PMID- 23554930
OWN - NLM
STAT- MEDLINE
DCOM- 20131017
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 8
IP  - 3
DP  - 2013
TI  - Classify hyperdiploidy status of multiple myeloma patients using gene expression 
      profiles.
PG  - e58809
LID - 10.1371/journal.pone.0058809 [doi]
LID - e58809
AB  - Multiple myeloma (MM) is a cancer of antibody-making plasma cells. It frequently 
      harbors alterations in DNA and chromosome copy numbers, and can be divided into 
      two major subtypes, hyperdiploid (HMM) and non-hyperdiploid multiple myeloma 
      (NHMM). The two subtypes have different survival prognosis, possibly due to 
      different but converging paths to oncogenesis. Existing methods for identifying 
      the two subtypes are fluorescence in situ hybridization (FISH) and copy number 
      microarrays, with increased cost and sample requirements. We hypothesize that 
      chromosome alterations have their imprint in gene expression through dosage 
      effect. Using five MM expression datasets that have HMM status measured by FISH 
      and copy number microarrays, we have developed and validated a K-nearest-neighbor 
      method to classify MM into HMM and NHMM based on gene expression profiles. 
      Classification accuracy for test datasets ranges from 0.83 to 0.88. This 
      classification will enable researchers to study differences and commonalities of 
      the two MM subtypes in disease biology and prognosis using expression datasets 
      without need for additional subtype measurements. Our study also supports the 
      advantages of using cancer specific characteristics in feature design and pooling 
      multiple rounds of classification results to improve accuracy. We provide R 
      source code and processed datasets at www.ChengLiLab.org/software.
FAU - Li, Yingxiang
AU  - Li Y
AD  - Department of Bioinformatics, School of Life Science and Technology, Tongji 
      University, Shanghai, China.
FAU - Wang, Xujun
AU  - Wang X
FAU - Zheng, Haiyang
AU  - Zheng H
FAU - Wang, Chengyang
AU  - Wang C
FAU - Minvielle, Stephane
AU  - Minvielle S
FAU - Magrangeas, Florence
AU  - Magrangeas F
FAU - Avet-Loiseau, Herve
AU  - Avet-Loiseau H
FAU - Shah, Parantu K
AU  - Shah PK
FAU - Zhang, Yong
AU  - Zhang Y
FAU - Munshi, Nikhil C
AU  - Munshi NC
FAU - Li, Cheng
AU  - Li C
LA  - eng
GR  - P01-78378/PHS HHS/United States
GR  - R01-124929/PHS HHS/United States
GR  - P01 CA078378/CA/NCI NIH HHS/United States
GR  - P01 CA155258/CA/NCI NIH HHS/United States
GR  - R01 GM077122/GM/NIGMS NIH HHS/United States
GR  - P50 CA100707/CA/NCI NIH HHS/United States
GR  - P50-100007/PHS HHS/United States
GR  - P01-155258/PHS HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20130315
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
SB  - IM
MH  - Gene Dosage
MH  - *Gene Expression Profiling
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Multiple Myeloma/diagnosis/*genetics/mortality
MH  - *Polyploidy
MH  - Reproducibility of Results
MH  - Trisomy
PMC - PMC3598955
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2013/04/05 06:00
MHDA- 2013/10/18 06:00
PMCR- 2013/03/15
CRDT- 2013/04/05 06:00
PHST- 2012/10/06 00:00 [received]
PHST- 2013/02/07 00:00 [accepted]
PHST- 2013/04/05 06:00 [entrez]
PHST- 2013/04/05 06:00 [pubmed]
PHST- 2013/10/18 06:00 [medline]
PHST- 2013/03/15 00:00 [pmc-release]
AID - PONE-D-12-30811 [pii]
AID - 10.1371/journal.pone.0058809 [doi]
PST - ppublish
SO  - PLoS One. 2013;8(3):e58809. doi: 10.1371/journal.pone.0058809. Epub 2013 Mar 15.