scholarly journals frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections

2018 ◽  
Author(s):  
Geoff Macintyre ◽  
Anna M Piskorz ◽  
Edith Ross ◽  
David B Morse ◽  
Ke Yuan ◽  
...  
Keyword(s):  
Copy Number ◽  
Process Model ◽  
In Situ Hybridisation ◽  
Poisson Model ◽  
Correction Method ◽  
Fluorescence In Situ Hybridisation ◽  
Dna Copy Number ◽  
Tissue Sections ◽  
Poisson Models

Chromosomal aberration and DNA copy number change are robust hallmarks of cancer. Imaging of spots generated using fluorescence in situ hybridisation (FISH) of locus specific probes is routinely used to detect copy number changes in tumour nuclei. However, it often does not perform well on solid tumour tissue sections, where partially represented or overlapping nuclei are common. 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 homogenous Poisson Point Process model for automated spot counting. We benchmarked the performance of FrenchFISH against previous approaches in a controlled simulation scenario and exemplify its use in 12 ovarian cancer FFPE-tissue sections, for which we assess copy number alterations in three loci (c-Myc, hTERC and SE7). We show that FrenchFISH outperforms standard spot counting approaches and that the automated spot counting is significantly faster than manual without loss of performance. FrenchFISH is a general approach that can be used to enhance clinical diagnosis on sections of any tissue.

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.

scholarly journals Clinical significance of ESR1 gene copy number changes in breast cancer as measured by fluorescence in situ hybridisation

2012 ◽  
Vol 66 (2) ◽  
pp. 140-145 ◽  
Author(s):  
Ching-Hung Lin ◽  
Jacqueline M Liu ◽  
Yen-Shen Lu ◽  
Chieh Lan ◽  
Wei-Chung Lee ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Clinical Significance ◽  
Copy Number ◽  
In Situ Hybridisation ◽  
Gene Copy Number ◽  
Disease Free Survival ◽  
Gene Copy ◽  
Fluorescence In Situ Hybridisation ◽  
Copy Number Changes

AimsThe ESR1 gene encodes for oestrogen receptor (ER) α, which plays a crucial role in mammary carcinogenesis and clinical outcome in patients with breast cancer. However, the clinical significance of the ESR1 gene copy number change for breast cancer has not been clarified.MethodsESR1 gene copy number was determined by fluorescence in situ hybridisation (FISH) on tissue sections. A minimum of 20 tumour cells were counted per section, and a FISH ratio of ESR1 gene to CEP6 ≥2.0 was considered ESR1 amplification. A ratio >1.2 but <2.0 was considered ESR1 gain. The ESR1 copy number was further measured by quantitative real-time PCR (Q-PCR) with ASXL2 as a reference.ResultsFISH revealed ESR1 amplification in six cases (4.0%) and ESR1 gain in 13 cases (8.7%) from a total of 150 cases. ESR1 gain and amplification were more common in older patients (p<0.001), and correlated well with ER protein expression (p=0.03) measured by immunohistochemistry, and ESR1 copy number (p<0.001) measured by Q-PCR. Furthermore, the multivariate analysis revealed that ESR1 amplification was associated with a shorter disease-free survival (HR=5.56, p=0.03) and a shorter overall survival (HR=5.11, p=0.04).ConclusionsIn general, the frequency of ESR1 amplification in breast cancer is low when measured by FISH in large sections. ESR1 gain and amplification in breast cancer may be associated with older age and poorer outcomes.

scholarly journals Rapid Multi-Hybridisation FISH Screening for Balanced Porcine Reciprocal Translocations Suggests a Much Higher Abnormality Rate Than Previously Appreciated

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 250
Author(s):  
Rebecca E O’Connor ◽  
Lucas G Kiazim ◽  
Claudia C Rathje ◽  
Rebecca L Jennings ◽  
Darren K Griffin
Keyword(s):  
Semen Analysis ◽  
In Situ Hybridisation ◽  
Economic Loss ◽  
Environmental Damage ◽  
Fluorescence In Situ Hybridisation ◽  
Reciprocal Translocations ◽  
Chromosome Translocations ◽  
Farrowing Rate ◽  
Significant Economic Loss

With demand rising, pigs are the world’s leading source of meat protein; however significant economic loss and environmental damage can be incurred if boars used for artificial insemination (AI) are hypoprolific (sub-fertile). Growing evidence suggests that semen analysis is an unreliable tool for diagnosing hypoprolificacy, with litter size and farrowing rate being more applicable. Once such data are available, however, any affected boar will have been in service for some time, with significant financial and environmental losses incurred. Reciprocal translocations (RTs) are the leading cause of porcine hypoprolificacy, reportedly present in 0.47% of AI boars. Traditional standard karyotyping, however, relies on animal specific expertise and does not detect more subtle (cryptic) translocations. Previously, we reported development of a multiple hybridisation fluorescence in situ hybridisation (FISH) strategy; here, we report on its use in 1641 AI boars. A total of 15 different RTs were identified in 69 boars, with four further animals XX/XY chimeric. Therefore, 4.5% had a chromosome abnormality (4.2% with an RT), a 0.88% incidence. Revisiting cases with both karyotype and FISH information, we reanalysed captured images, asking whether the translocation was detectable by karyotyping alone. The results suggest that chromosome translocations in boars may be significantly under-reported, thereby highlighting the need for pre-emptive screening by this method before a boar enters a breeding programme.

Monitoring HIV-1 treatment in immune-cell subsets with ultrasensitive fluorescence-in-situ hybridisation

The Lancet ◽  
1999 ◽  
Vol 353 (9148) ◽  
pp. 211-212 ◽  
Author(s):  
Bruce K Patterson ◽  
Mary Ann Czerniewski ◽  
John Pottage ◽  
Michelle Agnoli ◽  
Harold Kessler ◽  
...  
Keyword(s):  
Immune Cell ◽  
In Situ Hybridisation ◽  
Fluorescence In Situ Hybridisation ◽  
Immune Cell Subsets ◽  
Hiv 1

Assignment of the human slow skeletal muscle troponin gene (TNNI1) to 1q32 by fluorescence in situ hybridisation

1993 ◽  
Vol 62 (2-3) ◽  
pp. 181-182 ◽  
Author(s):  
H.J. Eyre ◽  
P.A. Akkari ◽  
C. Meredith ◽  
S.D. Wilton ◽  
D.C. Callen ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
In Situ Hybridisation ◽  
Fluorescence In Situ Hybridisation ◽  
Slow Skeletal Muscle
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