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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

A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes

Biology, 2022
As one of the major structural constituents, mobile elements comprise more than half of the human genome, among which Alu, L1, and SVA elements are still active and continue to generate new offspring.
Reza Halabian, Wojciech Makałowski
doaj   +1 more source

A genotype–phenotype correlation in split-hand/foot malformation type 1: further refinement of the phenotypic subregions within the 7q21.3 locus

Frontiers in Molecular Biosciences, 2023
Background: Split-hand/foot malformation type 1 (SHFM1) refers to the group of rare congenital limb disorders defined by the absence or hypoplasia of the central rays of the autopods with or without accompanying anomalies, such as hearing loss ...
Anna Sowińska-Seidler, Magdalena Socha, Anna Szoszkiewicz, Anna Materna-Kiryluk, Anna Materna-Kiryluk, Aleksander Jamsheer, Aleksander Jamsheer   +6 more
doaj   +1 more source

Detection of mobile elements insertions for routine clinical diagnostics in targeted sequencing data

Molecular Genetics & Genomic Medicine, 2021
Background Targeted sequencing approaches such as gene panel or exome sequencing have become standard of care for the diagnosis of rare and common genetic disease.
German Demidov, Joohyun Park, Sorin Armeanu‐Ebinger, Cristiana Roggia, Ulrike Faust, Isabell Cordts, Maria Blandfort, Tobias B. Haack, Christopher Schroeder, Stephan Ossowski   +9 more
doaj   +1 more source