PMID- 23812984
OWN - NLM
STAT- MEDLINE
DCOM- 20131217
LR  - 20220309
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 29
IP  - 13
DP  - 2013 Jul 1
TI  - Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from 
      tumor cell populations.
PG  - i189-98
LID - 10.1093/bioinformatics/btt205 [doi]
AB  - MOTIVATION: Development and progression of solid tumors can be attributed to a 
      process of mutations, which typically includes changes in the number of copies of 
      genes or genomic regions. Although comparisons of cells within single tumors show 
      extensive heterogeneity, recurring features of their evolutionary process may be 
      discerned by comparing multiple regions or cells of a tumor. A useful source of 
      data for studying likely progression of individual tumors is fluorescence in situ 
      hybridization (FISH), which allows one to count copy numbers of several genes in 
      hundreds of single cells. Novel algorithms for interpreting such data 
      phylogenetically are needed, however, to reconstruct likely evolutionary 
      trajectories from states of single cells and facilitate analysis of tumor 
      evolution. RESULTS: In this article, we develop phylogenetic methods to infer 
      likely models of tumor progression using FISH copy number data and apply them to 
      a study of FISH data from two cancer types. Statistical analyses of topological 
      characteristics of the tree-based model provide insights into likely tumor 
      progression pathways consistent with the prior literature. Furthermore, tree 
      statistics from the resulting phylogenies can be used as features for prediction 
      methods. This results in improved accuracy, relative to unstructured gene copy 
      number data, at predicting tumor state and future metastasis. AVAILABILITY: 
      Source code for software that does FISH tree building (FISHtrees) and the data on 
      cervical and breast cancer examined here are available at 
      ftp://ftp.ncbi.nlm.nih.gov/pub/FISHtrees. SUPPLEMENTARY INFORMATION: 
      Supplementary data are available at Bioinformatics online.
FAU - Chowdhury, Salim Akhter
AU  - Chowdhury SA
AD  - Joint Carnegie Mellon/University of Pittsburgh Ph.D. Program in Computational 
      Biology, Lane Center for Computational Biology, Carnegie Mellon University, 
      Pittsburgh, PA 15213, USA. sachowdh@andrew.cmu.edu
FAU - Shackney, Stanley E
AU  - Shackney SE
FAU - Heselmeyer-Haddad, Kerstin
AU  - Heselmeyer-Haddad K
FAU - Ried, Thomas
AU  - Ried T
FAU - Schaffer, Alejandro A
AU  - Schaffer AA
FAU - Schwartz, Russell
AU  - Schwartz R
LA  - eng
GR  - 1R01AI076318/AI/NIAID NIH HHS/United States
GR  - R01 AI076318/AI/NIAID NIH HHS/United States
GR  - 1R01CA140214/CA/NCI NIH HHS/United States
GR  - R01 CA140214/CA/NCI NIH HHS/United States
GR  - Z99 CA999999/Intramural NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, N.I.H., Intramural
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Algorithms
MH  - Breast Neoplasms/classification/*genetics/pathology
MH  - Disease Progression
MH  - Female
MH  - *Gene Dosage
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - *Phylogeny
MH  - Software
MH  - Uterine Cervical Neoplasms/classification/*genetics/pathology
PMC - PMC3694640
EDAT- 2013/07/03 06:00
MHDA- 2013/12/18 06:00
PMCR- 2013/06/19
CRDT- 2013/07/02 06:00
PHST- 2013/07/02 06:00 [entrez]
PHST- 2013/07/03 06:00 [pubmed]
PHST- 2013/12/18 06:00 [medline]
PHST- 2013/06/19 00:00 [pmc-release]
AID - btt205 [pii]
AID - 10.1093/bioinformatics/btt205 [doi]
PST - ppublish
SO  - Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.