Transcription profiling of biopsies from human squamous cell carcinomas to quantify intra-tumoral heterogeneity

ABSTRACT: 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 intra-tumoral heterogeneity in mRNA expression. The aim of our study was to quantify intra-tumoral heterogeneity in head and cancer. Methods: Forty-four fresh frozen biopsies were taken from 22 patients, two 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 80-90% 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 < 0.00001). Conclusions: Two biopsies from the same tumor show far greater similarity in gene expression than biopsies from different tumors, supporting the use of one biopsy for expression profiling.

ORGANISM(S): Homo sapiens

SUBMITTER: Cor Lieftink 

PROVIDER: E-NCMF-7 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress