Imperial College London
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ProfessorIainMcNeish

Faculty of Medicine, Department of Surgery & Cancer

Chair in Oncology
 
 
 
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Contact

 

+44 (0)20 7594 2185i.mcneish Website

 
 
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Assistant

 

Ms Sophie Lions +44 (0)20 7594 2792

 
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Location

 

G036Institute of Reproductive and Developmental BiologyHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Macintyre:2021:10.1200/CCI.20.00075,
author = {Macintyre, G and Piskorz, AM and Berman, A and Ross, E and Morse, DB and Yuan, K and Ennis, D and Pike, JA and Goranova, T and McNeish, I and Brenton, JD and Markowetz, F},
doi = {10.1200/CCI.20.00075},
journal = {Journal of Clinical Oncology},
pages = {176--186},
title = {FrenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections},
url = {http://dx.doi.org/10.1200/CCI.20.00075},
volume = {5},
year = {2021}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - PURPOSEChromosomal 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 METHODSTo 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.RESULTSWe 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.CONCLUSIONFrenchFISH 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.
AU  - Macintyre,G
AU  - Piskorz,AM
AU  - Berman,A
AU  - Ross,E
AU  - Morse,DB
AU  - Yuan,K
AU  - Ennis,D
AU  - Pike,JA
AU  - Goranova,T
AU  - McNeish,I
AU  - Brenton,JD
AU  - Markowetz,F
DO  - 10.1200/CCI.20.00075
EP  - 186
PY  - 2021///
SN  - 0732-183X
SP  - 176
TI  - FrenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections
T2  - Journal of Clinical Oncology
UR  - http://dx.doi.org/10.1200/CCI.20.00075
UR  - http://hdl.handle.net/10044/1/86012
VL  - 5
ER  -
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