Computer methods for visualization chromosome-specific DNA sequences in FISH images

Anton Bogomolov, Tatyana Karamysheva, Nikolay Rubtsov

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

Abstract

A great number of interspersed repetitive sequences in chromosomes make it difficult to identify chromosomal material via fluorescence in situ hybridization (FISH). The traditional approach to solve this problem is chromosome in situ suppression hybridization (CISS-hybridization). Unfortunately, it is impossible to be performed or fails with chromosomes of many eukaryote species. The aim of this study was to consider the image enhance procedure [1] and the in silico method of chromosome specific signal visualization (method VISSIS) [2] as alternatives to CISS-hybridization. The effectiveness of approaches for identification of specific signals was estimated by signal-to-background ratio (SNR). The computer methods were applied to images of human chromosomes, obtained with FISH of the whole chromosome painting DNA probes. Results showed that effectiveness of image processing methods depends on ratio of short and line interspersed elements (SINEs/LINEs) in DNA probes. The closer chromosomes in ratio of SINEs/LINEs, the higher specific signal intensities and signal-to-background ratios could be achieved. This suggests that computer methods can be efficient only with application of DNA probes derived from chromosomes characterized with similar ratio of SINE and LINE contents.

Original languageEnglish
Title of host publicationProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages76-79
Number of pages4
ISBN (Electronic)9781728195971
DOIs
Publication statusPublished - Jul 2020
Event2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020 - Novosibirsk, Russian Federation
Duration: 6 Jul 202010 Jul 2020

Publication series

NameProceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

Conference

Conference2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
CountryRussian Federation
CityNovosibirsk
Period06.07.202010.07.2020

Keywords

  • chromosomal in situ suppression hybridization (CISS hybridization)
  • chromosome-specific DNA sequences
  • fluorescence in situ hybridization (FISH)
  • image analysis
  • interspersed repetitive DNA

OECD FOS+WOS

  • 1.01 MATHEMATICS
  • 1.02 COMPUTER AND INFORMATION SCIENCES
  • 1.03 PHYSICAL SCIENCES AND ASTRONOMY
  • 1.06 BIOLOGICAL SCIENCES
  • 3.01 BASIC MEDICAL RESEARCH
  • 5.09 OTHER SOCIAL SCIENCES

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