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A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome

We have carried out complete sequencing of the genome of the human male maligant melanoma cell line COLO-829 using the Illumina Genome Analyzer II. We generated a sequencing library with a median insert size of ~200 bp following random fragmentation and gel fractionation of the genomic DNA. We sequenced 75 bases from both ends of these templates to cover the COLO-829 genome to an average depth of more than 40x. We have carried out purity-filtering (PF) to remove mixed reads, where two or more different template molecules are close enough on the surface of the flow-cell to form a mixed or overlapping cluster. No other filtering of the data has been carried out prior to submission. We have also submitted sequence data for a lymphoblastoid control cell line COLO-829BL from the same individual.

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
EGAD00000000055 Illumina Genome Analyzer II 2
Publications Citations
A comprehensive catalogue of somatic mutations from a human cancer genome.
Nature 463: 2010 191-196
Shimmer: detection of genetic alterations in tumors using next-generation sequence data.
Bioinformatics 29: 2013 1498-1503
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.
Bioinformatics 30: 2014 3302-3309
Towards accurate characterization of clonal heterogeneity based on structural variation.
BMC Bioinformatics 15: 2014 299
novoBreak: local assembly for breakpoint detection in cancer genomes.
Nat Methods 14: 2017 65-67
Deep convolutional neural networks for accurate somatic mutation detection.
Nat Commun 10: 2019 1041
Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data.
Gigascience 10: 2021 giab080