Computational analysis of cancer genome sequencing data

I Cortés-Ciriano, DC Gulhan, JJK Lee… - Nature Reviews …, 2022 - nature.com
Distilling biologically meaningful information from cancer genome sequencing data requires
comprehensive identification of somatic alterations using rigorous computational methods …

Expanding the computational toolbox for mining cancer genomes

L Ding, MC Wendl, JF McMichael… - Nature Reviews …, 2014 - nature.com
High-throughput DNA sequencing has revolutionized the study of cancer genomics with
numerous discoveries that are relevant to cancer diagnosis and treatment. The latest …

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

BJ Raphael, JR Dobson, L Oesper, F Vandin - Genome medicine, 2014 - Springer
High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the
measurement of the somatic mutations that drive cancer development. However, the …

Analysis of next-generation genomic data in cancer: accomplishments and challenges

L Ding, MC Wendl, DC Koboldt… - Human molecular …, 2010 - academic.oup.com
The application of next-generation sequencing technology has produced a transformation in
cancer genomics, generating large data sets that can be analyzed in different ways to …

Emerging patterns of somatic mutations in cancer

IR Watson, K Takahashi, PA Futreal, L Chin - Nature Reviews Genetics, 2013 - nature.com
Recent advances in technological tools for massively parallel, high-throughput sequencing
of DNA have enabled the comprehensive characterization of somatic mutations in a large …

Advances in understanding cancer genomes through second-generation sequencing

M Meyerson, S Gabriel, G Getz - Nature Reviews Genetics, 2010 - nature.com
Cancers are caused by the accumulation of genomic alterations. Therefore, analyses of
cancer genome sequences and structures provide insights for understanding cancer …

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

Q Wang, P Jia, F Li, H Chen, H Ji, D Hucks… - Genome medicine, 2013 - Springer
Background Driven by high throughput next generation sequencing technologies and the
pressing need to decipher cancer genomes, computational approaches for detecting …

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

F Cheng, J Zhao, Z Zhao - Briefings in bioinformatics, 2016 - academic.oup.com
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide
variants, small insertions or deletions, gene fusions, copy-number variations, and large …

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

J Kuipers, K Jahn, BJ Raphael… - Genome …, 2017 - genome.cshlp.org
Intra-tumor heterogeneity poses substantial challenges for cancer treatment. A tumor's
composition can be deduced by reconstructing its mutational history. Central to current …

A somatic reference standard for cancer genome sequencing

DW Craig, S Nasser, R Corbett, SK Chan, L Murray… - Scientific reports, 2016 - nature.com
Large-scale multiplexed identification of somatic alterations in cancer has become feasible
with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools …