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
Cell Biology
Maoni Guo, San Ming Wang
Summary: A computational approach was developed to identify a prognostic signature of 11 genes in TNBC, which successfully classified TNBC cases into high- and low-risk groups and showed predictive power in multiple datasets. This novel signature provides a better understanding of genome instability in TNBC and can serve as prognostic markers for clinical TNBC management.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Genetics & Heredity
Jill Rafalko, Erica Soster, Samantha Caldwell, Eyad Almasri, Thomas Westover, Vivian Weinblatt, Philip Cacheris
Summary: This study found that genome-wide cfDNA screening can detect chromosomal abnormalities beyond traditional screening, with an overall PPV of >70% for cases with subchromosomal CNVs. Isolated CNVs had a lower PPV of 61.0% compared to complex CNVs at 93.9%. Detected abnormalities included isolated deletions/duplications and unbalanced structural rearrangements.
GENETICS IN MEDICINE
(2021)
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
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
Genetics & Heredity
Kiely N. James, Shimul Chowdhury, Yan Ding, Sergey Batalov, Kelly Watkins, Yong Hyun Kwon, Lucitia Van Der Kraan, Katarzyna Ellsworth, Stephen F. Kingsmore, Lucia Guidugli
Summary: This study used genome sequencing to detect a wide range of copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types. These genetic alterations accounted for 15.8% of reported variants, with deletions being the most common type. The study also found that additional genetic tests were ordered in some cases, but failed to report the variants detected by genome sequencing.
GENETICS IN MEDICINE
(2024)
Article
Agronomy
Elizabeth Ihien Katche, Antje Schierholt, Heiko C. Becker, Jacqueline Batley, Annaliese S. Mason
Summary: Rapeseed (Brassica napus) is formed by hybridization between Brassica rapa and Brassica oleracea. However, rapeseed has limited genetic diversity due to a limited number of hybridization events and strong breeding selection. Resynthesized B. napus lines could increase genetic variation, but most of them are meiotically unstable and infertile.
Article
Biology
Tejashree H. Modak, Robert Literman, Jonathan B. Puritz, Kevin M. Johnson, Erin M. Roberts, Dina Proestou, Ximing Guo, Marta Gomez-Chiarri, Rachel S. Schwartz
Summary: Genomic structural variations are widely observed in the eastern oyster, showing high interindividual variability and potential impacts on gene function; these variations may play a significant role in genetic diversity and evolutionary success.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Barbara De Kegel, Colm J. Ryan
Summary: Genomic instability is a hallmark of cancer, and the dispensability of paralogs influences tumor genome evolution. It was found that genes with paralogs are more likely to be homozygously deleted, and paralogs that are essential in cancer cell lines are less frequently deleted in tumors.
MOLECULAR SYSTEMS BIOLOGY
(2023)
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
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
Linyong Hu, Liangzhi Zhang, Qi Li, Hongjin Liu, Tianwei Xu, Na Zhao, Xueping Han, Shixiao Xu, Xinquan Zhao, Cunfang Zhang
Summary: This study characterized copy number variations (CNVs) in Tibetan sheep using resequencing data and found a large number of CNVs that are associated with genetic structure, dosage regulation, and expression in the sheep genome. The shared CNV regions (CNVRs) were found to be significantly enriched in various pathways and GO terms related to transporters, sensory perception, and oxygen transport. Several CNVRs were also found to overlap with quantitative trait loci (QTLs) related to growth, body weight, and other traits. Vst analysis revealed significant divergence of certain genes between different ecotypic populations of Tibetan sheep. These findings provide valuable genetic variation resources for further elucidating the genetic basis of distinct phenotypic traits and local adaptation in Tibetan sheep.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
E. Guang-Xin, Dong-Ke Zhou, Zhu-Qing Zheng, Bai-Gao Yang, Xiang-Long Li, Lan-Hui Li, Rong-Yan Zhou, Wen-Hui Nai, Xun-Ping Jiang, Jia-Hua Zhang, Qiong-Hua Hong, Yue-Hui Ma, Ming-Xing Chu, Hui-Jiang Gao, Yong-Ju Zhao, Xing-Hai Duan, Yong-Meng He, Ri-Su Na, Yan-Guo Han, Yan Zeng, Yu Jiang, Yong-Fu Huang
Summary: The study used whole-genome next-generation sequencing technology to investigate the selective sweep of intersex goats from China, revealing candidate genes related to the intersexuality phenotype. It was confirmed that a duplicated fragment downstream of the PIS region was inserted into the PIS locus in intersex Chinese goats. The study suggested that this novel complex PIS variant genome could serve as a clinical diagnostic marker for XX intersexuality in goats from Europe and China.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Seongmin Hong, Yong Pyo Lim, Suk-Yoon Kwon, Ah-Young Shin, Yong-Min Kim
Summary: In polyploids, whole genome duplication plays a significant role in genome expansion, evolution, and diversification. The flowering-time gene family, one of the largest expanded gene families in plants, has functionally diversified through evolution, providing advantages for plant adaptation and survival.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu, Xiangyu Zhao, Wei Ning, Guangshuai Wang, Jinyu Wang, Jing Chen, Kaixuan Diao, Fuxiang Chen, Xue-Song Liu
Summary: This study developed a mechanism-agnostic method to categorize CNAs based on various fragment properties and revealed novel patterns of CNA. The activities of some CNA signatures consistently predicted cancer patients' prognosis. This study provides important insights into the role of CNA in cancer and its potential implications for cancer prognosis, evolution, and etiology.
BRIEFINGS IN BIOINFORMATICS
(2023)