Journal:CytoConverter: A web-based tool to convert karyotypes to genomic coordinates
| Full article title | CytoConverter: A web-based tool to convert karyotypes to genomic coordinates |
|---|---|
| Journal | BMC Bioinformatics |
| Author(s) | Wang, Janet; LaFramboise, Thomas |
| Author affiliation(s) | Case Western Reserve University |
| Primary contact | Email: Thomas dot LaFramboise at case dot edu |
| Year published | 2019 |
| Volume and issue | 20 |
| Page(s) | 467 |
| DOI | [ https://doi.org/10.1186/s12859-019-3062-4 10.1186/s12859-019-3062-4] |
| ISSN | 1471-2105 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://link.springer.com/article/10.1186/s12859-019-3062-4 |
| Download | https://link.springer.com/content/pdf/10.1186%2Fs12859-019-3062-4.pdf (PDF) |
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This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
Abstract
Background: Cytogenetic 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 it 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.
Results: Our 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.
Conclusions: CytoConverter is available as a web-based application and as an R script. Supplemental Material detailing the underlying algorithms is available.
Keywords: cytogenetics, chromosomal abnormalities, karyotypes, text parsing
Background
Many human diseases, particularly cancer, are caused by or driven by gains and losses of chromosomes or chromosomal segments.[1] In cancer, oncogenes are often found within regions of gain, while tumor suppressor genes are frequently deleted.[2] Chromosomal abnormalities also cause many known syndromes, and may be suspected as causes of undiagnosed diseases.[3] As such, testing for gains and losses is an important component of both research and clinical practice.
Abbreviations
AML: Acute myeloid leukemia
ISCN: International System for Human Cytogenomic Nomenclature
NCBI: National Center for Biotechnology Information
NGS: Next-generation sequencing
References
- ↑ Beroukhim, R.; Mermel, C.H.; Porter, D. et al. (2010). "The landscape of somatic copy-number alteration across human cancers". Nature 463 (7283): 899–905. doi:10.1038/nature08822. PMC PMC2826709. PMID 20164920. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826709.
- ↑ Smith, J.C.; Sheltzer, J.M. (2018). "Systematic identification of mutations and copy number alterations associated with cancer patient prognosis". eLife 7: e39217. doi:10.7554/eLife.39217. PMC PMC6289580. PMID 30526857. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289580.
- ↑ Theisen, A.; Shaffer, L.G. (2010). "Disorders caused by chromosome abnormalities". The Application of Clinical Genetics 3: 159–74. doi:10.2147/TACG.S8884. PMC PMC3681172. PMID 23776360. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681172.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. We also added PMCID and DOI when they were missing from the original reference. The original article lists references alphabetically, but this version—by design—lists them in order of appearance.
