Dataset Information

2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_genome_DNAseq_Medulloblastoma_ICGC - samples

ABSTRACT: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.

OTHER RELATED OMICS DATASETS IN: PRJNA213744PRJNA213380PRJNA214321

PROVIDER: EGAD00001000697 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Publications

Dissecting the genomic complexity underlying medulloblastoma.

Jones David T W DT Jäger Natalie N Kool Marcel M Zichner Thomas T Hutter Barbara B Sultan Marc M Cho Yoon-Jae YJ Pugh Trevor J TJ Hovestadt Volker V Stütz Adrian M AM Rausch Tobias T Warnatz Hans-Jörg HJ Ryzhova Marina M Bender Sebastian S Sturm Dominik D Pleier Sabrina S Cin Huriye H Pfaff Elke E Sieber Laura L Wittmann Andrea A Remke Marc M Witt Hendrik H Hutter Sonja S Tzaridis Theophilos T Weischenfeldt Joachim J Raeder Benjamin B Avci Meryem M Amstislavskiy Vyacheslav V Zapatka Marc M Weber Ursula D UD Wang Qi Q Lasitschka Bärbel B Bartholomae Cynthia C CC Schmidt Manfred M von Kalle Christof C Ast Volker V Lawerenz Chris C Eils Jürgen J Kabbe Rolf R Benes Vladimir V van Sluis Peter P Koster Jan J Volckmann Richard R Shih David D Betts Matthew J MJ Russell Robert B RB Russell Robert B RB Coco Simona S Tonini Gian Paolo GP Schüller Ulrich U Hans Volkmar V Graf Norbert N Kim Yoo-Jin YJ Monoranu Camelia C Roggendorf Wolfgang W Unterberg Andreas A Herold-Mende Christel C Milde Till T Kulozik Andreas E AE von Deimling Andreas A Witt Olaf O Maass Eberhard E Rössler Jochen J Ebinger Martin M Schuhmann Martin U MU Frühwald Michael C MC Hasselblatt Martin M Jabado Nada N Rutkowski Stefan S von Bueren André O AO Williamson Dan D Clifford Steven C SC McCabe Martin G MG Collins V Peter VP Wolf Stephan S Wiemann Stefan S Lehrach Hans H Brors Benedikt B Scheurlen Wolfram W Felsberg Jörg J Reifenberger Guido G Northcott Paul A PA Taylor Michael D MD Meyerson Matthew M Pomeroy Scott L SL Yaspo Marie-Laure ML Korbel Jan O JO Korshunov Andrey A Eils Roland R Pfister Stefan M SM Lichter Peter P

Nature 20120801 7409

Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles ar ...[more]

PMID: 22832583

Publication: 1/4

Similar Datasets

Project description:While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a training data set, which is typically either from a part of the data set being M-bM-^@M-^\recalibratedM-bM-^@M-^] (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 units, and by as much as 13 units M-BM- at CpG sites. In addition, since reads mapping to the genome are not used for recalibration, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration. Four human RNA samples with equimolar ERCC spike-in standards were sequenced on Illumina. Two human brain/liver/muscle RNA mixtures with dynamic range of ERCC spike-in standards were sequenced on SOLiD.

Dataset Information

2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_genome_DNAseq_Medulloblastoma_ICGC - samples

Publications

Dissecting the genomic complexity underlying medulloblastoma.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets