Heterogeneity of gene expression profiles in head and neck cancer.
BACKGROUND
Results of gene expression profiling studies from different institutes often lack consistency. This could be due to the use of different microarray platforms and protocols, or to intratumoral heterogeneity in mRNA expression. The aim of our study was to quantify intratumoral heterogeneity in head and neck cancer.


METHODS
Forty-four fresh frozen biopsies were taken from 22 patients, 2 per tumor. RNA was extracted, tested for quality, amplified, labeled, and hybridized to a 35k oligoarray.


RESULTS
Unsupervised clustering analyses using all genes, the most variable genes, or random gene sets showed that 80% to 90% of biopsy pairs clustered together. A within-pair-between-pair scatter ratio analysis showed that the similarity between matching pairs was significantly greater than that between random pairs (p <.00001).


CONCLUSIONS
Two biopsies from the same tumor show far greater similarity in gene expression than biopsies from different tumors, supporting the use of 1 biopsy for expression profiling.
Pramana
Jimmy
J
Division of Experimental Therapy, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
Pimentel
Nuno
N
Hofland
Ingrid
I
Wessels
Lodewijk F A
LF
van Velthuysen
Marie-Louise F
ML
Atsma
Douwe
D
Rasch
Coen R N
CR
van den Brekel
Michiel W M
MW
Begg
Adrian C
AC
D000368:Aged; D000369:Aged, 80 and over; D001706:Biopsy; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling; D018740:Genetic Heterogeneity; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000473:pathology; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000302:isolation & purification
D012313:RNA