Abstract LB190: DNAscopeTM: A novel chromogenic in-situ hybridization technology for high-resolution detection of DNA copy number and structural variations

2021 ◽  
Author(s):  
Li-Chong Wang ◽  
Farzaneh Tondnevis ◽  
Courtney Todorov ◽  
Jayson Gaspar ◽  
Aparna Sahajan ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Copy Number ◽  
Structural Variations ◽  
Dna Copy Number ◽  
Chromogenic In Situ Hybridization

scholarly journals FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In Situ Hybridization of Tissue Sections

2021 ◽  
pp. 176-186
Author(s):  
Geoff Macintyre ◽  
Anna M. Piskorz ◽  
Adam Berman ◽  
Edith Ross ◽  
David B. Morse ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Copy Number ◽  
Process Model ◽  
Poisson Model ◽  
Correction Method ◽  
Dna Copy Number ◽  
Tissue Sections ◽  
Poisson Models

PURPOSE Chromosomal aberration and DNA copy number change are robust hallmarks of cancer. The gold standard for detecting copy number changes in tumor cells is fluorescence in situ hybridization (FISH) using locus-specific probes that are imaged as fluorescent spots. However, spot counting often does not perform well on solid tumor tissue sections due to partially represented or overlapping nuclei. MATERIALS AND METHODS To overcome these challenges, we have developed a computational approach called FrenchFISH, which comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes or a homogeneous Poisson point process model for automated spot counting. RESULTS We benchmarked the performance of FrenchFISH against previous approaches using a controlled simulation scenario and tested it experimentally in 12 ovarian carcinoma FFPE-tissue sections for copy number alterations at three loci (c-Myc, hTERC, and SE7). FrenchFISH outperformed standard spot counting with 74% of the automated counts having < 1 copy number difference from the manual counts and 17% having < 2 copy number differences, while taking less than one third of the time of manual counting. CONCLUSION FrenchFISH is a general approach that can be used to enhance clinical diagnosis on sections of any tissue by both speeding up and improving the accuracy of spot count estimates.

Ultrastructural analysis of the spatial distribution of MRNA

1992 ◽  
Vol 50 (1) ◽  
pp. 552-553
Author(s):  
Gary Bassell ◽  
Robert H. Singer
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Nucleic Acids ◽  
Colloidal Gold ◽  
Dna Probe ◽  
Nucleotide Analogs ◽  
Gold Particles

We have been investigating the spatial distribution of nucleic acids intracellularly using in situ hybridization. The use of non-isotopic nucleotide analogs incorporated into the DNA probe allows the detection of the probe at its site of hybridization within the cell. This approach therefore is compatible with the high resolution available by electron microscopy. Biotinated or digoxigenated probe can be detected by antibodies conjugated to colloidal gold. Because mRNA serves as a template for the probe fragments, the colloidal gold particles are detected as arrays which allow it to be unequivocally distinguished from background.

An automatic analysis method for in situ hybridization using high-resolution image analysis

1989 ◽  
Vol 281 (5) ◽  
pp. 336-341 ◽  
Author(s):  
W. Stolz ◽  
K. Scharffetter ◽  
W. Abmayr ◽  
W. K�ditz ◽  
T. Krieg
Keyword(s):  
Image Analysis ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Automatic Analysis ◽  
Analysis Method ◽  
Resolution Image ◽  
High Resolution Image

scholarly journals Ultrastructural visualization of cytoskeletal mRNAs and their associated proteins using double-label in situ hybridization.

1989 ◽  
Vol 108 (6) ◽  
pp. 2343-2353 ◽  
Author(s):  
R H Singer ◽  
G L Langevin ◽  
J B Lawrence
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Colloidal Gold ◽  
Messenger Rna ◽  
Signal To Noise Ratio ◽  
Simultaneous Detection ◽  
Gold Particles ◽  
Rna Molecules ◽  
Nucleic Acid Molecule

