Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: In this study, we introduce SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. We demonstrate that SCONCE2 outperforms existing methods in copy number calling and phylogeny estimation. The method enables the inference of tumor phylogenies, providing deeper insights into tumor evolution.
BMC BIOINFORMATICS
(2022)
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
Oncology
Alexa Childs, Christopher D. Steele, Clare Vesely, Francesca M. Rizzo, Leah Ensell, Helen Lowe, Pawan Dhami, Heli Vaikkinen, Tu Vinh Luong, Lucia Conde, Javier Herrero, Martyn Caplin, Christos Toumpanakis, Christina Thirlwell, John A. Hartley, Nischalan Pillay, Tim Meyer
Summary: The study compared single-cell copy number variation (CNV) data of circulating tumor cells (CTCs) with tissue samples to define genomic heterogeneity, revealing recurrent chromosomal alterations and significant intra- and inter-patient genomic heterogeneity. This has implications for identifying therapeutic targets and implementing CTC-biomarkers in cancer.
ENDOCRINE-RELATED CANCER
(2021)
Article
Biotechnology & Applied Microbiology
Wilson Nandolo, Gabor Meszaros, Maria Wurzinger, Liveness J. Banda, Timothy N. Gondwe, Henry A. Mulindwa, Helen N. Nakimbugwe, Emily L. Clark, M. Jennifer Woodward-Greene, Mei Liu, George E. Liu, Curtis P. Van Tassell, Benjamin D. Rosen, Johann Solkner
Summary: This study focused on African goats and developed a detailed copy number variation map, identifying a large number of CNVs with substantial differentiation between populations and population-specific selective pressures. A total of 6231 global CNV regions were identified across all animals, containing genes enriched in important biological functions and cellular components.
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
Biotechnology & Applied Microbiology
Chao Yuan, Zengkui Lu, Tingting Guo, Yaojing Yue, Xijun Wang, Tianxiang Wang, Yajun Zhang, Fujun Hou, Chune Niu, Xiaopin Sun, Hongchang Zhao, Shaohua Zhu, Jianbin Liu, Bohui Yang
Summary: This study identified a large number of CNVs in 32 fine-wool sheep, with CNVRs mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Functional enrichment analysis showed overlap with previously reported sheep CNVRs, with 1855 CNVRs associated with 166 quantitative trait loci.
Article
Biochemistry & Molecular Biology
Xinyi Guo, Terezie Mandakova, Karolina Trachtova, Baris Ozudogru, Jianquan Liu, Martin A. Lysak
Summary: This study reveals the complex genomic history of the mustard family tribe Biscutelleae, showing contentious relationships within this plant family. Genome evolution in Biscutelleae was influenced by pervasive hybridizations and subsequent genome duplications, leading to a complex pattern of relationships among the genera.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Oncology
Michael Menzel, Stephan Ossowski, Sebastian Kral, Patrick Metzger, Peter Horak, Ralf Marienfeld, Melanie Boerries, Steffen Wolter, Markus Ball, Olaf Neumann, Sorin Armeanu-Ebinger, Christopher Schroeder, Uta Matysiak, Hannah Goldschmid, Vincent Schipperges, Axel Fuerstberger, Michael Allgaeuer, Timo Eberhardt, Jakob Niewoehner, Andreas Blaumeiser, Carolin Ploeger, Tobias Bernd Haack, Timothy Kwang Yong Tay, Olga Kelemen, Thomas Pauli, Martina Kirchner, Klaus Kluck, Alexander Ott, Marcus Renner, Jakob Admard, Axel Gschwind, Silke Lassmann, Hans Kestler, Falko Fend, Anna Lena Illert, Martin Werner, Peter Moeller, Thomas Theodor Werner Seufferlein, Nisar Malek, Peter Schirmacher, Stefan Froehling, Daniel Kazdal, Jan Budczies, Albrecht Stenzinger
Summary: With the increasing number of druggable targets and national initiatives for precision oncology, broad genomic profiling for cancer patients has become necessary. Whole exome sequencing (WES) provides unbiased analysis of coding sequences and accurate determination of complex biomarkers. Evaluating the inter-institution variability of clinical WES is important for the development of quality control frameworks.
NPJ PRECISION ONCOLOGY
(2023)
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
Veterinary Sciences
Yangkai Liu, Yanan Mu, Wenxiang Wang, Zulfiqar Ahmed, Xudong Wei, Chuzhao Lei, Zhijie Ma
Summary: In this study, we investigated the copy number variants (CNVs) in Qaidam cattle and found that duplications were more common than deletions in their genome, which may have less harmful effects on gene formation and function. We also identified differential CNVRs and functional genes related to immunity, growth, and adaptability in the Qaidam cattle population compared to other cattle breeds. Our findings provide valuable insights into the genomic characteristics of Chinese cattle breeds and can be used as customized molecular markers in cattle breeding and production.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Genetics & Heredity
Jing Tu, Yue Zhou, Yuhan Tao, Na Lu, Yixuan Yang, Zuhong Lu
Summary: This study evaluated the sensitivity of copy number variation detection in single-cell genomics and suggested that 0.75x sequencing depth with moderate resolution (250 kb bin size) may be a practical guideline. The performance of copy number calling can be optimized based on amplification approach, cell type, and sample complexity.
Article
Genetics & Heredity
Andre E. Minoche, Ben Lundie, Greg B. Peters, Thomas Ohnesorg, Mark Pinese, David M. Thomas, Andreas Zankl, Tony Roscioli, Nicole Schonrock, Sarah Kummerfeld, Leslie Burnett, Marcel E. Dinger, Mark J. Cowley
Summary: ClinSV is a WGS-based framework for integration, annotation, prioritization, and visualization of structural variants with low false positive rates and high reproducibility. In clinical practice, ClinSV identified reportable variants that were undetectable by current clinical microarray designs in a significant percentage of cases.
Article
Multidisciplinary Sciences
Xiaotao Wang, Yu Luan, Feng Yue
Summary: The Hi-C technique is promising for detecting structural variations in human genomes, but lacks algorithms for full-range SV detection. EagleC combines deep-learning and ensemble-learning strategies to predict a full range of SVs at high resolution, uniquely capturing a set of fusion genes. EagleC also effectively captures SVs in other chromatin interaction platforms.
Article
Biotechnology & Applied Microbiology
Huibin Shi, Taotao Li, Manchun Su, Huihui Wang, Qiao Li, Xia Lang, Youji Ma
Summary: In this study, the distribution characteristics of copy number variations (CNVs) in Tibetan sheep were investigated using whole-genome resequencing. The results showed a large number of CNV events in Tibetan sheep, which were associated with their adaptability and complex traits. Functional enrichment analysis revealed that these CNV regions were related to organ development, neural regulation, immune regulation, digestion, and metabolism. In addition, some CNV regions overlapped with quantitative trait loci (QTLs) associated with body weight and growth traits in sheep. Furthermore, significant differences were observed between different breeds, indicating that CNVs may play an important role in population differences in sheep.
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
Oncology
Darawalee Wangsa, Salim Akhter Chowdhury, Michael Ryott, E. Michael Gertz, Goran Elmberger, Gert Auer, Elisabeth Avall Lundqvist, Stefan Kueffer, Philipp Stroebel, Alejandro A. Schaeffer, Russell Schwartz, Eva Munck-Wikland, Thomas Ried, Kerstin Heselmeyer-Haddad
INTERNATIONAL JOURNAL OF CANCER
(2016)
Article
Biotechnology & Applied Microbiology
Theodore Roman, Lu Xie, Russell Schwartz
Article
Biochemical Research Methods
Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schaffer, Russell Schwartz
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2016)
Article
Multidisciplinary Sciences
Gregory R. Smith, Lu Xie, Russell Schwartz
Editorial Material
Biochemical Research Methods
Lonnie Welch, Cath Brooksbank, Russell Schwartz, Sarah L. Morgan, Bruno Gaeta, Alastair M. Kilpatrick, Daniel Mietchen, Benjamin L. Moore, Nicola Mulder, Mark Pauley, William Pearson, Predrag Radivojac, Naomi Rosenberg, Anne Rosenwald, Gabriella Rustici, Tandy Warnow
PLOS COMPUTATIONAL BIOLOGY
(2016)
Article
Biochemical Research Methods
Lu Xie, Gregory R. Smith, Russell Schwartz
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2017)
Article
Biochemical Research Methods
Theodore Roman, Lu Xie, Russell Schwartz
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Mathematical & Computational Biology
Marcus Thomas, Russell Schwartz
BMC SYSTEMS BIOLOGY
(2018)
Article
Biochemical Research Methods
Nicola Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, Anne Rosenwald, Gabriella Rustici, Michael Sierk, Tandy Warnow, Lonnie Welch
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Multidisciplinary Sciences
E. Michael Gertz, Salim Akhter Chowdhury, Woei-Jyh Lee, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Russell Schwartz, Alejandro A. Schaffer
Article
Biochemical Research Methods
Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
Summary: This article discusses the impact of differences in mutational phenotypes among different patients on the risk of cancer progression, finding that nearly a third of the risk can be explained by these differences. Mutational phenotypes serve as important parameters for predicting cancer progression, even after considering other predictive information, showcasing their independent predictive power.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz
Summary: In this study, a tumor phylogeny method called TUSV-ext was developed, which integrates single-nucleotide variants (SNVs), copy number alterations (CNAs), and structural variations (SVs) into a single inference framework. The accuracy and usability of the method were demonstrated through simulations and application to real tumor data, revealing the evolutionary tree and clonal structure of the tumor.
Article
Biochemical Research Methods
Haoyun Lei, Xiaoyan A. Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian Lee, Russell Schwartz
Summary: This study developed a new method to interpret sample collections for which only bulk RNA-seq is available for some samples using reference scRNA-seq. By integrating this information in a Quadratic Programming framework, the method can recover more accurate cell types and corresponding cell type abundances in bulk samples.
Article
Biochemistry & Molecular Biology
Yifeng Tao, Xiaojun Ma, Drake Palmer, Russell Schwartz, Xinghua Lu, Hatice Ulku Osmanbeyoglu
Summary: CITRUS is a neural network-based model that simulates the impact of somatic alterations on transcription factors and transcriptional programs, aiding personalized therapeutic decisions and revealing transcriptional program variations between tumor types. Using self-attention mechanism and hidden nodes, CITRUS predicts patient-specific TF activities.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Xuecong Fu, Haoyun Lei, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Michael Dean, Thomas Ried, Russell Schwartz
Summary: The study developed a joint clustering method combining single-cell DNA sequencing and multiplex interphase fluorescence in situ hybridization data to better understand ploidy changes in tumor evolution.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)