Reliable detection of subclonal single-nucleotide variants in tumour cell populations

[1]  J. Stockman,et al.  A Mosaic Activating Mutation in AKT1 Associated with the Proteus Syndrome , 2013 .

[2]  Nancy R. Zhang,et al.  Ultrasensitive detection of rare mutations using next-generation targeted resequencing , 2011, Nucleic acids research.

[3]  H. Fine,et al.  Many tumors in one: a daunting therapeutic prospect. , 2011, Cancer cell.

[4]  Rebecca A Betensky,et al.  Mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma. , 2011, Cancer cell.

[5]  André Altmann,et al.  vipR: variant identification in pooled DNA using R , 2011, Bioinform..

[6]  K. Kinzler,et al.  Detection and quantification of rare mutations with massively parallel sequencing , 2011, Proceedings of the National Academy of Sciences.

[7]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[8]  Trevor J Pugh,et al.  Initial genome sequencing and analysis of multiple myeloma , 2011, Nature.

[9]  P. A. Futreal,et al.  Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma , 2010, Nature.

[10]  S. Nelson,et al.  Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation , 2010, Nature.

[11]  Andrew Menzies,et al.  The patterns and dynamics of genomic instability in metastatic pancreatic cancer , 2010, Nature.

[12]  M. Nowak,et al.  Distant Metastasis Occurs Late during the Genetic Evolution of Pancreatic Cancer , 2010, Nature.

[13]  Niko Beerenwinkel,et al.  Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies , 2010, Nucleic acids research.

[14]  Vikas Bansal,et al.  A statistical method for the detection of variants from next-generation resequencing of DNA pools , 2010, Bioinform..

[15]  Joshua F. McMichael,et al.  Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.

[16]  Olivier Harismendy,et al.  Accurate detection and genotyping of SNPs utilizing population sequencing data. , 2010, Genome research.

[17]  Gurpreet W. Tang,et al.  Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes , 2009, Nature.

[18]  Vikas Bansal,et al.  A statistical method for the detection of variants from next-generation resequencing of DNA pools. , 2010, Bioinformatics.

[19]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[20]  Klaus Nordhausen,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition by Trevor Hastie, Robert Tibshirani, Jerome Friedman , 2009 .

[21]  Ryan D. Morin,et al.  Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution , 2009, Nature.

[22]  R. Holt,et al.  Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. , 2009, Genome research.

[23]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[24]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[25]  Francesco Vallania,et al.  Quantification of rare allelic variants from pooled genomic DNA , 2009, Nature Methods.

[26]  Jeffrey E. Barrick,et al.  Genome-wide mutational diversity in an evolving population of Escherichia coli. , 2009, Cold Spring Harbor symposia on quantitative biology.

[27]  M. Stratton,et al.  Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing , 2008, Proceedings of the National Academy of Sciences.

[28]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[29]  C. Maley,et al.  Cancer is a disease of clonal evolution within the body1–3. This has profound clinical implications for neoplastic progression, cancer prevention and cancer therapy. Although the idea of cancer as an evolutionary problem , 2006 .

[30]  Thomas Lengauer,et al.  ROCR: visualizing classifier performance in R , 2005, Bioinform..

[31]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[32]  Robert C. Elston,et al.  On Fisher's Method of Combining p-Values , 1991 .

[33]  P. Nowell The clonal evolution of tumor cell populations. , 1976, Science.