TY - GEN

T1 - Computer methods for visualization chromosome-specific DNA sequences in FISH images

AU - Bogomolov, Anton

AU - Karamysheva, Tatyana

AU - Rubtsov, Nikolay

N1 - Funding Information: ACKNOWLEDGMENT The reported study was funded by RFBR according to the research project № 19-015-00084а and by project 0324-2019-0042 of IC&G SB RAS. We thank the Microscopic Center of the Siberian Branch of the Russian Academy of Sciences for granting access to microscopic equipment. Publisher Copyright: © 2020 IEEE. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/7

Y1 - 2020/7

N2 - 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.

AB - 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.

KW - chromosomal in situ suppression hybridization (CISS hybridization)

KW - chromosome-specific DNA sequences

KW - fluorescence in situ hybridization (FISH)

KW - image analysis

KW - interspersed repetitive DNA

UR - http://www.scopus.com/inward/record.url?scp=85094811925&partnerID=8YFLogxK

UR - https://elibrary.ru/item.asp?id=45183449

U2 - 10.1109/CSGB51356.2020.9214751

DO - 10.1109/CSGB51356.2020.9214751

M3 - Conference contribution

AN - SCOPUS:85094811925

T3 - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

SP - 76

EP - 79

BT - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020

Y2 - 6 July 2020 through 10 July 2020

ER -