PMID- 33570999
OWN - NLM
STAT- MEDLINE
DCOM- 20210831
LR  - 20240210
IS  - 2473-4276 (Electronic)
IS  - 2473-4276 (Linking)
VI  - 5
DP  - 2021 Feb
TI  - FrenchFISH: Poisson Models for Quantifying DNA Copy Number From Fluorescence In 
      Situ Hybridization of Tissue Sections.
PG  - 176-186
LID - 10.1200/CCI.20.00075 [doi]
LID - CCI.20.00075
AB  - 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.
FAU - Macintyre, Geoff
AU  - Macintyre G
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - Piskorz, Anna M
AU  - Piskorz AM
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - Berman, Adam
AU  - Berman A
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - Ross, Edith
AU  - Ross E
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - Morse, David B
AU  - Morse DB
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
AD  - Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, 
      UK.
FAU - Yuan, Ke
AU  - Yuan K
AD  - University of Glasgow, Glasgow, UK.
FAU - Ennis, Darren
AU  - Ennis D
AD  - Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
AD  - Department of Surgery and Cancer, Imperial College London, UK.
FAU - Pike, Jeremy A
AU  - Pike JA
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
AD  - Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham 
      and Nottingham, UK.
FAU - Goranova, Teodora
AU  - Goranova T
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - McNeish, Iain A
AU  - McNeish IA
AD  - Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
AD  - Department of Surgery and Cancer, Imperial College London, UK.
FAU - Brenton, James D
AU  - Brenton JD
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
FAU - Markowetz, Florian
AU  - Markowetz F
AD  - Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK.
LA  - eng
GR  - C14303/A17197/CRUK_/Cancer Research UK/United Kingdom
GR  - A18072/CRUK_/Cancer Research UK/United Kingdom
GR  - 28290/CRUK_/Cancer Research UK/United Kingdom
GR  - A19274/CRUK_/Cancer Research UK/United Kingdom
GR  - 19274/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - JCO Clin Cancer Inform
JT  - JCO clinical cancer informatics
JID - 101708809
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - *Chromosome Aberrations
MH  - Computer Simulation
MH  - DNA
MH  - *DNA Copy Number Variations/genetics
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
PMC - PMC8140799
EDAT- 2021/02/12 06:00
MHDA- 2021/09/01 06:00
PMCR- 2022/02/11
CRDT- 2021/02/11 17:12
PHST- 2021/02/11 17:12 [entrez]
PHST- 2021/02/12 06:00 [pubmed]
PHST- 2021/09/01 06:00 [medline]
PHST- 2022/02/11 00:00 [pmc-release]
AID - CCI.20.00075 [pii]
AID - 10.1200/CCI.20.00075 [doi]
PST - ppublish
SO  - JCO Clin Cancer Inform. 2021 Feb;5:176-186. doi: 10.1200/CCI.20.00075.