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Series GSE60542 Query DataSets for GSE60542
Status Public on Sep 01, 2015
Title Revisiting the transcriptional analysis of primary tumors and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The biology underlying nodal metastasis is poorly understood. Transcriptome profiling has helped to characterize both primary tumors seeding nodal metastasis and the metastasis themselves. The interpretation of these data, however, is not without ambiguities. Here we profiled the transcriptomes of 17 papillary thyroid cancer (PTC) nodal metastases, associated primary tumors and primary tumors from N0 patients. We also included patient-matched normal thyroid and lymph node samples as controls to address some limits of previous studies. We found that the transcriptomes of patient-matched primary tumors and metastases were more similar than of unrelated metastases/primary pairs, a result also reported in other organ systems, and that part of this similarity reflected patient background. We found that the comparison of patient-matched primary tumors and metastases was heavily confounded by the presence of lymphoid tissues in the metastasis samples. An original data adjustment procedure was developed to circumvent this problem. It revealed a differential expression of stroma-related gene expression signatures also regulated in other organ systems. The comparison of N0 vs. N+ primary tumors uncovered a signal irreproducible across independent PTC datasets. This signal was also detectable when comparing the normal thyroid tissues adjacent to N0 and N+ tumors, suggesting a cohort specific bias also likely to be present in previous studies with similar statistical power. Classification of N0 vs. N+ yielded an accuracy of 63%, but additional statistical controls not presented in previous studies, revealed that this is likely to occur by chance alone. To address this issue, we used large datasets from The Cancer Genome Atlas and showed that N0 vs. N+ classification rates could not be reached randomly for most cancers. Yet, it was significant, but of limited accuracy (<70%) for thyroid, breast and head and neck cancers.
 
Overall design We profiled the transcriptomes of 11 primary PTCs with no detectable nodal invasion, 17 primary PTCs with nodal invasion and 17 patient-matched nodal metastases. We also profiled a number of control samples. These included 24 patient-matched normal thyroid tissues (11 from N0, 13 from N+ patients), and 4 normal lymph nodes; technical and biological replicates including additional nodal metastasis for 3 patients, adjacent blocks for 5 primary tumors, 4 normal thyroid tissues and 1 nodal metastasis.
 
Contributor(s) Tarabichi M, Saiselet M, Trésallet C, Hoang C, Larsimont D, Andry G, Maenhaut C, Detours V
Citation(s) 25965298
Submission date Aug 20, 2014
Last update date Mar 25, 2019
Contact name Maxime Tarabichi
E-mail(s) Maxime.Tarabichi@ulb.ac.be
Phone 003225556769
Organization name IRIBHM
Street address Route de Lennik 808
City Anderlecht
State/province Bruxelles
ZIP/Postal code 1070
Country Belgium
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (92)
GSM1481838 23-N,Normal thyroid,N0
GSM1481839 1-PT-N1,Papillary thyroid carcinoma,N1
GSM1481840 9-LNM,Lymph node metastasis,N1
Relations
BioProject PRJNA258507

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60542_RAW.tar 645.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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