An overview of mutational and copy number signatures in human cancer

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

(2022) Erik N. Bergstrom et al.   NATURE

Biallelic mutations in cancer genomes reveal local mutational determinants

(2022) Jonas Demeulemeester et al.   NATURE GENETICS

Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers

(2022) Arnoud Boot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signatures of TOP1 transcription-associated mutagenesis in cancer and germline

(2022) Martin A. M. Reijns et al.   NATURE

Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes

(2021) Shixiang Wang et al.   PLoS Genetics

Copy Number Variant Detection with Low-Coverage Whole-Genome Sequencing Represents a Viable Alternative to the Conventional Array-CGH

(2021) Marcel Kucharík et al.   Diagnostics

Copy number signatures predict chromothripsis and clinical outcomes in newly diagnosed multiple myeloma

(2021) Kylee H. Maclachlan et al.   Nature Communications

Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures

(2021) Ammal Abbasi et al.   DNA REPAIR

Pan-cancer analysis of whole genomes

(2020)   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

(2020) Isidro Cortés-Ciriano et al.   NATURE GENETICS

Homologous recombination deficiency status-based classification of high-grade serous ovarian carcinoma

(2020) Hisamitsu Takaya et al.   Scientific Reports

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer

(2020) Paulina J. Dziubańska-Kusibab et al.   NATURE MEDICINE

Mechanisms generating cancer genome complexity from a single cell division error

(2020) Neil T. Umbreit et al.   SCIENCE

Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer

(2020) Neha Chopra et al.   Nature Communications

Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers

(2020) Dominik Glodzik et al.   Nature Communications

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

(2020) Kevin Hadi et al.   CELL

Clinical assays for assessment of homologous recombination DNA repair deficiency

(2020) Elizabeth H. Stover et al.   GYNECOLOGIC ONCOLOGY

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

(2020) Simone Zaccaria et al.   NATURE BIOTECHNOLOGY

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

(2020) Hoon Kim et al.   NATURE GENETICS

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

(2020) Simone Zaccaria et al.   Nature Communications

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways

(2019) Christopher D. Steele et al.   CANCER CELL

Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype

(2019) Judith E. Grolleman et al.   CANCER CELL

Portrait of a cancer: mutational signature analyses for cancer diagnostics

(2019) Arne Van Hoeck et al.   BMC CANCER

A Compendium of Mutational Signatures of Environmental Agents

(2019) Jill E. Kucab et al.   CELL

Ongoing chromosomal instability and karyotype evolution in human colorectal cancer organoids

(2019) Ana C. F. Bolhaqueiro et al.   NATURE GENETICS

Detecting the mutational signature of homologous recombination deficiency in clinical samples

(2019) Doga C. Gulhan et al.   NATURE GENETICS

Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

(2019) Natalya P. Degtyareva et al.   PLOS BIOLOGY

The immune response‐related mutational signatures and driver genes in non‐small‐cell lung cancer

(2019) Hao Chen et al.   CANCER SCIENCE

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

(2019) Johan Staaf et al.   NATURE MEDICINE

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

(2018) Carolyn Hutter et al.   CELL

Validating the concept of mutational signatures with isogenic cell models

(2018) Xueqing Zou et al.   Nature Communications

Copy number signatures and mutational processes in ovarian carcinoma

(2018) Geoff Macintyre et al.   NATURE GENETICS

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

(2017) Jack Kuipers et al.   GENOME RESEARCH

Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors

(2017) Mi Ni Huang et al.   GENOME RESEARCH

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

(2017) Helen Davies et al.   NATURE MEDICINE

Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer

(2017) Yue Wang et al.   Scientific Reports

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer

(2016) E. K. Law et al.   Science Advances

Detection of Chromosomal Aberrations in Clinical Practice: From Karyotype to Genome Sequence

(2015) Christa Lese Martin et al.   Annual Review of Genomics and Human Genetics

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

Mutational signatures: the patterns of somatic mutations hidden in cancer genomes

(2014) Ludmil B Alexandrov et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

(2014) Serena Nik-Zainal et al.   NATURE GENETICS

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

Genome-wide transcriptome profiling of homologous recombination DNA repair

(2014) Guang Peng et al.   Nature Communications

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Exceptionally long-term persistence of DNA adducts formed by carcinogenic aristolochic acid I in renal tissue from patients with aristolochic acid nephropathy

(2013) Heinz H. Schmeiser et al.   INTERNATIONAL JOURNAL OF CANCER

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool

(2013) S. L. Poon et al.   Science Translational Medicine

Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing

(2013) M. L. Hoang et al.   Science Translational Medicine

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Linking abnormal mitosis to the acquisition of DNA damage

(2012) Neil J. Ganem et al.   JOURNAL OF CELL BIOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Olaparib Maintenance Therapy in Platinum-Sensitive Relapsed Ovarian Cancer

(2012) Jonathan Ledermann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines

(2008) Edurne Arriola et al.   LABORATORY INVESTIGATION