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E-GEOD-16597 - Identification of novel candidate target genes at 3q26.2-q29 in squamous cell carcinoma of the lung

Status
Submitted on 12 June 2009, released on 18 May 2010, last updated on 1 May 2014
Organism
Homo sapiens
Samples (72)
Array (1)
Protocols (8)
Description
High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at 3q26.2-q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs. Array-CGH was performed to compare the different patterns of genetic alterations. DNA from NSCLC patients (n=36) and human reference DNA (Promega) were differentially labeled and cohybridized on the array. The Fisher exact test utilized two categories, normal and abnormal (loss and gain), with the null hypothesis that the relative proportions of each of the two imbalance categories would be expected to be the same in the groups. The counts of abnormal versus normal were summarized by subtype of NSCLC for each BAC, providing 2x2 tables for analysis. A multiple testing correction (Benjamini-Hochberg false discovery rate (FDR)) was applied to correct for the high number of false positive calls.
Experiment type
comparative genomic hybridization by array 
Contacts
Jiun Kang <ju2497@gmail.com>, JinMan Kim, JiUn Kang, JongWoo Park, KyeChul Kwon, SunHoe Koo
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-16597.idf.txt
Sample and data relationshipE-GEOD-16597.sdrf.txt
Raw data (1)E-GEOD-16597.raw.1.zip
Processed data (1)E-GEOD-16597.processed.1.zip
Array designA-GEOD-8690.adf.txt
Links