ArticleBMC bioinformatics2019
CytoConverter: a web-based tool to convert karyotypes to genomic coordinates.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Pervasive chromosomal instability drives the karyotypic evolution of hypodiploid tumours.Genome medicine · 2026Article
- Anti-Neoplastic Activity of Estrogen Receptor Beta in Chemoresistant Triple-Negative Breast Cancer.Cancers · 2025Article
- A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Review
- Article
- Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer.International journal of molecular sciences · 2024Review
- A cloud-based resource for genome coordinate-based exploration and large-scale analysis of chromosome aberrations and gene fusions in cancer.Genes, chromosomes & cancer · 2023Article
- Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.Cell stem cell · 2022Article
- RCytoGPS: an R package for reading and visualizing cytogenetics data.Bioinformatics (Oxford, England) · 2021Article
- Cancer Cytogenetics: Deep Roots, New Branches in the Age of Omics.Cancer genomics & proteomicsReview
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells' karyotype. The nomenclature identifies locations on chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype.
resultsOur tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments.
conclusionsCytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/ . Supplemental Material detailing the underlying algorithms is available.
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