Dataset Information

Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing.

ABSTRACT: 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.

SUBMITTER: Garcia-Chequer AJ

PROVIDER: S-EPMC4993565 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing.

García-Chequer A J AJ Méndez-Tenorio A A Olguín-Ruiz G G Sánchez-Vallejo C C Isa P P Arias C F CF Torres J J Hernández-Angeles A A Ramírez-Ortiz M A MA Lara C C Cabrera-Muñoz M L ML Sadowinski-Pine S S Bravo-Ortiz J C JC Ramón-García G G Diegopérez-Ramírez J J Ramírez-Reyes G G Casarrubias-Islas R R Ramírez J J Orjuela M A MA Ponce-Castañeda M V MV

Cancer genetics 20151215 3

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 ...[more]

PMID: 26883451

Similar Datasets

Project description:BackgroundNext-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches.ResultsWe have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (assay for transposase-accessible chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~?100 Gb size) in minutes, outperforming currently available tools.ConclusionsBAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice-aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).

Dataset Information

Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing.

Publications

Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets