Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma

2010 ◽  
Vol 51 (10) ◽  
pp. 4884 ◽  
Author(s):  
Sarah L. Lake ◽  
Sarah E. Coupland ◽  
Azzam F. G. Taktak ◽  
Bertil E. Damato
Keyword(s):  
Loss Of Heterozygosity ◽  
Uveal Melanoma ◽  
Chromosome 3 ◽  
Whole Genome ◽  
Whole Genome Microarray

Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis

2016 ◽  
Vol 46 (5) ◽  
pp. 371-376 ◽  
Author(s):  
Marina Gonçalves Diniz ◽  
Alessandra Pires Duarte ◽  
Rolando A. Villacis ◽  
Bruna V. A. Guimarães ◽  
Luiz Cláudio Pires Duarte ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Microarray Analysis ◽  
Copy Number ◽  
Neutral Loss ◽  
High Density ◽  
Whole Genome ◽  
Copy Number Alterations ◽  
Whole Genome Microarray

Identification of genomic islands in Synechococcus sp. WH8102 using genomic barcode and whole-genome microarray analyses

2020 ◽  
Vol 15 ◽  
Author(s):  
Jiahui Pan ◽  
Xizi Luo ◽  
Tong Shao ◽  
Chaoying Li ◽  
Tingting Zhao ◽  
...  
Keyword(s):  
Genomic Islands ◽  
Whole Genome ◽  
Photosynthetic Organisms ◽  
Depth Study ◽  
Whole Genome Microarray ◽  
Integrated Methods ◽  
Synechococcus Sp ◽  
Intuitive View ◽  
Genomic Regions ◽  
Different Origins

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes. Results: Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain. Conclusion: Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.

scholarly journals Monosomy 3 Is Linked to Resistance to MEK Inhibitors in Uveal Melanoma

2021 ◽  
Vol 22 (13) ◽  
pp. 6727
Author(s):  
Svenja Mergener ◽  
Jens T. Siveke ◽  
Samuel Peña-Llopis
Keyword(s):  
Cell Lines ◽  
Uveal Melanoma ◽  
Survival Data ◽  
Translation Initiation Factor ◽  
The Cancer Genome Atlas ◽  
Initiation Factor ◽  
Chromosome 3 ◽  
Mek Inhibitors ◽  
Mek Inhibition ◽  
Insight Into

The use of MEK inhibitors in the therapy of uveal melanoma (UM) has been investigated widely but has failed to show benefits in clinical trials due to fast acquisition of resistance. In this study, we investigated a variety of therapeutic compounds in primary-derived uveal melanoma cell lines and found monosomy of chromosome 3 (M3) and mutations in BAP1 to be associated with higher resistance to MEK inhibition. However, reconstitution of BAP1 in a BAP1-deficient UM cell line was unable to restore sensitivity to MEK inhibition. We then compared UM tumors from The Cancer Genome Atlas (TCGA) with mutations in BAP1 with tumors with wild-type BAP1. Principal component analysis (PCA) clearly differentiated both groups of tumors, which displayed disparate overall and progression-free survival data. Further analysis provided insight into differential expression of genes involved in signaling pathways, suggesting that the downregulation of the eukaryotic translation initiation factor 2A (EIF2A) observed in UM tumors with BAP1 mutations and M3 UM cell lines might lead to a decrease in ribosome biogenesis while inducing an adaptive response to stress. Taken together, our study links loss of chromosome 3 with decreased sensitivity to MEK inhibition and gives insight into possible related mechanisms, whose understanding is fundamental to overcome resistance in this aggressive tumor.

scholarly journals Whole genome microarray analysis ofC. elegans rrf-3anderi-1mutants

FEBS Letters ◽  
2007 ◽  
Vol 581 (26) ◽  
pp. 5050-5054 ◽  
Author(s):  
Suvi Asikainen ◽  
Markus Storvik ◽  
Merja Lakso ◽  
Garry Wong
Keyword(s):  
Microarray Analysis ◽  
Whole Genome ◽  
Whole Genome Microarray

scholarly journals Multiple locations on chromosome 3 are the targets of specific deletions in uveal melanoma

Eye ◽  
2005 ◽  
Vol 20 (4) ◽  
pp. 476-481 ◽  
Author(s):  
N A Cross ◽  
A Ganesh ◽  
M Parpia ◽  
A K Murray ◽  
I G Rennie ◽  
...  
Keyword(s):  
Uveal Melanoma ◽  
Chromosome 3
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