scholarly journals FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations

2014 ◽  
Vol 13 ◽  
pp. CIN.S19519 ◽  
Author(s):  
Oscar Krijgsman ◽  
Christian Benner ◽  
Gerrit A. Meijer ◽  
Mark A. van de Wiel ◽  
Bauke Ylstra
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Software Package ◽  
Array Comparative Genomic Hybridization ◽  
Germ Line ◽  
R Package ◽  
Copy Number Variations ◽  
Comparative Genomic ◽  
Sequencing Data ◽  
Copy Number Aberrations

In order to identify somatic focal copy number aberrations (CNAs) in cancer specimens and to distinguish them from germ-line copy number variations (CNVs), we developed the software package FocalCall. FocalCall enables user-defined size cutoffs to recognize focal aberrations and builds on established array comparative genomic hybridization segmentation and calling algorithms. To distinguish CNAs from CNVs, the algorithm uses matched patient normal signals as references or, if this is not available, a list with known CNVs in a population. Furthermore, FocalCall differentiates between homozygous and heterozygous deletions as well as between gains and amplifications and is applicable to high-resolution array and sequencing data. AVAILABILITY AND IMPLEMENTATION: FocalCall is available as an R-package from: https://github.com/OscarKrijgsman/focalCall . The R-package will be available in Bioconductor.org as of release 3.0.

scholarly journals A customized high-resolution array-comparative genomic hybridization to explore copy number variations in Parkinson’s disease

Neurogenetics ◽  
2016 ◽  
Vol 17 (4) ◽  
pp. 233-244 ◽  
Author(s):  
Valentina La Cognata ◽  
Giovanna Morello ◽  
Giulia Gentile ◽  
Velia D’Agata ◽  
Chiara Criscuolo ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
High Resolution ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Copy Number Variations ◽  
Comparative Genomic ◽  
Genomic Hybridization

scholarly journals Increased Frequency of Copy Number Variations Revealed by Array Comparative Genomic Hybridization in the Offspring of Male Mice Exposed to Low Dose-Rate Ionizing Radiation

2021 ◽  
Vol 22 (22) ◽  
pp. 12437
Author(s):  
Keiji Ogura ◽  
Yoshiko Ayabe ◽  
Chihiro Harada ◽  
Ignacia Braga Tanaka ◽  
Satoshi Tanaka ◽  
...  
Keyword(s):  
Ionizing Radiation ◽  
Dose Rate ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Low Dose ◽  
De Novo ◽  
Copy Number Variations ◽  
Comparative Genomic ◽  
Male Mice ◽  
Low Dose Rate

There is very little information on the transgenerational or genetic effects of low dose-rate ionizing radiation. We report the detection of the transgenerational effects of chronic low dose-rate irradiation in mice, at the molecular level in the whole genome, using array comparative genomic hybridization technology. We observed that the number of the mice with de novo copy number variations (specifically, deletions) was significantly increased in the offspring of C57BL/6J male mice exposed to 20 mGy/day gamma-rays for 400 days (total dose: 8000 mGy), as compared to non-irradiated controls. We did not detect any difference in the size of the de novo deletions between the irradiated and the non-irradiated groups. An analysis of the life span of the offspring suggested a possibility that de novo copy-number variations may be associated with shorter life spans.

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