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Genetic Analysis of Desmoplastic Melanoma

UID: 11295

Author(s): Bastian, Boris C., Shain, Alan H., Murali, Rajmohan*, Cho, Raymond J. * MSK affiliated

Description
Description from dbGaP:

"Desmoplastic melanoma is an infrequent variant of melanoma with sarcomatous histology, distinct clinical behavior, and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes to validate candidate genes. A high mutation burden (median 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate UV-radiation as the dominant mutagen, indicating a superficially located cell of origin. Novel alterations included recurrent promoter mutations of NF-kappa B inhibitor epsilon, NFKBIE (IkBε) in 14.5% of samples. Commonly mutated oncogenes in melanomas, in particular BRAF(V600E) and NRAS(Q61K/R), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS, and PIK3CA, some of which being candidates for targeted therapies."
Subject of Study
Homo sapiens
Subject(s)
Exome Sequencing
Melanoma
Melanoma/genetics
Mutation
Proto-Oncogene Proteins B-raf
OncoTree Cancer Type(s)
Melanoma
Access via dbGaP


Accession #: phs000977.v1.p1

Access Restrictions
Application Required
Access Instructions
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Associated Publications
Shain A, Garrido M, Botton T, Talevich E, Yeh I, Sanborn J, Chung J, Wang N, Kakavand H, Mann G, Thompson J, Wiesner T, Roy R, Olshen A, Gagnon A, Gray J, Huh N, Hur J, Busam K, Scolyer R, Cho R, Murali R, Bastian B. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics. 2015; 47(10):1194-1199.
Bastian BC. The molecular pathology of melanoma: an integrated taxonomy of melanocytic neoplasia. Annu Rev Pathol. 2014;9:239-71. PMID: 24460190; PMCID: PMC4831647.
Equipment Used
Agilent SureSelect Human All Exon V4
Illumina HiSeq 2500

High throughput sequencing system

SeqCap EZ Choice Library

solution-based capture method that enables enrichment of the whole exome or customer regions of interest in a single test tube

Dataset Format(s)
PDF, XML, gzip, TXT
Dataset Size
387.38 KB
Data Catalog Record Updated
2024-07-08