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| Status |
Public on Oct 01, 2006 |
| Title |
Survey of Intra- and Inter-Tumour Heterogeneity of Gene Expression in Cervical Cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Purpose: To explore intratumor heterogeneity in gene expression profiles from patients with cervical cancer.
Experimental Design: A total of 33 biopsies were obtained from 11 patients, sampling between two and five different areas for each tumor.The extracted RNAwas hybridized onto the Affymetrix U133 Plus 2.0 oligonucleotide chip. The variance of expression within a patient (W), between patients (B) and the total variance (T =W + B) were calculated for each ProbeSet, and the ratio W/T was used as a measure of intratumor heterogeneity. Gene Ontology functional analysis was done to assess the function of genes that had high W/T (top 10%) and low W/T (bottom 10%) values.
Results: In total, 448 ProbeSets (2.2% of the total) had W/T < 0.10, indicating low intratumor heterogeneity, and 537 ProbeSets (2.7% of the total) had W/T > 0.90, indicating high intratumor heterogeneity. In total 14,473 ProbeSets (72.4%) had higher intertumor than intratumor heterogeneity (W/T < 0.5). Genes with low intratumor heterogeneity were characterized by a statistically significant enrichment of immune-related functions (P < 0.0001). Genes with high intratumor heterogeneity were characterized by a significant tendency towards nuclear localization and nucleic acid binding (both P < 0.0001). For genes with W/T > 0.5, more than six biopsies would be required to minimize the intratumoral heterogeneity to <0.15; if W/T is 0.3 to 0.4, four biopsies are required; and for low W/T of 0.16 to 0.3, only two to three biopsies would be needed.
Conclusion: Although the intratumor heterogeneity was low for the majority of the tested ProbeSets, for many genes, multiple biopsies are required to obtain a reliable estimate of gene expression.
Keywords: disease state comparison
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| Overall design |
Sixty-six flash-frozen punch biopsies were obtained from 16 patients with cervical cancer who were undergoing examination under general anesthesia as part of their pretreatment evaluation for cervical cancer.
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| Contributor(s) |
Bachtiary B, Boutros PC, Pintilie M, Shi W, Bastianutto C, Li JH, Schwock J, Zhang W, Penn LZ, Jurisica I, Fyles A, Liu FF |
| Citation(s) |
17020965 |
| Submission date |
Sep 07, 2006 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Paul C Boutros |
| E-mail(s) |
Paul.Boutros@utoronto.ca
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| Organization name |
Ontario Institute for Cancer Research
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| Street address |
101 College Street, Suite 800
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (33)
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| GSM135229 |
Cervical Cancer Patient 10, Biopsy 6 |
| GSM135230 |
Cervical Cancer Patient 10, Biopsy 3 |
| GSM135231 |
Cervical Cancer Patient 6, Biopsy 2 |
| GSM135232 |
Cervical Cancer Patient 4, Biopsy 2 |
| GSM135233 |
Cervical Cancer Patient 1, Biopsy 3 |
| GSM135234 |
Cervical Cancer Patient 1, Biopsy 6 |
| GSM135235 |
Cervical Cancer Patient 4, Biopsy 1 |
| GSM135236 |
Cervical Cancer Patient 4, Biopsy 3 |
| GSM135237 |
Cervical Cancer Patient 12, Biopsy 1 |
| GSM135238 |
Cervical Cancer Patient 12, Biopsy 4 |
| GSM135239 |
Cervical Cancer Patient 12, Biopsy 5 |
| GSM135240 |
Cervical Cancer Patient 15, Biopsy 2 |
| GSM135241 |
Cervical Cancer Patient 16, Biopsy 1 |
| GSM135242 |
Cervical Cancer Patient 6, Biopsy 1 |
| GSM135243 |
Cervical Cancer Patient 6, Biopsy 4 |
| GSM135244 |
Cervical Cancer Patient 7, Biopsy 1 |
| GSM135245 |
Cervical Cancer Patient 10, Biopsy 2 |
| GSM135246 |
Cervical Cancer Patient 10, Biopsy 7 |
| GSM135247 |
Cervical Cancer Patient 11, Biopsy 6 |
| GSM135248 |
Cervical Cancer Patient 15, Biopsy 3 |
| GSM135249 |
Cervical Cancer Patient 16, Biopsy 2 |
| GSM135250 |
Cervical Cancer Patient 11, Biopsy 7 |
| GSM135251 |
Cervical Cancer Patient 6, Biopsy 5 |
| GSM135252 |
Cervical Cancer Patient 6, Biopsy 3 |
| GSM135253 |
Cervical Cancer Patient 15, Biopsy 4 |
| GSM135254 |
Cervical Cancer Patient 9, Biopsy 2 |
| GSM135255 |
Cervical Cancer Patient 9, Biopsy 3 |
| GSM135256 |
Cervical Cancer Patient 13, Biopsy 5 |
| GSM135257 |
Cervical Cancer Patient 13, Biopsy 3 |
| GSM135258 |
Cervical Cancer Patient 10, Biopsy 5 |
| GSM135259 |
Cervical Cancer Patient 7, Biopsy 4 |
| GSM135260 |
Cervical Cancer Patient 1, Biopsy 4 |
| GSM135261 |
Cervical Cancer Patient 9, Biopsy 5 |
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| Relations |
| BioProject |
PRJNA97143 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE5787_RAW.tar |
250.2 Mb |
(http)(custom) |
TAR (of CEL, EXP) |
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