We have been able to visualize cytoskeletal messenger RNA molecules at high resolution using nonisotopic in situ hybridization followed by whole-mount electron microscopy. Biotinated cDNA probes for actin, tubulin, or vimentin mRNAs were hybridized to Triton-extracted chicken embryo fibroblasts and myoblasts. The cells were then exposed to antibodies against biotin followed by colloidal gold-conjugated antibodies and then critical-point dried. Identification of mRNA was possible using a probe fragmented to small sizes such that hybridization of several probe fragments along the mRNA was detected as a string of colloidal gold particles qualitatively and quantitatively distinguishable from nonspecific background. Extensive analysis showed that when eight gold particles were seen in this iterated array, the signal to noise ratio was greater than 30:1. Furthermore, these gold particles were colinear, often spiral, or circular suggesting detection of a single nucleic acid molecule. Antibodies against actin, vimentin, or tubulin proteins were used after in situ hybridization, allowing simultaneous detection of the protein and its cognate message on the same sample. This revealed that cytoskeletal mRNAs are likely to be extremely close to actin protein (5 nm or less) and unlikely to be within 20 nm of vimentin or tubulin filaments. Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. These results indicate that this high resolution in situ hybridization approach is a powerful tool by which to investigate the association of mRNA with the cytoskeleton.

Genome-Wide High-Resolution Screening in Dupuytren's Disease Reveals Common Regions of DNA Copy Number Alterations

2010 ◽  
Vol 35 (7) ◽  
pp. 1172-1183.e7 ◽  
Author(s):  
Barbara B. Shih ◽  
May Tassabehji ◽  
James S. Watson ◽  
Angus D. McGrouther ◽  
Ardeshir Bayat
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Dupuytren’S Disease ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Dupuytren's Disease ◽  
Genome Wide ◽  
Dna Copy Number Alterations

scholarly journals Quantitative real-time RT-PCR and chromogenic in situ hybridization: precise methods to detect HER-2 status in breast carcinoma

BMC Cancer ◽  
2009 ◽  
Vol 9 (1) ◽  
Author(s):  
Fabíola E Rosa ◽  
Sara M Silveira ◽  
Cássia GT Silveira ◽  
Nádia A Bérgamo ◽  
Francisco A Moraes Neto ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Breast Carcinoma ◽  
Real Time ◽  
Rt Pcr ◽  
Her 2 ◽  
Chromogenic In Situ Hybridization

scholarly journals Evaluating HER2 Gene Amplification Using Chromogenic In Situ Hybridization (CISH) Method In Comparison To Immunohistochemistry Method in Breast Carcinoma

2018 ◽  
Vol 6 (11) ◽  
pp. 1977-1981 ◽  
Author(s):  
Hadi Atabati ◽  
Amir Raoofi ◽  
Abdollah Amini ◽  
Reza Masteri Farahani
Keyword(s):  
Breast Cancer ◽  
In Situ Hybridization ◽  
Gene Amplification ◽  
Method Comparison ◽  
Her2 Expression ◽  
Her2 Gene ◽  
Cross Sectional ◽  
Exact Test ◽  
Chromogenic In Situ Hybridization

BACKGROUND: In patients with breast cancer, HER2 gene expression is of a great importance in reacting to Herceptin treatment. To evaluate this event, immunohistochemistry (IHC) has been done routinely on the basis of scoring it and so the patients were divided into 4 groups. Lately, as there have been disagreements about how to treat score 2 patients, chromogenic in situ hybridization (CISH) and florescence in situ hybridization (FISH) are introduced. Since CISH method is more convenient than FISH for gene amplification study, FISH has been substituted by CISH. AIM: The current study is conducted in order to investigate whether using CISH is a better method comparison to IHC method for determines HER2 expression in patients with breast cancer in. METHODS: In this cross-sectional descriptive analytical study, information of 44 female patients with invasive ductal breast cancer were gathered from Imam Reza and Omid Hospital in Mashhad. IHC staining was done for all patients in order to determine the level of HER2 expression, and after scoring them into 4 groups of 0, +1, +2 and +3, CISH staining was carried out for all 4 groups. At the end, results from both methods were statistically evaluated using SPSS software V.22.0. RESULTS: The average age of patients was 50.2 with the standard deviation of 10.96. Using IHC method was observed that 2.6% (1 patient), 26.3% (10 patients), 65.8% (25 patients) and 5.3% (2 patients) percentage of patients had scores of 0, +1, +2 and +3. On the other hand, CISH method showed 36 patients (90%) with no amplifications and 4 (10%) with sever amplifications. In a comparative study using Fisher's exact test (p = 0.000), we found a significant relation between IHC method and CISH method indicating that all patients showing severe amplifications in CISH method, owned scores of +2 and +3 in IHC method. CONCLUSION: According to the present study and comparing the results with similar previous studies, it can be concluded that CISH method works highly effective in determining HER2 expression level in patients with breast cancer. This method is also able to determine the status of patients with score +2 in IHC for their treatment with herceptin

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