PMID- 19351364
OWN - NLM
STAT- MEDLINE
DCOM- 20090506
LR  - 20090408
IS  - 1440-1827 (Electronic)
IS  - 1320-5463 (Linking)
VI  - 59
IP  - 4
DP  - 2009 Apr
TI  - Copy number estimation algorithms and fluorescence in situ hybridization to 
      describe copy number alterations in human tumors.
PG  - 218-28
LID - 10.1111/j.1440-1827.2009.02354.x [doi]
AB  - The platforms of high-resolution genetic analysis of human tumors have become 
      popular, and several copy number estimation algorithms have been applied to the 
      data generated by single-nucleotide polymorphism microarrays. Although 
      comparisons have been made between several different platforms or methodologies, 
      there has never been a robust comparison of different copy number estimation 
      algorithms, and the validity of the estimations in comparison with multiple 
      fluorescence in situ hybridization (FISH) data in tumors has rarely been 
      addressed. In the present study the dataset that the Affymetrix 250K Nsp array 
      generated in two cancer cases was used to compare the two widely used algorithms 
      for estimating copy number alterations (CNA): the genotyping microarray-based 
      copy number variation (CNV) analysis (GEMCA) algorithm and the copy number 
      analyzer for Affymetrix Genechip mapping (CNAG) algorithm. Considerable 
      differences were noticed between the estimations by these two algorithms, because 
      of the difference in the formula used to calculate the threshold values. Both 
      algorithms yielded highly consistent data with the FISH results, but CNAG was 
      more stringent for detecting loss. There were areas in which both algorithms 
      provided gains, but FISH showed no change. It will be interesting to pursue the 
      reasons for these remaining discrepancies.
FAU - Suzuki, Masaya
AU  - Suzuki M
AD  - Department of Pathology, Hamamatsu University School of Medicine, Hamamatsu, 
      Japan.
FAU - Nagura, Kiyoko
AU  - Nagura K
FAU - Igarashi, Hisaki
AU  - Igarashi H
FAU - Tao, Hong
AU  - Tao H
FAU - Midorikawa, Yutaka
AU  - Midorikawa Y
FAU - Kitayama, Yasuhiko
AU  - Kitayama Y
FAU - Sugimura, Haruhiko
AU  - Sugimura H
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - Australia
TA  - Pathol Int
JT  - Pathology international
JID - 9431380
SB  - IM
MH  - *Algorithms
MH  - Female
MH  - *Gene Dosage
MH  - Gene Expression Profiling
MH  - Humans
MH  - *In Situ Hybridization, Fluorescence
MH  - Male
MH  - Middle Aged
MH  - Neoplasms/*genetics
MH  - Oligonucleotide Array Sequence Analysis/*methods
MH  - Polymorphism, Single Nucleotide
EDAT- 2009/04/09 09:00
MHDA- 2009/05/07 09:00
CRDT- 2009/04/09 09:00
PHST- 2009/04/09 09:00 [entrez]
PHST- 2009/04/09 09:00 [pubmed]
PHST- 2009/05/07 09:00 [medline]
AID - PIN2354 [pii]
AID - 10.1111/j.1440-1827.2009.02354.x [doi]
PST - ppublish
SO  - Pathol Int. 2009 Apr;59(4):218-28. doi: 10.1111/j.1440-1827.2009.02354.x.