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Series GSE5828 Query DataSets for GSE5828
Status Public on May 01, 2007
Title Gene expression profiling classifies lung squamous cell carcinomas with N1 positive lymph nodes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Using gene expression microarrays, we tested whether lung SCCs that have metastasised to loco-regional lymph nodes (N1/2m) are different to those that directly invade and involve local nodes (N1d). Using 22,323 element microarrays, a non-parametric test identified 126 genes/transcripts that discriminated between N0 (n=35) and N1/2m (n=16) tumours (Wilcoxon-Mann-Whitney U test, P<0.01). Hiearchical clustering of all 59 tumours (including 8 N1d tumours) demonstrated the N1d tumours clustered with the N0 tumours rather than the N1/2m tumours. Next, we built class prediction models from the 35 N0 tumours and 16 N1/2m tumours to predict the class of N1d tumours. All models consistently classified N1d tumours as similar to N0 tumours. This could explain some of the variable response of some N1 tumours to adjuvant chemotherapy, and suggest refinement of the TNM "N" stage nomenclature to adjust for this biological observation to ensure appropriate patients benefit from treatment.
Keywords: non-small cell lung carcinoma, squamous cell, nodal metastasis, TNM staging, expression profiling
 
Overall design Expression profiling using 22K element microarrays of 59 primary lung squamous cell carcinomas.
 
Contributor(s) Larsen JE, Pavey SJ, Clarke BC, Colosimo ML, Bowman RV, Yang IA, Hayward NK, Fong KM
Citation(s) 17601969
Submission date Sep 13, 2006
Last update date Jan 18, 2013
Contact name Jill Everland Larsen
E-mail(s) j.larsen@uq.edu.au
Phone +61731394110
Fax +61731394957
Organization name The Prince Charles Hospital
Department Thoracic Medicine
Lab Thoracic Research Lab
Street address Rode Road, Chermside
City Brisbane
State/province Queensland
ZIP/Postal code 4032
Country Australia
 
Platforms (1)
GPL3877 PRHU05-S1-0006 (PC Human Operon v2 21k)
Samples (59)
GSM115459 Primary Lung SCC Carcinoma Sample_N1
GSM115460 Primary Lung SCC Carcinoma Sample_N2
GSM115461 Primary Lung SCC Carcinoma Sample_N3
Relations
BioProject PRJNA97219

Clinical data header descriptions
SCC Sample ID
Histology
Sex
Age
Pack-year
Differentiation
Stage
Survival time (months)
Survival status

Data table
SCC Sample ID Histology Sex Age Pack-year Differentiation Stage Survival time (months) Survival status
Sample_N1 Squamous cell carcinoma M 72 11 W IB 61.11 D
Sample_N10 Squamous cell carcinoma F 58 80 P IIIB 96.76 A
Sample_N11 Squamous cell carcinoma M 67 50 M IB 80.23 A
Sample_N12 Squamous cell carcinoma F 66 25 P IIB 120.41 A
Sample_N13 Squamous cell carcinoma M 65 53 W IB 100.14 D
Sample_N14 Squamous cell carcinoma M 64 50 M IA 99.58 A
Sample_N15 Squamous cell carcinoma M 60 71 P IA 82.07 A
Sample_N16 Squamous cell carcinoma M 69 50 M IB 92.94 A
Sample_N17 Squamous cell carcinoma M 71 8 W IB 157.54 A
Sample_N18 Squamous cell carcinoma F 75 57 M IA 98.86 A
Sample_N19 Squamous cell carcinoma F 74 15 P IB 92.06 A
Sample_N2 Squamous cell carcinoma M 68 40 W IA 153.63 D
Sample_N20 Squamous cell carcinoma F 50 30 P IB 46.59 D
Sample_N21 Squamous cell carcinoma M 69 43 P IB 70.05 A
Sample_N22 Squamous cell carcinoma M 84 38 P IA 60.29 A
Sample_N23 Squamous cell carcinoma M 64 171 M IIIB 62.98 A
Sample_N24 Squamous cell carcinoma F 75 45 P IB 64.6 A
Sample_N25 Squamous cell carcinoma M 68 75 P IB 46.75 A
Sample_N26 Squamous cell carcinoma F 44 . W IIA 161.45 A
Sample_N27 Squamous cell carcinoma M 72 83 M IIIA 61.5 D

Total number of rows: 59

Table truncated, full table size 4 Kbytes.




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