ena-STUDY-UMCU-10-07-2018-16:02:45:755-2183
Whole genome sequencing of the COLO829 reference cancer cell line
Cancer genome sequencing has taken central stage in personalized cancer care. A major issue with respect to cancer genome sequencing is the reliable detection of somatic structural genomic variations. Here, we have generated whole genome sequencing data for the COLO829 tumor cell line and the corresponding reference cell line, using 5 different sequencing platforms: 10x genomics, Illumina HiSeq, Oxford Nanopore, Pacific Biosciences and Bionano Genomics. We performed an integrated analysis of the somatic structural variations in the data and define a gold-standard reference structural variation call set. We use this set to estimate the performance of each of the sequencing platforms in capturing somatic SVs. Furthermore, we define the effects of sequencing coverage and tumor cell percentage on structural variation detection sensitivity.
Cancer genome sequencing has taken central stage in personalized cancer care. A major issue with respect to cancer genome sequencing is the reliable detection of somatic structural genomic variations. Here, we have generated whole genome sequencing data for the COLO829 tumor cell line and the corresponding reference cell line, using 5 different sequencing platforms: 10x genomics, Illumina HiSeq, Oxford Nanopore, Pacific Biosciences and Bionano Genomics. We performed an integrated analysis of the somatic structural variations in the data and define a gold-standard reference structural variation call set. We use this set to estimate the performance of each of the sequencing platforms in capturing somatic SVs. Furthermore, we define the effects of sequencing coverage and tumor cell percentage on structural variation detection sensitivity.