We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.
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http://dx.doi.org/10.5808/GI.2012.10.1.65 | DOI Listing |
NAR Genom Bioinform
March 2025
School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel.
Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications.
View Article and Find Full Text PDFNAR Genom Bioinform
March 2025
Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking.
View Article and Find Full Text PDFEnvironmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA.
View Article and Find Full Text PDFNPJ Antimicrob Resist
January 2025
Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, G1V 0A6 Canada.
Faced with the burden of increasing resistance to antifungals in many fungal pathogens and the constant emergence of new drug-resistant strains, it is essential to assess the importance of various resistance mechanisms. Fungi have relatively plastic genomes and can tolerate genomic copy number variation (CNV) caused by aneuploidy and gene amplification or deletion. In many cases, these genomic changes lead to adaptation to stressful conditions, including those caused by antifungal drugs.
View Article and Find Full Text PDFClin Case Rep
January 2025
Copy number variations (CNVs) contribute to various disorders including intellectual disability, developmental disorders, and cancer. This study identifies a de novo 2.62 Mb deletion at 6q22.
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