Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing
| Autor: | C. Lara, R. Casarrubias-Islas, Alfonso Méndez-Tenorio, J. Diegopérez-Ramírez, Adriana Hernández-Angeles, Cabrera-Muñoz Ml, S. Sadowinski-Pine, Javier Mancilla Ramírez, Gabriela Edith Olguín-Ruiz, Pavel Isa, Javier Torres, Carlos F. Arias, Marco A. Ramirez-Ortiz, G. Ramírez-Reyes, Carlos Javier Sánchez-Vallejo, Juan Carlos Bravo-Ortiz, Guillermo Ramón-García, Manuela Orjuela, Adda Jeanette García-Chéquer, M.V. Ponce-Castañeda |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
Male
0301 basic medicine Cancer Research Retinal Neoplasms In silico Biology Malignancy Genome Article DNA sequencing 03 medical and health sciences 0302 clinical medicine Recurrence Genetics medicine Humans Molecular Biology Oligonucleotide Array Sequence Analysis Chromosome 13 Retinoblastoma High-Throughput Nucleotide Sequencing Chromosome medicine.disease 030104 developmental biology 030220 oncology & carcinogenesis Female Human genome Chromosome Deletion Medulloblastoma |
| Zdroj: | Cancer Genetics. 209:57-69 |
| ISSN: | 2210-7762 |
| Popis: | Genes are frequently lost or gained in malignant tumors and the analysis of these changes can be informative about the underlying tumor biology. Retinoblastoma is a pediatric intraocular malignancy, and since deletions in chromosome 13 have been described in this tumor, we performed genome wide sequencing with the Illumina platform to test whether recurrent losses could be detected in low coverage data from DNA pools of Rb cases. An in silico reference profile for each pool was created from the human genome sequence GRCh37p5; a chromosome integrity score and a graphics 40 Kb window analysis approach, allowed us to identify with high resolution previously reported non random recurrent losses in all chromosomes of these tumors. We also found a pattern of gains and losses associated to clear and dark cytogenetic bands respectively. We further analyze a pool of medulloblastoma and found a more stable genomic profile and previously reported losses in this tumor. This approach facilitates identification of recurrent deletions from many patients that may be biological relevant for tumor development. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect