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Series GSE123011 Query DataSets for GSE123011
Status Public on Nov 25, 2019
Title Conjunctival melanoma copy number alterations and correlation with mutation status, tumor features and clinical outcome
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Relatively little is known about the genetic aberrations of conjunctival melanomas (CoM) and their correlation with clinical and histomorphological features as well as prognosis. The aim of this large collaborative multicentre study was to determine potential key biomarkers for metastatic risk and any druggable targets for high-risk metastatic CoM. Using Affymetrix Single Nucleotide Polymorphism genotyping arrays on 59 CoM, we detected frequent amplifications on chromosome (chr) 6p and deletions on 7q, and characterised mutation-specific copy number alterations. Deletions on chr 10q11.21-26.2, a region harbouring the tumor suppressor genes, PDCD4, SUFU, NEURL1, PTEN, RASSF4, DMBT1 and C10orf90 & 99 significantly correlated with metastases (Fisher’s Exact, p≤0.04), lymphatic invasion (Fisher’s Exact, p≤0.02), increasing tumor thickness (Mann-Whitney, p≤0.02) and BRAF mutation (Fisher’s Exact, p≤0.05). This enhanced insight into CoM biology is a step towards identifying patients at risk of metastasis and potential therapeutic targets for systemic disease.
 
Overall design 59 samples in total: 52 primary and 7 locally recurrent conjuncitval melanoma (CoM)
 
Contributor(s) Kenawy N, Kalirai H, Sacco JJ, Lake SL, Heegaard S, Larsen A, Finger PT, Milman T, Chin K, Mosci C, Lanza F, Moulin A, Schmitt CA, Caujolle JP, Maschi C, Marincovic M, Taktak AF, Heimann H, Damato BE, Coupland SE
Citation(s) 30672666
Submission date Nov 27, 2018
Last update date Nov 25, 2019
Contact name Sarah E Coupland
E-mail(s) s.e.coupland@liverpool.ac.uk
Organization name University of Liverpool
Department Molecular and Clinical Cancer Medicine
Lab Liverpool Ocular Oncology Group
Street address West Derby Street
City Liverpool
ZIP/Postal code L7 8TX
Country United Kingdom
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (59)
GSM3490630 Primary conjunctival melanoma [SAMPLE 1]
GSM3490631 Primary conjunctival melanoma [SAMPLE 2]
GSM3490632 Primary conjunctival melanoma [SAMPLE 3]
Relations
BioProject PRJNA507249

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
GSE123011_RAW.tar 3.2 Gb (http)(custom) TAR (of CEL, CHP, TXT)
Processed data provided as supplementary file

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