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Genomic Alteration Burden in Advanced Prostate Cancer and Therapeutic Implications [PDF]

Frontiers in Oncology, 2019
The increasing number of patients with sequenced prostate cancer genomes enables us to study not only individual oncogenic mutations, but also capture the global burden of genomic alterations.
Matthew J. Ryan, Matthew J. Ryan, Matthew J. Ryan, Rohit Bose, Rohit Bose, Rohit Bose, Rohit Bose, Rohit Bose   +7 more
doaj   +4 more sources

A Murine Database of Structural Variants Identifies A Candidate Gene for a Spontaneous Murine Lymphoma Model [PDF]

Advanced Science
A more complete map of the pattern of genetic variation among inbred mouse strains is essential for characterizing the genetic architecture of the many available mouse genetic models of important biomedical traits.
Wenlong Ren, Zhuoqing Fang, Egor Dolzhenko, Christopher T. Saunders, Zhuanfen Cheng, Victoria Popic, Gary Peltz   +6 more
doaj   +2 more sources

MetaSVs: A pipeline combining long and short reads for analysis and visualization of structural variants in metagenomes

iMeta, 2023
Structural variants (SVs, including large‐scale insertions, deletions, inversions, and translocations) significantly impact the functions of genes in the microbial genome, and SVs in the microbiome are associated with diverse biological processes and ...
Yuejuan Li, Jiabao Cao, Jun Wang
doaj   +2 more sources

Editorial: Exploring structural variants in plant pangenomics: innovations and applications [PDF]

Frontiers in Plant Science
Jinglong Wang, Qilong Zhou, Yunfei Liu, Risheng Li, Lan Lan, Junliang Zhao, Zefeng Yang, Yong Jia, Haifei Hu   +8 more
doaj   +2 more sources

Experience of Low-Pass Whole-Genome Sequencing-Based Copy Number Variant Analysis: A Survey of Chinese Tertiary Hospitals

Diagnostics, 2022
In China, low-pass whole-genome sequencing (low-pass WGS) is emerging as an alternative diagnostic test to detect copy number variants (CNVs). This survey aimed to study the laboratory practice, service quality, and case volumes of low-pass WGS-based CNV
Yu Zheng, Baosheng Zhu, Jichun Tan, Yichun Guan, The Chinese Genomic Structural Variants Consortium, Cynthia C. Morton, Guangxiu Lu   +6 more
doaj   +1 more source

Rearrangement-mediated cis-regulatory alterations in advanced patient tumors reveal interactions with therapy

Cell Reports, 2021
Summary: The global impact of somatic structural variants (SVs) on gene regulation in advanced tumors with complex treatment histories has been mostly uncharacterized.
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J. Grisdale, Emma Titmuss, Janessa Laskin, Steven J.M. Jones, Isidro Cortes-Ciriano, Marco A. Marra, Chad J. Creighton   +10 more
doaj   +1 more source

Evolutionary genomics: Insights from the invasive European starlings

Frontiers in Genetics, 2023
Two fundamental questions for evolutionary studies are the speed at which evolution occurs, and the way that this evolution may present itself within an organism’s genome.
Katarina C. Stuart, William B. Sherwin, Richard J. Edwards, Lee A Rollins   +3 more
doaj   +1 more source

Enhancers dysfunction in the 3D genome of cancer cells

Frontiers in Cell and Developmental Biology, 2023
Eukaryotic genomes are spatially organized inside the cell nucleus, forming a threedimensional (3D) architecture that allows for spatial separation of nuclear processes and for controlled expression of genes required for cell identity specification and ...
Giulia Della Chiara, Carlos Jiménez, Mohit Virdi, Nicola Crosetto, Nicola Crosetto, Nicola Crosetto, Magda Bienko, Magda Bienko, Magda Bienko   +8 more
doaj   +1 more source

VariantSurvival: a tool to identify genotype–treatment response

Frontiers in Bioinformatics, 2023
Motivation: For a number of neurological diseases, such as Alzheimer’s disease, amyotrophic lateral sclerosis, and many others, certain genes are known to be involved in the disease mechanism. A common question is whether a structural variant in any such
Thomas Krannich, Marina Herrera Sarrias, Hiba Ben Aribi, Moustafa Shokrof, Alfredo Iacoangeli, Ammar Al-Chalabi, Fritz J. Sedlazeck, Ben Busby, Ahmad Al Khleifat   +8 more
doaj   +1 more source

Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases

Biomedicines, 2022
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells.
Valentina La Cognata, Sebastiano Cavallaro   +1 more
doaj   +1 more source