, Huan Zhang, Daren Zhao, Ao Li, Furhan Iqbal, Qinghua Shi, Yuanwei Zhang
Summary: Researchers have reviewed existing linkage analysis tools and introduced PedMiner, a web-based application designed to narrow down candidate variants from family-based whole-exome sequencing (WES) data through linkage analysis. PedMiner integrates linkage analysis, variant annotation, and prioritization in an automated pipeline, providing comprehensive annotation of variants and genes within linked regions. This efficient application will benefit the scientific community studying Mendelian inherited disorders using family-based WES data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medical Laboratory Technology
Yingdi Liu, Yanling Teng, Zhuo Li, Jingyi Cui, Desheng Liang, Lingqian Wu
Summary: By reanalyzing whole-exome sequencing data with updated algorithms and databases, optimizing processes and strategies, the diagnostic yield can be improved and missed diagnoses reduced.
CLINICA CHIMICA ACTA
(2021)
Article
Cell Biology
Yufen Xu, Di Che, Xiaoyu Zuo, Lanyan Fu, Lei Pi, Huazhong Zhou, Yaqian Tan, Kejian Wang, Xiaoqiong Gu
Summary: Kawasaki disease is an autoimmune disease that causes acquired heart disease in children. It is more common in males, but the reason for this sex bias is unknown. A study using whole-exome sequencing identified several genetic variants associated with male and female Kawasaki disease patients, and further validation showed that four of these variants were associated with Kawasaki disease susceptibility. These findings provide insight into the sex bias in Kawasaki disease and may contribute to the development of sex-specific precision therapies.
Article
Oncology
Ashwini Kumar, Sadiksha Adhikari, Matti Kankainen, Caroline A. Heckman
Summary: This study compared the performance of whole-exome sequencing and linked-read exome sequencing in detecting structural variants and short variants in multiple myeloma patient samples, showing that whole-exome sequencing detected more short variants and different types of structural variants, and demonstrated higher performance. While linked-read sequencing detected more large structural variants, mainly inversions, it showed poor detection of other types of structural variants.
Article
Genetics & Heredity
Atefe Papi, Mina Zamani, Gholamreza Shariati, Alireza Sedaghat, Tahere Seifi, Samira Negahdari, Sahar Sadat Sedighzadeh, Jawaher Zeighami, Alihossein Saberi, Mohammad Hamid, Hamid Galehdari
Summary: In this study, pathogenic variants in Iranian patients with GSD and CDG were identified using whole exome sequencing. These findings can provide valuable information for patient management and family counseling.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2023)
Article
Genetics & Heredity
Paola Granata, Dario Cocciadiferro, Alessandra Zito, Chiara Pessina, Alessandro Bassani, Fabio Zambonin, Antonio Novelli, Mauro Fasano, Rosario Casalone
Summary: 16p13.11 microdeletion is a predisposing factor to neurodevelopmental disorders, with varying prevalence in different diseases. By using whole exome sequencing, this study identified gene signatures potentially capable of explaining the clinical phenotype.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Gabriella Doddato, Floriana Valentino, Annarita Giliberti, Filomena Tiziana Papa, Rossella Tita, Lucia Pia Bruno, Sara Resciniti, Chiara Fallerini, Elisa Benetti, Maria Palmieri, Maria Antonietta Mencarelli, Alessandra Fabbiani, Mirella Bruttini, Alfredo Orrico, Margherita Baldassarri, Francesca Fava, Diego Lopergolo, Caterina Lo Rizzo, Vittoria Lamacchia, Sara Mannucci, Anna Maria Pinto, Aurora Curro, Virginia Mancini, Francesca Mari, Alessandra Renieri, Francesca Ariani
Summary: This study identified pathogenic and potentially pathogenic genes in HBOC patients through whole exome sequencing and MLPA testing, expanding the spectrum of causative variants. This helps to improve personalized risk assessment and clinical surveillance in HBOC families.
FRONTIERS IN ONCOLOGY
(2021)
Article
Cell Biology
Yixia Xie, Baowei Hu, Yue Gao, Yaxin Tang, Guohe Chen, Jiayuan Shen, Zhikai Jiang, He Jiang, Jiwei Han, Junyan Yan, Lifang Jin
Summary: This study investigates the development and mechanism of ductular reactions in Glycogen storage disease type Ia (GSD-Ia), improving our understanding of the pathophysiology of the disease and highlighting the potential of drug targeting of ductular reactions.
ANIMAL CELLS AND SYSTEMS
(2022)
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
Genetics & Heredity
Angham Abdulrhman Abdulkareem, Qaiser Zaman, Hamza Khan, Sabar Khan, Gauhar Rehman, Nabeel Tariq, Mashal Ahmad, Muhammad Owais, Osama Yousef Najumuddin, Osama Yousef Muthaffar, Fehmida Bibi, Rin Khang, Seung Woo Ryu, Muhammad Imran Naseer, Musharraf Jelani
Summary: This study identified four novel variants in CARS2, ARSA, CNTN2 and CLCN4 genes associated with epilepsy in five Pakistani families. These variants were found to be pathogenic and molecular diagnosis was successfully achieved through whole exome sequencing and Sanger sequencing. This study suggests that exome sequencing should be performed as a first-line molecular diagnostic test in familial cases.
