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Mutational signatures
Mutational signatures provide a powerful alternative for understanding the pathophysiology of cancer. Currently, experimental efforts aimed at validating and understanding the etiologies of cancer-derived mutational signatures...
Published by: Genome biology
Holistic cancer genome profiling for every patient.
Technological advances in the ability to read the human genome have accelerated the speed of sequencing, such that today we can perform whole genome sequencing (WGS) in one day. Until recently, genomic studies have largely been...
From genome integrity to cancer.
Serena Nik-Zainal
Mar 04, 2019
The genome in each of our normal cells acquires somatic genetic changes throughout life [1]. The burden of DNA damage from exogenous and endogenous sources is considerable, but highly competent DNA repair pathways operate in...
Mutational signatures
Mutational signatures provide a powerful alternative for understanding the pathophysiology of cancer. Currently, experimental efforts aimed at validating and understanding the etiologies of cancer-derived mutational signatures...
DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.
Benjamin Jm Taylor, Serena Nik-Zainal, Yee Ling Wu, Lucy A Stebbings, Keiran Raine, Peter J Campbell, Cristina Rada, Michael R Stratton, Michael S Neuberger
Sep 29, 2018
Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions...
Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers.
BACKGROUND: Complex clusters of rearrangements are a challenge in interpretation of cancer genomes. Some clusters of rearrangements demarcate clear amplifications of driver oncogenes but others are less well understood. A...
Adult Age Distribution Aged Aged 80 and over Algorithms Breast Breast Neoplasms Carrier Proteins Chromosomes Human Pair 11 Chromosomes Human Pair 8 Cyclin D1 Datasets as Topic Female Gene Amplification Genetic Loci Genomics Humans Middle Aged Oncogenes Receptor Fibroblast Growth Factor Type 1 Translocation Genetic whole genome sequencing
A mutational signature in gastric cancer suggests therapeutic strategies.
Ludmil B Alexandrov, Serena Nik-Zainal, Hoi Cheong Siu, Suet Yi Leung, Michael R Stratton
Nov 01, 2018
Targeting defects in the DNA repair machinery of neoplastic cells, for example, those due to inactivating BRCA1 and/or BRCA2 mutations, has been used for developing new therapies in certain types of breast, ovarian and...
Deciphering signatures of mutational processes operative in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Peter J Campbell, Michael R Stratton
Nov 17, 2020
The genome of a cancer cell carries somatic mutations that are the cumulative consequences of the DNA damage and repair processes operative during the cellular lineage between the fertilized egg and the cancer cell. Remarkably...
Short inverted repeats contribute to localized mutability in human somatic cells.
Xueqing Zou, Sandro Morganella, Dominik Glodzik, Helen Davies, Yilin Li, Michael R Stratton, Serena Nik-Zainal
Sep 05, 2018
Selected repetitive sequences termed short inverted repeats (SIRs) have the propensity to form secondary DNA structures called hairpins. SIRs comprise palindromic arm sequences separated by short spacer sequences that form the...
Validating the concept of mutational signatures with isogenic cell models.
Xueqing Zou, Michel Owusu, Rebecca Harris, Stephen P Jackson, Joanna I Loizou, Serena Nik-Zainal
Jun 29, 2018
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they...
Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts
Ilias Georgakopoulos-Soares, Gene Koh, Sophie E. Momen, Josef Jiricny, Martin Hemberg, Serena Nik-Zainal
Apr 24, 2021
Abstract: The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. Here, we introduce a method...
Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature.
Helen R Davies, Kevin D Broad, Zerrin Onadim, Elizabeth A Price, Xueqing Zou, Ibrahim Sheriff, Esin Kotiloğlu Karaa, Irene Scheimberg, M Ashwin Reddy, Mandeep S Sagoo, Shin-Ichi Ohnuma, Serena Nik-Zainal
Feb 17, 2021
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We...
Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts.
Ilias Georgakopoulos-Soares, Gene Koh, Sophie E Momen, Josef Jiricny, Martin Hemberg, Serena Nik-Zainal
Mar 31, 2020
Amino Acid Motifs Computational Biology DNA Breaks Double-Stranded DNA Mutational Analysis DNA Repair DNA Replication Gene Deletion Gene Expression Regulation Neoplastic genetic variation Genome Human Genomics Humans INDEL Mutation Mutagenesis Neoplasms Polynucleotides Repetitive Sequences Nucleic Acid Sequence Analysis RNA Transcription Genetic
APOBEC3A/B deletion polymorphism and cancer risk.
Liv B Gansmo, Paal Romundstad, Kristian Hveem, Lars Vatten, Serena Nik-Zainal, Per Eystein Lønning, Stian Knappskog
Jul 24, 2018
Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature
Helen R. Davies, Kevin D. Broad, Zerrin Onadim, Elizabeth A. Price, Xueqing Zou, Ibrahim Sheriff, Esin Kotiloğlu Karaa, Irene Scheimberg, M. Ashwin Reddy, Mandeep S. Sagoo, Shin-Ichi Ohnuma, Serena Nik-Zainal
Feb 12, 2021
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We...
Benjamin G Challis, Narayanan Kandasamy, Andrew S Powlson, Olympia Koulouri, Anand Kumar Annamalai, Lisa Happerfield, Alison J Marker, Mark J Arends, Serena Nik-Zainal, Mark Gurnell
May 12, 2016
A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer.
Marine Inglebert, Martina Dettwiler, Kerstin Hahn, Anna Letko, Cord Drogemuller, John Doench, Adam Brown, Yasin Memari, Helen R Davies, Andrea Degasperi, Serena Nik-Zainal, Sven Rottenberg
Oct 27, 2022
Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression...
A practical guide for mutational signature analysis in hematological malignancies
Francesco Maura, Andrea Degasperi, Ferran Nadeu, Daniel Leongamornlert, Helen Davies, Luiza Moore, Romina Royo, Bachisio Ziccheddu, Xose S. Puente, Herve Avet-Loiseau, Peter J. Campbell, Serena Nik-Zainal, Elias Campo, Nikhil Munshi, Niccolò Bolli
Jul 04, 2020
Abstract: Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis...
Dramatic response of metastatic cutaneous angiosarcoma to an immune checkpoint inhibitor in a patient with xeroderma pigmentosum
Sophie Momen, Hiva Fassihi, Helen R Davies, Christos Nikolaou, Andrea Degasperi, Catherine M Stefanato, Joao ML Dias, Dhruba Dasgupta, Emma Craythorne, Robert Sarkany, Sophie Papa, Serena Nik-Zainal
Nov 13, 2019
"Mutational signatures" are patterns of mutations that report DNA damage and subsequent repair processes that have occurred. Whole-genome sequencing (WGS) can provide additional information to standard diagnostic techniques and...
metastatic angiosarcoma Adult Antibodies Monoclonal Antibodies Monoclonal Humanized B7-H1 Antigen DNA Mutational Analysis DNA Polymerase II Hemangiosarcoma Humans Male Microsatellite Instability Mutation Poly-ADP-Ribose Binding Proteins Programmed Cell Death 1 Receptor Skin Neoplasms whole genome sequencing Xeroderma Pigmentosum
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