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Series GSE5123

Query DataSets for GSE5123

Status

Public on Nov 21, 2006

Title

Expression profiling defines a recurrence signature in lung squamous cell carcinoma

Organism

Homo sapiens

Experiment type

Expression profiling by array

Summary

Lung cancer remains the leading cause of cancer death worldwide. Overall 5-year survival is about 10-15% and despite curative intent surgery, treatment failure is primarily due to recurrent disease. Conventional prognostic markers are unable to determine which patients with completely resected disease within each stage group are likely to relapse. To identify a gene signature associated with recurrent squamous cell carcinoma (SCC) of lung, we analyzed primary tumour gene expression for a total of fifty-one SCCs (stage I-III) on 22,323 element microarrays, comparing expression profiles for individuals who remained disease-free for a minimum of 36 months with those from individuals whose disease recurred within 18 months of complete resection. Cox proportional hazards modeling with leave-one-out cross-validation identified a 70-gene capable of predicting the likelihood of tumor recurrence and a 79-gene signature predictive for overall survival. These two signatures were pooled to generate a 111-gene classifier which achieved an overall predictive accuracy for disease recurrence of 72% (77% sensitivity, 67% specificity) in an independent set of fifty-eight stage I-III SCCs. This classifier also predicted differences in survival (log-rank P=0.0008, hazard ratio (HR), 3.8 [95% confidence interval, 1.6-8.7]), and was superior to conventional prognostic markers such as TNM stage or N stage in predicting patient outcome. Genome-wide profiling has revealed a distinct gene expression profile for recurrent lung SCC which may be clinically useful as a prognostic tool.
Keywords: non-small cell lung carcinoma, squamous cell, tumor recurrence, expression profiling

Overall design

Expression profiling using 22K element microarrays of 51 primary lung squamous cell carcinomas.

Contributor(s)

Larsen JE, Pavey SJ, Passmore LH, Bowman RV, Clarke BE, Hayward NK, Fong KM

Citation(s)

17082175

Submission date

Jun 21, 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 (51)

More...

GSM115459	Primary Lung SCC Carcinoma Sample_N1
GSM115460	Primary Lung SCC Carcinoma Sample_N2
GSM115461	Primary Lung SCC Carcinoma Sample_N3

GSM115462	Primary Lung SCC Carcinoma Sample_N4
GSM115463	Primary Lung SCC Carcinoma Sample_N5
GSM115464	Primary Lung SCC Carcinoma Sample_N6
GSM115465	Primary Lung SCC Carcinoma Sample_N7
GSM115466	Primary Lung SCC Carcinoma Sample_N8
GSM115467	Primary Lung SCC Carcinoma Sample_N9
GSM115468	Primary Lung SCC Carcinoma Sample_N10
GSM115469	Primary Lung SCC Carcinoma Sample_N11
GSM115470	Primary Lung SCC Carcinoma Sample_N12
GSM115471	Primary Lung SCC Carcinoma Sample_N13
GSM115472	Primary Lung SCC Carcinoma Sample_N14
GSM115473	Primary Lung SCC Carcinoma Sample_N15
GSM115474	Primary Lung SCC Carcinoma Sample_N16
GSM115475	Primary Lung SCC Carcinoma Sample_N17
GSM115476	Primary Lung SCC Carcinoma Sample_N18
GSM115477	Primary Lung SCC Carcinoma Sample_N19
GSM115478	Primary Lung SCC Carcinoma Sample_N20
GSM115479	Primary Lung SCC Carcinoma Sample_N21
GSM115480	Primary Lung SCC Carcinoma Sample_N22
GSM115481	Primary Lung SCC Carcinoma Sample_N23
GSM115482	Primary Lung SCC Carcinoma Sample_N24
GSM115483	Primary Lung SCC Carcinoma Sample_N25
GSM115484	Primary Lung SCC Carcinoma Sample_N26
GSM115485	Primary Lung SCC Carcinoma Sample_N27
GSM115486	Primary Lung SCC Carcinoma Sample_N28
GSM115487	Primary Lung SCC Carcinoma Sample_N29
GSM115488	Primary Lung SCC Carcinoma Sample_N30
GSM115489	Primary Lung SCC Carcinoma Sample_N31
GSM115490	Primary Lung SCC Carcinoma Sample_N32
GSM115491	Primary Lung SCC Carcinoma Sample_R1
GSM115492	Primary Lung SCC Carcinoma Sample_R2
GSM115493	Primary Lung SCC Carcinoma Sample_R3
GSM115494	Primary Lung SCC Carcinoma Sample_R4
GSM115495	Primary Lung SCC Carcinoma Sample_R5
GSM115496	Primary Lung SCC Carcinoma Sample_R6
GSM115497	Primary Lung SCC Carcinoma Sample_R7
GSM115498	Primary Lung SCC Carcinoma Sample_R8
GSM115499	Primary Lung SCC Carcinoma Sample_R9
GSM115500	Primary Lung SCC Carcinoma Sample_R10
GSM115501	Primary Lung SCC Carcinoma Sample_R11
GSM115502	Primary Lung SCC Carcinoma Sample_R12
GSM115503	Primary Lung SCC Carcinoma Sample_R13
GSM115504	Primary Lung SCC Carcinoma Sample_R14
GSM115505	Primary Lung SCC Carcinoma Sample_R15
GSM115506	Primary Lung SCC Carcinoma Sample_R16
GSM115507	Primary Lung SCC Carcinoma Sample_R17
GSM115508	Primary Lung SCC Carcinoma Sample_R18
GSM115509	Primary Lung SCC Carcinoma Sample_R19

Relations

BioProject

PRJNA96621

Supplementary_Data_SCCRec 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	1	61.11	D
Sample_N10	Squamous cell carcinoma	F	58	80	P	3	96.76	A
Sample_N11	Squamous cell carcinoma	M	67	50	M	1	80.23	A
Sample_N12	Squamous cell carcinoma	F	66	25	P	2	120.41	A
Sample_N13	Squamous cell carcinoma	M	65	53	W	1	100.14	D
Sample_N14	Squamous cell carcinoma	M	64	50	M	1	99.58	A
Sample_N15	Squamous cell carcinoma	M	60	71	P	1	82.07	A
Sample_N16	Squamous cell carcinoma	M	69	50	M	1	92.94	A
Sample_N17	Squamous cell carcinoma	M	71	8	W	1	157.54	A
Sample_N18	Squamous cell carcinoma	F	75	57	M	1	98.86	A
Sample_N19	Squamous cell carcinoma	F	74	15	P	1	92.06	A
Sample_N2	Squamous cell carcinoma	M	68	40	W	1	153.63	D
Sample_N20	Squamous cell carcinoma	F	50	30	P	1	46.59	D
Sample_N21	Squamous cell carcinoma	M	69	43	P	1	70.05	A
Sample_N22	Squamous cell carcinoma	M	84	38	P	1	60.29	A
Sample_N23	Squamous cell carcinoma	M	64	171	M	3	62.98	A
Sample_N24	Squamous cell carcinoma	F	75	45	P	1	64.6	A
Sample_N25	Squamous cell carcinoma	M	68	75	P	1	46.75	A
Sample_N26	Squamous cell carcinoma	F	44	0	W	2	161.45	A
Sample_N27	Squamous cell carcinoma	M	72	83	M	3	61.5	D

Total number of rows: 51

Table truncated, full table size 3 Kbytes.

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