Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
Abstract Background Structural variations (SVs) or copy number variations (CNVs) greatly
impact the functions of the genes encoded in the genome and are responsible for diverse …
impact the functions of the genes encoded in the genome and are responsible for diverse …
Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication
Comparative population genomics offers an excellent opportunity for unraveling the genetic
history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an …
history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an …
SvABA: genome-wide detection of structural variants and indels by local assembly
JA Wala, P Bandopadhayay, NF Greenwald… - Genome …, 2018 - genome.cshlp.org
Structural variants (SVs), including small insertion and deletion variants (indels), are
challenging to detect through standard alignment-based variant calling methods. Sequence …
challenging to detect through standard alignment-based variant calling methods. Sequence …
[HTML][HTML] From DNA human sequence to the chromatin higher order organisation and its biological meaning: using biomolecular interaction networks to understand the …
The three-dimensional structure of the human genome has been proven to have a
significant functional impact on gene expression. The high-order spatial chromatin is …
significant functional impact on gene expression. The high-order spatial chromatin is …
PGBD5 promotes site-specific oncogenic mutations in human tumors
Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac
transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase …
transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase …
Childhood cancer mutagenesis caused by transposase-derived PGBD5
Genomic rearrangements are a hallmark of most childhood tumors, including
medulloblastoma, one of the most common brain tumors in children, but their causes remain …
medulloblastoma, one of the most common brain tumors in children, but their causes remain …
Analysis of structural variants reveal novel selective regions in the genome of Meishan pigs by whole genome sequencing
H Du, X Zheng, Q Zhao, Z Hu, H Wang, L Zhou… - Frontiers in …, 2021 - frontiersin.org
Structural variants (SVs) represent essential forms of genetic variation, and they are
associated with various phenotypic traits in a wide range of important livestock species …
associated with various phenotypic traits in a wide range of important livestock species …
[HTML][HTML] Emerging functions of DNA transposases and oncogenic mutators in childhood cancer development
AG Henssen, A Kentsis - JCI insight, 2018 - ncbi.nlm.nih.gov
Our understanding of the molecular pathogenesis of childhood cancers has advanced
substantially, but their fundamental causes remain poorly understood. Recently, multiple …
substantially, but their fundamental causes remain poorly understood. Recently, multiple …
Seeksv: an accurate tool for somatic structural variation and virus integration detection
Y Liang, K Qiu, B Liao, W Zhu, X Huang, L Li… - …, 2017 - academic.oup.com
Motivation Many forms of variations exist in the human genome including single nucleotide
polymorphism, small insert/deletion (DEL)(indel) and structural variation (SV). Somatically …
polymorphism, small insert/deletion (DEL)(indel) and structural variation (SV). Somatically …
[HTML][HTML] DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data
T Yuan, J Dong, B Jia, H Jiang, Z Zhao, M Zhou - PeerJ, 2024 - peerj.com
Background Tandem duplication (TD) is a common and important type of structural variation
in the human genome. TDs have been shown to play an essential role in many diseases …
in the human genome. TDs have been shown to play an essential role in many diseases …