Article
Agriculture, Dairy & Animal Science
Harshit Kumar, Manjit Panigrahi, K. A. Saravanan, Divya Rajawat, Subhashree Parida, Bharat Bhushan, G. K. Gaur, Triveni Dutt, B. P. Mishra, R. K. Singh
Summary: This study used the Illumina BovineSNP 50 K BeadChip to detect copy number variations (CNVs) in the Tharparkar cattle genome and identified 447 CNV regions. These findings provide crucial information for a better understanding of the indigenous cattle genome.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Snehasmita Panda, Amit Kumar, Gyanendra Kumar Gaur, Sheikh Firdous Ahmad, Anuj Chauhan, Arnav Mehrotra, Triveni Dutt
Summary: In this study, genotype data of Porcine 60K SNP from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) in autosomes. A total of 386 CNVs were identified and aggregated into 115 CNV regions (CNVRs). Approximately 75% of the detected CNVRs were novel. Functional annotation and pathway analysis revealed the enrichment of 267 well-annotated Sus scrofa genes in CNVRs, involved in various biological functions. This study provides a comprehensive overview of CNV distribution in the Indian porcine genome for the first time.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Nora Laseca, Antonio Molina, Mercedes Valera, Alicia Antonini, Sebastian Demyda-Peyras
Summary: This study provides a detailed characterization of CNV regions in the Pura Raza Espanola horse breed, revealing a unique pattern of genomic regions enriched in CNVs and the incidence of CNVs across the entire genome. The study also identifies genes related to olfactory pathways and immune response. The findings contribute to our understanding of CNVs in equines and their impact on genetic and phenotypic variations.
Article
Cell Biology
Yaxi Xu, Jian Hu, Wenlei Fan, Hehe Liu, Yunsheng Zhang, Zhanbao Guo, Wei Huang, Xiaolin Liu, Shuisheng Hou
Summary: This study discovered the existence of variations in the number of cervical vertebrae in duck populations. Most ducks had 15 cervical vertebrae, while a small number had 14 or 16. The number of cervical vertebrae had a positive influence on neck production, with each additional cervical vertebra resulting in an increase of 11 g or 2 cm in duck neck length. Through genome-wide analysis, six copy number variations (CNVs) associated with the number of cervical vertebrae were identified, with the associated CNV regions containing 15 genes including WNT10A and WNT6. These findings are important for understanding variations in the number of vertebrae in ducks and provide a foundation for future duck breeding.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Wei Zhang, Mei Zhou, Linqing Liu, Shiguang Su, Lin Dong, Xinxin Meng, Xueting Li, Chonglong Wang
Summary: This study conducted a genome-wide comparison of CNVs between Wannan black pigs and Asian wild boars, identifying selected CNVs related to muscle, reproduction, residual feed intake, and ear size. The findings provide important information for further research on the genetic basis of complex phenotypic traits in Wannan black pigs and offer guidance for their protection and utilization.
Article
Genetics & Heredity
Li Zhang, Jingru Shi, Jian Ouyang, Riquan Zhang, Yiran Tao, Dongsheng Yuan, Chengkai Lv, Ruiyuan Wang, Baitang Ning, Ruth Roberts, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: The research team developed the X-CNV computational framework, integrating multiple informative features to predict the pathogenicity of CNVs, outperforming other tools. They also proposed an MVP score to quantitatively measure the pathogenic effect of CNVs, demonstrating high discriminative power.
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
Oncology
Shun Yamada, Mitsumasa Osakabe, Noriyuki Uesugi, Naoki Yanagawa, Takayuki Matsumoto, Hiromu Suzuki, Tamotsu Sugai
Summary: This study investigates the association between somatic copy number alterations (SCNAs) and neoplastic progression in colorectal cancer (CRC) tumors. The results suggest that specific SCNAs are required for the acquisition of invasive ability in CRC and certain genes affected by SCNAs can serve as potential markers for invasion.
Article
Genetics & Heredity
Feyza Yilmaz, Megan Null, David Astling, Hung-Chun Yu, Joanne Cole, Stephanie A. Santorico, Benedikt Hallgrimsson, Mange Manyama, Richard A. Spritz, Audrey E. Hendricks, Tamim H. Shaikh
Summary: This study conducted a genome-wide copy number analysis on over 3400 healthy Bantu Africans from Tanzania, identifying more than 400,000 CNVs. Some of the CNVs detected overlapped with genomic regions associated with congenital anomaly syndromes and developmental disorders.
BMC MEDICAL GENOMICS
(2021)
Article
Genetics & Heredity
Md. Panir Choudhury, Zihao Wang, Min Zhu, Shaohua Teng, Jing Yan, Shuwei Cao, Guoqiang Yi, Yuwen Liu, Yuying Liao, Zhonglin Tang
Summary: This study conducted a comprehensive analysis of copy number variations (CNVs) in different horse breeds, and identified genomic regions associated with miniature features. Functional annotation revealed the biological functions and adaptations related to these CNVs.
Article
Computer Science, Information Systems
Tian Zheng, Xinyang Qian, Jiayin Wang
Summary: This paper introduces a transfer learning-based method to accurately genotype structural variations while considering copy number variations (CNVs). By adjusting the weights of instances with different allelic copy numbers, the method maximizes the contribution of all instances to genotyping and minimizes the genotyping errors caused by CNVs.
FRONTIERS OF COMPUTER SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Colin Jackson, Nanette Christie, Sharon Melissa Reynolds, Gerhard C. Marais, Yokateme Tii-kuzu, Madison Caballero, Tamanique Kampman, Erik A. Visser, Sanushka Naidoo, Dominic Kain, Ross W. Whetten, Fikret Isik, Jill Wegrzyn, Gary R. Hodge, Juan J. Acosta, Alexander A. Myburg
Summary: This study focused on gene and genome targeted SNP discovery to develop a genome-wide, multispecies genotyping array for tropical pines. The developed Pitro50K SNP chip will be valuable for population genomics and molecular breeding in a group of pine species, which represent the majority of fast-growing tropical and subtropical pine plantations globally.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agriculture, Dairy & Animal Science
Nitesh Kumar Sharma, Prashant Singh, Bibek Saha, Anuradha Bhardwaj, Mir Asif Iquebal, Yash Pal, Varij Nayan, Sarika Jaiswal, Shiv Kumar Giri, Ram Avatar Legha, T. K. Bhattacharya, Dinesh Kumar, Anil Rai, Bhupendra Nath Tripathi
Summary: Copy number variants (CNVs) are large DNA fragments (>1 kb) that are duplicated or deleted. There is a lack of research on CNVs in animals, especially equine. This study investigates the genomes of Bhutia equines and identifies 619 CNVs, which could have significant implications for economically advantageous genetic features in this breed.
INDIAN JOURNAL OF ANIMAL SCIENCES
(2023)
Article
Dermatology
Q. Zhen, Y. Zhang, Y. Yu, H. Yang, T. Zhang, X. Li, X. Mo, B. Li, J. Wu, Y. Liang, H. Ge, Q. Xu, W. Chen, W. Qian, H. Xu, G. Chen, B. Bai, J. Zhang, Y. Lu, S. Chen, H. Zhang, X. Chen, X. Jin, X. Lin, L. Yong, M. Fang, J. Zhao, S. Wu, D. Jiang, J. Shi, H. Cao, Y. Qiu, S. Li, X. Kang, J. Shen, H. Ma, S. Sun, Y. Fan, M. Bai, Q. Jiang, W. Li, C. Lv, M. Chen, F. Li, Y. Li, L. Sun
Summary: The study identified novel structural variations (SVs) associated with psoriasis through genome-wide screening, enriching the understanding of the genetic architecture and pathogenesis of the disease. The impact of SVs on complex diseases, such as psoriasis, was highlighted, emphasizing the importance of considering SVs in genetic studies of complex diseases.
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Article
Medical Laboratory Technology
Nian Liu, Hui Li, Manman Li, Yanduo Gao, Hong Yan
Summary: This study retrospectively analyzed a series of cases from a single tertiary referral center that performed prenatal single nucleotide polymorphism (SNP) array testing from April 2017 to December 2021. A total of 30 fetuses carrying 16p11.2 copy number variations (CNVs) were identified. The results showed that 16p11.2 CNVs have variable prenatal phenotypes and are frequently inherited from parents with a milder or normal phenotype.
CLINICA CHIMICA ACTA
(2023)