Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy 1

Xiaoyang Lan, David J. Jörg, Florence M. G. Cavalli, Laura M. Richards, Long V. 2 Nguyen, Robert J. Vanner, Paul Guilhamon, Lilian Lee, Michelle Kushida, Davide 3 Pellacani, Nicole I. Park, Fiona J. Coutinho, Heather Whetstone, Hayden J. 4 Selvadurai, Clare Che, Betty Luu, Annaick Carles, Michelle Moksa, Naghmeh 5 Rastegar, Renee Head, Sonam Dolma, Panagiotis Prinos, Michael D. Cusimano, 6 Sunit Das, Mark Bernstein, Cheryl H. Arrowsmith, Andrew J. Mungall, Richard A. 7 Moore, Yussanne Ma, Marco Gallo, Mathieu Lupien, Trevor J. Pugh, Michael D. 8 Taylor, Martin Hirst, Connie J. Eaves, Benjamin D. Simons, and Peter B. 9 Dirks 10

[1]  I. Glauche,et al.  Limitations and challenges of genetic barcode quantification , 2017, Scientific Reports.

[2]  Giovanni Coppola,et al.  Identification of an Efficient Gene Expression Panel for Glioblastoma Classification , 2016, PloS one.

[3]  Renata Walewska,et al.  Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks , 2016, Nature Communications.

[4]  Marc J. Williams,et al.  Identification of neutral tumor evolution across cancer types , 2016, Nature Genetics.

[5]  B. Simons.  Deep sequencing as a probe of normal stem cell fate and preneoplasia in human epidermis , 2015, Proceedings of the National Academy of Sciences.

[6]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[7]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[8]  M. Stratton,et al.  High burden and pervasive positive selection of somatic mutations in normal human skin , 2015, Science.

[9]  Trevor J Pugh,et al.  Oncotator: Cancer Variant Annotation Tool , 2015, Human mutation.

[10]  Martin A. Nowak,et al.  A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity , 2015, Nature.

[11]  Sohrab P. Shah,et al.  Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution , 2014, Nature.

[12]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[13]  Nicolai J. Birkbak,et al.  Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data , 2014, Annals of oncology : official journal of the European Society for Medical Oncology.

[14]  Peter Rodgers,et al.  eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses , 2014, PloS one.

[15]  M. Hirst,et al.  Clonal analysis via barcoding reveals diverse growth and differentiation of transplanted mouse and human mammary stem cells. , 2014, Cell stem cell.

[16]  Steven J. M. Jones,et al.  Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma , 2014, Science.

[17]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[18]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[19]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[20]  Joachim M. Buhmann,et al.  TMARKER: A free software toolkit for histopathological cell counting and staining estimation , 2013, Journal of pathology informatics.

[21]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[22]  Joaquín Dopazo,et al.  Qualimap: evaluating next-generation sequencing alignment data , 2012, Bioinform..

[23]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[24]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[25]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[26]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[27]  Andrew Mugler,et al.  Analytic methods for modeling stochastic regulatory networks. , 2010, Methods in molecular biology.

[28]  G. Smyth,et al.  ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays. , 2009, Journal of immunological methods.

[29]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[30]  C. Gardiner.  Stochastic Methods: A Handbook for the Natural and Social Sciences , 2009 .

[31]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[32]  Martin A Nowak,et al.  The age incidence of chronic myeloid leukemia can be explained by a one-mutation model , 2006, Proceedings of the National Academy of Sciences.

[33]  J. Herman,et al.  Predicting lung cancer by detecting aberrant promoter methylation in sputum. , 2000, Cancer research.

[34]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[35]  Norman T. J. Bailey,et al.  The Elements of Stochastic Processes with Applications to the Natural Sciences , 1964 .

[36]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[37]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[38]  Jos Jonkers,et al.  A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites , 2009, Nature Protocols.

[39]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..