A combined comparative genomic hybridization and expression microarray analysis of gastric cancer reveals novel molecular subtypes.
Comparative genomic hybridization (CGH), microsatellite instability (MSI) assays, and expression microarrays were used to molecularly subclassify a common set of gastric tumor samples. We identified a number of novel genomic aberrations associated with gastric cancer and discovered that gastric tumors could be grouped by their expression profiles into three broad classes: "tumorigenic," "reactive," and "gastric-like." Patients with gastric-like tumors exhibited a significantly better overall survival than patients belonging to the other two classes (P < 0.05). A novel supervised learning methodology for multiclass prediction was used to identify optimal predictor gene sets that accurately predicted the class of an unknown tumor sample. These predictor sets may prove useful in the development of new diagnostic applications for gastric cancer staging and prognostication.
Tay
Su Ting
ST
Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Republic of Singapore.
Leong
Siew Hong
SH
Yu
Kun
K
Aggarwal
Amit
A
Tan
Soo Yong
SY
Lee
Chee How
CH
Wong
Keith
K
Visvanathan
Jaya
J
Lim
Dennis
D
Wong
Wai Keong
WK
Soo
Khee Chee
KC
Kon
Oi Lian
OL
Tan
Patrick
P
D000230:Adenocarcinoma / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000401:mortality; D000465:Algorithms; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D015993:Life Tables; D008285:Major Histocompatibility Complex; D008679:Metaplasia; D018895:Microsatellite Repeats; D009363:Neoplasm Proteins / Q000032:analysis / Q000145:classification / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D013272:Stomach Diseases / Q000235:genetics / Q000378:metabolism; D013274:Stomach Neoplasms / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000401:mortality; D016019:Survival Analysis
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins