Genomics

Dataset Information

40

Affymetrix SNP array data for esophageal squamous cell carcinoma samples


ABSTRACT: A proportion of superficial esophageal squamous cell carcinoma, a type of less invasive esophageal squamous cell carcinoma (ESCC), would have metastasis after esophagectomy or endoscopic resection with poor prognosis. The purpose of this study was to discover the whole-genome copy number alteration (CNA) profiles of superficial ESCC and compare the CNAs of superficial ESCC patients with and without metastasis after surgery. Thirty eight superficial ESCC cases, including 19 cases with metastasis and 19 cases without metastasis within 5 years after surgery, were analyzed CNAs by Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was initially constructed to identify high risk of metastasis in superficial ESCC patients. In addition, amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were identified as recurrent CNAs across all 38 superficial ESCC cases. And amplifications of 3p26.33 (SOX2-OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were identified as recurrent CNAs among metastasis cases only. Our study provided a 39-gene signature tool to identified high risk metastasis in superficial ESCC and suggested that amplifications of SOX2-OT, MYC, FOXA1 genes and deletion of GBE1 gene might play a vital role in metastasis among superficial ESCC. Overall design: Copy number analysis of Affymetrix FFPE Oncoscan Array was performed for 38 superficial esophageal squamous cell carcinoma (pT1N0M0) samples, including 19 cases with metastasis after surgery within 5 years after surgery and 19 cases without metastasis.

INSTRUMENT(S): [OncoScan] Affymetrix OncoScan FFPE Assay

SUBMITTER: Jianming Ying 

PROVIDER: GSE78926 | GEO | 2017-06-10

SECONDARY ACCESSION(S): PRJNA314447

REPOSITORIES: GEO

altmetric image

Publications

Genome wide copy number analyses of superficial esophageal squamous cell carcinoma with and without metastasis.

Wang Pengjiao P   Shan Ling L   Xue Liyan L   Zheng Bo B   Ying Jianming J   Lu Ning N  

Oncotarget 20170101 3


Superficial esophageal squamous cell carcinoma (ESCC) is generally considered a subtype of less invasive ESCC. Yet a subset of these superficial ESCC would have metastasis after esophagostomy or endoscopic resection and lead to poor prognosis. The objective of this study is to determine biomarkers that can identify such subset of superficial ESCC that would have metastasis after surgery using genome wide copy number alteration (CNA) analyses. The CNAs of 38 cases of superficial ESCCs originated  ...[more]

Similar Datasets

2015-08-07 | E-GEOD-59973 | ArrayExpress
2014-03-11 | E-GEOD-54995 | ArrayExpress
2014-03-11 | E-GEOD-54994 | ArrayExpress
2014-03-11 | E-GEOD-54993 | ArrayExpress
2014-08-01 | E-GEOD-45670 | ArrayExpress
2013-03-23 | E-GEOD-37949 | ArrayExpress
2015-07-27 | E-GEOD-59974 | ArrayExpress
2011-11-04 | E-GEOD-33426 | ArrayExpress
2014-09-20 | E-GEOD-61587 | ArrayExpress
| GSE61588 | GEO