E-MTAB-1159 - Genotyping by array of tumour-normal pairs from two paediatric medulloblastoma patients to identify single nucleotide variations in each pair of samples

Status
Released on 1 June 2013, last updated on 3 May 2014
Organism
Homo sapiens
Samples (2)
Array (1)
Protocols (5)
Description
We sequenced two tumor/normal pairs obtained from two paediatric medulloblastoma patients (MB14 and MB24) with at least 30x coverage on all commonly used next-generation sequencing platforms for whole genome sequencing (SOLiD 4, 5500xl SOLiD, Illumina's HiSeq2000, and Complete Genomic' technology). The normal tissue samples came from venous blood. We compared their ability to call single nucleotide variations (SNVs) in whole-genome sequencing data with high confidence. As gold standard for SNV calling, we used genotypes determined by Affymetrix SNP 6.0 Array Technology (total of 907,551 SNPs after quality filtering).
Experiment types
genotyping by array, array platform variation, genotyping, quality control testing
Contact
Citation
Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies. Marc Zapatka, Nora Rieber, B?rbel Lasitschka, David Jones, Paul Northcott, Barbara Hutter, Natalie J?ger, Marcel Kool, Michael Taylor, Peter Lichter, Stefan Pfister, Stephan Wolf, Benedikt Brors, Roland Eils.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-1159.idf.txt
Sample and data relationshipE-MTAB-1159.sdrf.txt
Processed data (1)E-MTAB-1159.processed.1.zip
Array designA-AFFY-142.adf.txt
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