Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations

[1]  Sohrab P. Shah,et al.  TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data , 2014, Genome research.

[2]  Yu Cao,et al.  Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing , 2014, Science.

[3]  Obi L. Griffith,et al.  SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution , 2014, PLoS Comput. Biol..

[4]  N. Navin,et al.  Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing , 2014, Nature.

[5]  A. Bouchard-Côté,et al.  PyClone: statistical inference of clonal population structure in cancer , 2014, Nature Methods.

[6]  P. A. Futreal,et al.  Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing , 2014, Nature Genetics.

[7]  Nicholas B. Larson,et al.  PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data , 2013, Bioinform..

[8]  Linghua Wang,et al.  From human genome to cancer genome: The first decade , 2013, Genome research.

[9]  Joseph T. Chang,et al.  A Melanoma Brain Metastasis with a Donor-Patient Hybrid Genome following Bone Marrow Transplantation: First Evidence for Fusion in Human Cancer , 2013, PloS one.

[10]  Ryan M. Layer,et al.  Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms , 2013, Genome research.

[11]  Serafim Batzoglou,et al.  Genome evolution during progression to breast cancer , 2013, Genome research.

[12]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[13]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[14]  C. Dupuy,et al.  The emerging role of ROS-generating NADPH oxidase NOX4 in DNA-damage responses. , 2012, Mutation research.

[15]  Jesse J. Salk,et al.  Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.

[16]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[17]  Peter Van Loo,et al.  ABSOLUTE cancer genomics , 2012, Nature Biotechnology.

[18]  A. Sivachenko,et al.  Sequence analysis of mutations and translocations across breast cancer subtypes , 2012, Nature.

[19]  A. Børresen-Dale,et al.  The Life History of 21 Breast Cancers , 2012, Cell.

[20]  Michael Wigler,et al.  Genome-wide copy number analysis of single cells , 2012, Nature Protocols.

[21]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[22]  Joshua F. McMichael,et al.  Whole Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition , 2012, Nature.

[23]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[24]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[25]  Huanming Yang,et al.  Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor , 2012, Cell.

[26]  R. Durbin,et al.  Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.

[27]  David Pellman,et al.  Causes and consequences of aneuploidy in cancer , 2012, Nature Reviews Genetics.

[28]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[29]  Steven Salzberg,et al.  BIOINFORMATICS ORIGINAL PAPER , 2004 .

[30]  Michael C. Rusch,et al.  CREST maps somatic structural variation in cancer genomes with base-pair resolution , 2011, Nature Methods.

[31]  C. Osipo,et al.  NOTCH-1 and NOTCH-4 are novel gene targets of PEA3 in breast cancer: novel therapeutic implications , 2011, Breast Cancer Research.

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

[33]  Varda Rotter,et al.  Mutations in the p53 Tumor Suppressor Gene: Important Milestones at the Various Steps of Tumorigenesis. , 2011, Genes & cancer.

[34]  Mingming Jia,et al.  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..

[35]  C. Hudis,et al.  Triple-negative breast cancer: an unmet medical need. , 2011, The oncologist.

[36]  M. Gerlinger,et al.  How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine , 2010, British Journal of Cancer.

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

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

[39]  James Hicks,et al.  Tracing the tumor lineage , 2010, Molecular oncology.

[40]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[41]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[42]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[43]  J. Troge,et al.  Inferring tumor progression from genomic heterogeneity. , 2010, Genome research.

[44]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

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

[46]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[47]  B. Lakshmi,et al.  Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). , 2009, Blood.

[48]  Debra L Winkeljohn.  Triple-negative breast cancer. , 2008, Clinical journal of oncology nursing.

[49]  W. Birchmeier,et al.  Wnt signalling and its impact on development and cancer , 2008, Nature Reviews Cancer.

[50]  P. Polakis.  The many ways of Wnt in cancer. , 2007, Current opinion in genetics & development.

[51]  Xin Cai,et al.  A specific PP2A regulatory subunit, B56γ, mediates DNA damage‐induced dephosphorylation of p53 at Thr55 , 2007, The EMBO journal.

[52]  W. Gu,et al.  FBXO11 Promotes the Neddylation of p53 and Inhibits Its Transcriptional Activity* , 2007, Journal of Biological Chemistry.

[53]  J. Andersen,et al.  Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases , 2007, Breast Cancer Research and Treatment.

[54]  J. Downward,et al.  Phosphoinositide 3-Kinase C2beta regulates cytoskeletal organization and cell migration via Rac-dependent mechanisms. , 2006, Molecular biology of the cell.

[55]  N. Sonenberg,et al.  Upstream and downstream of mTOR. , 2004, Genes & development.

[56]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[57]  Y. Lazebnik,et al.  Cell fusion: a hidden enemy? , 2003, Cancer cell.

[58]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[59]  F. Paronetto,et al.  Image analysis versus flow cytometry for DNA ploidy quantitation of solid tumors: a comparison of six methods of sample preparation. , 1993, Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc.

[60]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.