Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis.

Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis.

Publication date: Mar 01, 2019

To clinically use the UCSF500, a pancancer, next-generation sequencing assay in uveal melanoma (UM) and to correlate results with gene expression profiling (GEP) and predictive factors for metastasis.

Cohort study. Tumor samples of adult UM patients were analyzed with the UCSF500 and GEP. Main outcomes were copy number changes in chromosomes 1, 3, 6, and 8 and mutations in GNAQ, GNA11, SF3B1, EIF1AX, BAP1, SRSF2, U2AF1, and PLCB4. Chromosome 3 loss (a metastasis predictor) was tested for correlation with GEP class, tumor characteristics (largest basal diameter, thickness, ciliary body involvement, and extraocular extension), and histology (presence of epithelioid cells, closed loops, and mitotic count).

The 62 patients had a mean age of 59 years (range, 24-89 years). Chromosome 3 loss was detected in 30 patients and was associated with larger basal tumor diameter (Wilcoxon rank sum test, P = 0.015), greater thickness (Wilcoxon rank sum test, P = 0.016) and tumor, node, metastasis stage (Fisher test, P = 0.006), epithelioid cytology (Fisher test, P

UCSF500 detects chromosomal copy number changes and missense mutations that correlate strongly with metastasis predictors, including GEP.

Next-generation sequencing of UM should enhance survival prognostication.

Open Access PDF

Afshar, A.R., Damato, B.E., Stewart, J.M., Zablotska, L.B., Roy, R., Olshen, A.B., Joseph, N.M., and Bastian, B.C. Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis. 22483. 2019 Transl Vis Sci Technol (8):2.

Concepts Keywords
Assay J. William Harbour
Basal DecisionDx-UM
Chromosome Cancer
Chromosomes BAP1
Ciliary Body Metastasis
Cohort Study Uveal melanoma
Correlation RTT
Cytology Health
Epithelioid Medicine
Epithelioid Cells Melanoma
Expression Profiling Branches of biology
Histology
Melanoma
Metastasis
Metastatic
Missense Mutations
Mitotic
Mutation
Next Generation Sequencing
Odds Ratio
Sci
Sequencing
Tumor
Uveal Melanoma
Vis

Semantics

Type Source Name
gene UNIPROT ENG
gene UNIPROT INTU
gene UNIPROT GOPC
gene UNIPROT FBLIM1
disease MESH growth
gene UNIPROT BCL2L11
gene UNIPROT SMC3
gene UNIPROT SGSM3
gene UNIPROT FASTK
disease DOID choroidal tumor
disease MESH visual
gene UNIPROT RORC
gene UNIPROT BRD2
gene UNIPROT EXOG
disease MESH blue nevi
gene UNIPROT MCL1
disease MESH cytogenetic abnormalities
disease MESH multi
gene UNIPROT COL9A3
gene UNIPROT COMP
gene UNIPROT COL9A1
gene UNIPROT COL9A2
gene UNIPROT SCN8A
gene UNIPROT LAT2
gene UNIPROT ZBTB8OS
disease MESH eye cancer
gene UNIPROT TNIP1
gene UNIPROT ABO
gene UNIPROT KRT23
gene UNIPROT ABCC6
gene UNIPROT FOXC1
gene UNIPROT PAK3
disease DOID Blindness
disease MESH Blindness
drug DRUGBANK Formaldehyde
gene UNIPROT ARSE
gene UNIPROT BANK1
gene UNIPROT KIT
gene UNIPROT LARGE1
disease MESH chromosome deletion
disease MESH oral cancer
gene UNIPROT THOP1
disease MESH neuroepithelial tumor
disease DOID medulloblastoma
disease MESH medulloblastoma
disease MESH ependymoma
disease DOID pineoblastoma
disease MESH pineoblastoma
pathway BSID Glioma
disease MESH glioma
disease MESH risk factors
disease MESH monosomy
gene UNIPROT CES2
gene UNIPROT CASP1
disease DOID cancer
gene UNIPROT MBP
gene UNIPROT PRG2
gene UNIPROT MBL2
disease MESH diagnosis
drug DRUGBANK Tantalum
drug DRUGBANK Tricyclazole
gene UNIPROT CYSLTR2
gene UNIPROT TBX3
disease MESH death
gene UNIPROT TENM1
disease DOID noma
disease MESH noma
gene UNIPROT MENT
drug DRUGBANK Trestolone
gene UNIPROT PLEKHG5
pathway BSID Melanoma
disease DOID melanoma
disease MESH melanoma
gene UNIPROT TNFSF13
gene UNIPROT ANP32B
gene UNIPROT NFKBIZ
gene UNIPROT NAA50
gene UNIPROT CTCFL
gene UNIPROT TNFRSF11A
gene UNIPROT PLCB4
gene UNIPROT U2AF1
gene UNIPROT SRSF2
gene UNIPROT MAGI1
gene UNIPROT BAP1
gene UNIPROT RNF2
gene UNIPROT EIF1AX
gene UNIPROT SF3B1
gene UNIPROT SF3B2
gene UNIPROT GNA11
gene UNIPROT GNAQ
disease MESH Tumor
gene UNIPROT GRN
gene UNIPROT GNA12
pathway BSID Gene Expression
disease MESH Metastasis
disease DOID Uveal Melanoma
disease MESH Uveal Melanoma

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