Literature DB >> 21076057

Mutation and epigenetic molecular clocks in cancer.

Darryl Shibata1.   

Abstract

A quandary of evolution is how to measure change over time. A natural inclination is to use morphologic criteria-the greater the differences between two phenotypes, the greater amount of time needed to evolve these differences. However, appearances may be deceiving, and another approach to infer time is with molecular clocks. Here, the greater the differences between two genomes, on average the greater the time since a common ancestor. Recent advances in DNA sequencing shed new light on how human cancers might evolve.

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Year:  2010        PMID: 21076057      PMCID: PMC3026845          DOI: 10.1093/carcin/bgq239

Source DB:  PubMed          Journal:  Carcinogenesis        ISSN: 0143-3334            Impact factor:   4.944


  37 in total

Review 1.  Molecular clock mirages.

Authors:  F J Ayala
Journal:  Bioessays       Date:  1999-01       Impact factor: 4.345

2.  Investigating stem cells in human colon by using methylation patterns.

Authors:  Y Yatabe; S Tavaré; D Shibata
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

3.  Pushing the envelope on molecular dating.

Authors:  Robert Shields
Journal:  Trends Genet       Date:  2004-05       Impact factor: 11.639

Review 4.  Counting divisions in a human somatic cell tree: how, what and why?

Authors:  Darryl Shibata; Simon Tavaré
Journal:  Cell Cycle       Date:  2006-03-15       Impact factor: 4.534

5.  A Gompertzian model of human breast cancer growth.

Authors:  L Norton
Journal:  Cancer Res       Date:  1988-12-15       Impact factor: 12.701

6.  A comprehensive catalogue of somatic mutations from a human cancer genome.

Authors:  Erin D Pleasance; R Keira Cheetham; Philip J Stephens; David J McBride; Sean J Humphray; Chris D Greenman; Ignacio Varela; Meng-Lay Lin; Gonzalo R Ordóñez; Graham R Bignell; Kai Ye; Julie Alipaz; Markus J Bauer; David Beare; Adam Butler; Richard J Carter; Lina Chen; Anthony J Cox; Sarah Edkins; Paula I Kokko-Gonzales; Niall A Gormley; Russell J Grocock; Christian D Haudenschild; Matthew M Hims; Terena James; Mingming Jia; Zoya Kingsbury; Catherine Leroy; John Marshall; Andrew Menzies; Laura J Mudie; Zemin Ning; Tom Royce; Ole B Schulz-Trieglaff; Anastassia Spiridou; Lucy A Stebbings; Lukasz Szajkowski; Jon Teague; David Williamson; Lynda Chin; Mark T Ross; Peter J Campbell; David R Bentley; P Andrew Futreal; Michael R Stratton
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

7.  A simple algebraic cancer equation: calculating how cancers may arise with normal mutation rates.

Authors:  Peter Calabrese; Darryl Shibata
Journal:  BMC Cancer       Date:  2010-01-05       Impact factor: 4.430

8.  Using DNA methylation patterns to infer tumor ancestry.

Authors:  You Jin Hong; Paul Marjoram; Darryl Shibata; Kimberly D Siegmund
Journal:  PLoS One       Date:  2010-08-09       Impact factor: 3.240

Review 9.  Influence of genetic background on genetically engineered mouse phenotypes.

Authors:  Thomas Doetschman
Journal:  Methods Mol Biol       Date:  2009

10.  High sensitivity mapping of methylated cytosines.

Authors:  S J Clark; J Harrison; C L Paul; M Frommer
Journal:  Nucleic Acids Res       Date:  1994-08-11       Impact factor: 16.971

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  20 in total

1.  Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change.

Authors:  Nicholas Chia; Nicholas Guttenberg
Journal:  Mob Genet Elements       Date:  2011-09-01

2.  Detection and quantification of rare mutations with massively parallel sequencing.

Authors:  Isaac Kinde; Jian Wu; Nick Papadopoulos; Kenneth W Kinzler; Bert Vogelstein
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-17       Impact factor: 11.205

Review 3.  Cancer in light of experimental evolution.

Authors:  Kathleen Sprouffske; Lauren M F Merlo; Philip J Gerrish; Carlo C Maley; Paul D Sniegowski
Journal:  Curr Biol       Date:  2012-09-11       Impact factor: 10.834

4.  Prognostic significance of histone methyltransferase enhancer of zeste homolog 2 in patients with cervical squamous cell carcinoma.

Authors:  Minfei Jin; Zujing Yang; Weiping Ye; Xiaowei Yu; Xiaolin Hua
Journal:  Oncol Lett       Date:  2015-06-04       Impact factor: 2.967

Review 5.  Evaluating the effects of genetic variants of DNA repair genes using cytogenetic mutagen sensitivity approaches.

Authors:  Sherif Z Abdel-Rahman; Randa A El-Zein
Journal:  Biomarkers       Date:  2011-05-20       Impact factor: 2.658

6.  Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.

Authors:  Ronan Chaligne; Federico Gaiti; Dana Silverbush; Joshua S Schiffman; Hannah R Weisman; Lloyd Kluegel; Simon Gritsch; Sunil D Deochand; L Nicolas Gonzalez Castro; Alyssa R Richman; Johanna Klughammer; Tommaso Biancalani; Christoph Muus; Caroline Sheridan; Alicia Alonso; Franco Izzo; Jane Park; Orit Rozenblatt-Rosen; Aviv Regev; Mario L Suvà; Dan A Landau
Journal:  Nat Genet       Date:  2021-09-30       Impact factor: 38.330

Review 7.  Advances for studying clonal evolution in cancer.

Authors:  Li Ding; Benjamin J Raphael; Feng Chen; Michael C Wendl
Journal:  Cancer Lett       Date:  2013-01-23       Impact factor: 8.679

8.  High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

Authors:  Kimberly D Siegmund; Paul Marjoram; Simon Tavaré; Darryl Shibata
Journal:  PLoS One       Date:  2011-06-28       Impact factor: 3.240

9.  Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization.

Authors:  Andrea Sottoriva; Inmaculada Spiteri; Darryl Shibata; Christina Curtis; Simon Tavaré
Journal:  Cancer Res       Date:  2012-10-22       Impact factor: 12.701

Review 10.  Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics.

Authors:  Anna S Nam; Ronan Chaligne; Dan A Landau
Journal:  Nat Rev Genet       Date:  2020-08-17       Impact factor: 53.242

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