High-throughput oncogene mutation profiling in human cancer

RK Thomas, AC Baker, RM DeBiasi, W Winckler… - Nature …, 2007 - nature.com
Systematic efforts are underway to decipher the genetic changes associated with tumor
initiation and progression,. However, widespread clinical application of this information is …

Computational approaches to identify functional genetic variants in cancer genomes

Nature methods, 2013 - nature.com
Abstract The International Cancer Genome Consortium (ICGC) aims to catalog genomic
abnormalities in tumors from 50 different cancer types. Genome sequencing reveals …

Defining the blueprint of the cancer genome

VE Velculescu - Carcinogenesis, 2008 - academic.oup.com
It is widely accepted that cancer is a disease caused by accumulation of mutations in
specific genes. These tumor-specific mutations provide clues to the cellular processes …

Cancer subtype identification using somatic mutation data

ML Kuijjer, JN Paulson, P Salzman, W Ding… - British journal of …, 2018 - nature.com
Background With the onset of next-generation sequencing technologies, we have made
great progress in identifying recurrent mutational drivers of cancer. As cancer tissues are …

Signatures of mutation and selection in the cancer genome

GR Bignell, CD Greenman, H Davies, AP Butler… - Nature, 2010 - nature.com
The cancer genome is moulded by the dual processes of somatic mutation and selection.
Homozygous deletions in cancer genomes occur over recessive cancer genes, where they …

Mechanisms underlying mutational signatures in human cancers

T Helleday, S Eshtad, S Nik-Zainal - Nature reviews genetics, 2014 - nature.com
The collective somatic mutations observed in a cancer are the outcome of multiple
mutagenic processes that have been operative over the lifetime of a patient. Each process …

Phase and context shape the function of composite oncogenic mutations

AN Gorelick, FJ Sánchez-Rivera, Y Cai, CM Bielski… - Nature, 2020 - nature.com
Cancers develop as a result of driver mutations, that lead to clonal outgrowth and the
evolution of disease,. The discovery and functional characterization of individual driver …

A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies

A Degasperi, TD Amarante, J Czarnecki, S Shooter… - Nature cancer, 2020 - nature.com
Mutational signatures are patterns of mutations that arise during tumorigenesis. We present
an enhanced, practical framework for mutational signature analyses. Applying these …

Identification of neutral tumor evolution across cancer types

MJ Williams, B Werner, CP Barnes, TA Graham… - Nature …, 2016 - nature.com
Despite extraordinary efforts to profile cancer genomes, interpreting the vast amount of
genomic data in the light of cancer evolution remains challenging. Here we demonstrate that …

Mutation patterns in cancer genomes

AF Rubin, P Green - … of the National Academy of Sciences, 2009 - National Acad Sciences
Recent large-scale cancer sequencing studies have focused primarily on identifying cancer-
associated genes, but as an important byproduct provide “passenger mutation” data that can …