Study

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies

Study ID Alternative Stable ID Type
EGAS00001000274 Whole Genome Sequencing

Study Description

Massively parallel sequencing has revolutionized research in cancer genetics and genomics and enhanced our understanding of natural human genetic variation. Recently, Lam et al. have performed a detailed comparison of two next-generation sequencing technologies with respect to their sensitivity to call single nucleotide variants (SNV) and indels. Here, we sequenced two tumor/normal pairs obtained from two paedriatic medulloblastoma patients with Life Technologies’ SOLiD 4 and 5500xl SOLiD, Illumina’s HiSeq2000, and Complete Genomics’ technology. We then compared their ability to call SNVs with high confidence. As gold standard for SNV calling, we used genotypes determined by an Affymetrix SNP array. Additionally, we performed a detailed analysis of how evenly each technology covers the genome and how the reads are distributed across functional genomic regions. Finally, we studied how a combination of data from different technologies might help to overcome the limitations in SNV calling by any of the four technologies alone.

Study Datasets 1 dataset.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001000174
DATA_SET_Coverage_bias_sensitivity_of_variant_calling_for_4_WG_seq_tech
AB SOLiD 4 System,Complete Genomics,Illumina HiSeq 2000,unspecified 4

Who archives the data?

Publications

Citations

Retrieving...
Retrieving...