FRONTIERS IN GENETICS
(2023)
Article
Pediatrics
Shimin Wu, Shusen Guo, Lina Fu, Caiqi Du, Xiaoping Luo
Summary: This case report describes a patient with glycogen storage disease type la who showed significant increase in height after growth hormone treatment. The results suggest that early diagnosis and growth hormone therapy are crucial for the growth and development of patients with GSD la.
FRONTIERS IN PEDIATRICS
(2022)
Article
Multidisciplinary Sciences
Erdem Turk, Akif Ayaz, Ayhan Yuksek, Baris E. Suzek
Summary: The study introduces a desktop application called DEVOUR, which analyzes read alignments in WES experiments to identify low-coverage regions and annotates known variants in these regions using clinical variant annotation databases. The application was used to analyze samples from a Hirschsprung disease-related WES project, revealing potentially disease-associated variants in low-coverage regions.
Article
Genetics & Heredity
Huling Jiang, Luming Wang, Jianjun Zhu, Zepeng Ping
Summary: This study aimed to identify the susceptibility genes for preeclampsia (PE) by performing whole-exome sequencing on nine families with severe PE. Compound heterozygous variants in the NPFFR2 gene were found to be potentially associated with severe PE. This study provides clinicians and researchers with a better understanding of the molecular mechanisms underlying severe PE in pregnant women.
Article
Geriatrics & Gerontology
Lin Sun, Jianye Zhang, Ning Su, Shaowei Zhang, Feng Yan, Xiang Lin, Jie Yu, Wei Li, Xia Li, Shifu Xiao
Summary: By conducting whole exome sequencing on 84 patients with degenerative dementia, new pathogenic and likely pathogenic gene variants were identified, indicating heterogeneity in the etiology and phenotype of dementia.
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Article
Multidisciplinary Sciences
Juan Cao, An'er Chen, Liyun Tian, Lulu Yan, Haibo Li, Bihua Zhou
Summary: This study investigated the role of whole exome sequencing (WES) technology in diagnosing fetuses with skeletal abnormalities. Several novel heterozygous mutations were identified, expanding the mutation spectrum for prenatal diagnosis. WES technology is essential for accurate diagnosis of skeletal abnormalities in fetuses.
Article
Plant Sciences
Maojun Wang, Pengcheng Wang, Fan Liang, Zhengxiu Ye, Jianying Li, Chao Shen, Liuling Pei, Feng Wang, Jiang Hu, Lili Tu, Keith Lindsey, Daohua He, Xianlong Zhang
Article
Biochemistry & Molecular Biology
Ta-na Wuyun, Lin Wang, Huimin Liu, Xuewen Wang, Liangsheng Zhang, Jeffrey L. Bennetzen, Tiezhu Li, Lirong Yang, Panfeng Liu, Lanying Du, Lu Wang, Mengzhen Huang, Jun Qing, Lili Zhu, Wenquan Bao, Hongguo Li, Qingxin Du, Jingle Zhu, Hong Yang, Shuguang Yang, Hui Liu, Hui Yue, Jiang Hu, Guoliang Yu, Yu Tian, Fan Liang, Jingjing Hu, Depeng Wang, Ruiwen Gao, Dejun Li, Hongyan Du
Article
Plant Sciences
Chuan Liu, Xuefeng Qu, Yanhao Zhou, Gaoyuan Song, Naghmeh Abiri, Yuhui Xiao, Fan Liang, Daiming Jiang, Zhongli Hu, Daichang Yang
PLANT CELL AND ENVIRONMENT
(2018)
Article
Genetics & Heredity
Sheng Zeng, Mei-yun Zhang, Xue-jing Wang, Zheng-mao Hu, Jin-chen Li, Nan Li, Jun-ling Wang, Fan Liang, Qi Yang, Qian Liu, Li Fang, Jun-wei Hao, Fu-dong Shi, Xue-bing Ding, Jun-fang Teng, Xiao-meng Yin, Hong Jiang, Wei-ping Liao, Jing-yu Liu, Kai Wang, Kun Xia, Bei-sha Tang
JOURNAL OF MEDICAL GENETICS
(2019)
Article
Biochemical Research Methods
Peng Ni, Neng Huang, Zhi Zhang, De-Peng Wang, Fan Liang, Yu Miao, Chuan-Le Xiao, Feng Luo, Jianxin Wang
Article
Genetics & Heredity
Yun Tian, Jun-Ling Wang, Wen Huang, Sheng Zeng, Bin Jiao, Zhen Liu, Zhao Chen, Yujing Li, Ying Wang, Hao-Xuan Min, Xue-Jing Wang, Yong You, Ru-Xu Zhang, Xiao-Yu Chen, Fang Yi, Ya-Fang Zhou, Hong-Yu Long, Chao-Jun Zhou, Xuan Hou, Jun-Pu Wang, Bin Xie, Fan Liang, Zhuan-Yi Yang, Qi-Ying Sun, Emily G. Allen, Andrew Mark Shafik, Ha Eun Kong, Ji-Feng Guo, Xin-Xiang Yan, Zheng-Mao Hu, Kun Xia, Hong Jiang, Hong-Wei Xu, Ran-Hui Duan, Peng Jin, Bei-Sha Tang, Lu Shen
AMERICAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Genetics & Heredity
Yuting Zheng, Lingrong Kong, Hui Xu, Yongjie Lu, Xuechao Zhao, Yuxia Yang, Guoliang Yu, Pidong Li, Fan Liang, Hongshuai Jin, Xiangdong Kong
PRENATAL DIAGNOSIS
(2020)
Article
Genetics & Heredity
Jianwen Deng, Jiaxi Yu, Pidong Li, Xinghua Luan, Li Cao, Juan Zhao, Meng Yu, Wei Zhang, He Lv, Zhiying Xie, LingChao Meng, Yiming Zheng, Yawen Zhao, Qiang Gang, Qingqing Wang, Jing Liu, Min Zhu, Xueyu Guo, Yanan Su, Yu Liang, Fan Liang, Tomohiro Hayashi, Meiko Hashimoto Maeda, Tatsuro Sato, Shigehisa Ura, Yasushi Oya, Masashi Ogasawara, Aritoshi Iida, Ichizo Nishino, Chang Zhou, Chuanzhu Yan, Yun Yuan, Daojun Hong, Zhaoxia Wang
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Plant Sciences
Shengli Yao, Fan Liang, Rafaqat Ali Gill, Junyan Huang, Xiaohui Cheng, Yueying Liu, Chaobo Tong, Shengyi Liu
Article
Genetics & Heredity
Xiao Du, Lili Li, Fan Liang, Sanyang Liu, Wenxin Zhang, Shuai Sun, Yuhui Sun, Fei Fan, Linying Wang, Xinming Liang, Weijin Qiu, Guangyi Fan, Ou Wang, Weifei Yang, Jiezhong Zhang, Yuhui Xiao, Yang Wang, Depeng Wang, Shoufang Qu, Fang Chen, Jie Huang
Summary: Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical research.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Haiming Ma, Juan Jiang, Jun He, Huifang Liu, Lingling Han, Yan Gong, Biao Li, Zonggang Yu, Shengguo Tang, Yuebo Zhang, Yehui Duan, Yulong Yin, Qinghua Zeng, Jiacheng Yi, Xinglong He, Yongbo Zeng, Kung Seok Kim, Kang Xu, Fan Liang, Jianhua He
Summary: Advances in sequencing technology have allowed for the sequencing and assembly of the Ningxiang pig genome, revealing structural variations compared to European pigs. These findings will be valuable for modern pig breeding and genetic conservation efforts.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Liang Chen, Na Zhao, Jiabao Cao, Xiaolin Liu, Jiayue Xu, Yue Ma, Ying Yu, Xuan Zhang, Wenhui Zhang, Xiangyu Guan, Xiaotong Yu, Zhipeng Liu, Yanqun Fan, Yang Wang, Fan Liang, Depeng Wang, Linhua Zhao, Moshi Song, Jun Wang
Summary: In this study, the researchers used a combination of short and long sequencing reads to analyze the genetic variations in human gut microbiomes. They found that these structural variations are highly distinct between individuals and stable within an individual, and they have significant impacts on the functional differences and correlations with metabolites.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Yu H. Sun, Hongxiao Cui, Chi Song, Jiafei Teng Shen, Xiaoyu Zhuo, Ruoqiao Huiyi Wang, Xiaohui Yu, Rudo Ndamba, Qian Mu, Hanwen Gu, Duolin Wang, Gayathri Guru Murthy, Pidong Li, Fan Liang, Lei Liu, Qing Tao, Ying Wang, Sara Orlowski, Qi Xu, Huaijun Zhou, Jarra Jagne, Omer Gokcumen, Nick Anthony, Xin Zhao, Xin Zhiguo Li
Summary: Unlike in other species, the majority of piRNAs in adult mammalian testes do not have obvious targets. However, piRNA sequences and loci evolve rapidly in mammals compared to the rest of the genome. Through comparative studies and sequencing, it is found that piRNA loci in amniotes experience high rates of structural variation, undergo positive selection to suppress transposable elements, and undergo negative selection to eliminate harmful structural variations. These findings demonstrate the importance of genetic instability at piRNA loci in maintaining genome integrity.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Lin Zhang, Meilan Liu, Hongxu Long, Wei Dong, Asher Pasha, Eddi Esteban, Wenying Li, Xiaoming Yang, Ze Li, Aixia Song, Duo Ran, Guang Zhao, Yanling Zeng, Hao Chen, Ming Zou, Jingjing Li, Fan Liang, Meili Xie, Jiang Hu, Depeng Wang, Heping Cao, Nicholas J. Provart, Liangsheng Zhang, Xiaofeng Tan
GENOMICS PROTEOMICS & BIOINFORMATICS
(2019)