@article {1638820, title = {Computational analysis of cancer genome sequencing data}, journal = {Nature Reviews Genetics}, volume = {23}, number = {5}, year = {2022}, month = {2022 May}, pages = {298-314}, abstract = {Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.}, keywords = {Chromosome Mapping, Computational Biology, DNA Copy Number Variations, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Mutation, Neoplasms}, issn = {1471-0064}, doi = {10.1038/s41576-021-00431-y}, author = {Cort{\'e}s-Ciriano, Isidro and Gulhan, Doga C and Lee, Jake June-Koo and Melloni, Giorgio EM and Park, Peter J*} }