THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

[1]  Benjamin J. Raphael,et al.  Advances for studying clonal evolution in cancer. , 2013, Cancer letters.

[2]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[3]  Benjamin J. Raphael,et al.  Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data , 2013, RECOMB.

[4]  V. Bafna,et al.  An algorithmic approach for breakage-fusion-bridge detection in tumor genomes , 2013, Proceedings of the National Academy of Sciences.

[5]  J. Korbel,et al.  Criteria for Inference of Chromothripsis in Cancer Genomes , 2013, Cell.

[6]  A. McKenna,et al.  Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia , 2012, Cell.

[7]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[8]  F. Markowetz,et al.  Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling , 2012, Science Translational Medicine.

[9]  Li Zhang,et al.  PurityEst: estimating purity of human tumor samples using next-generation sequencing data , 2012, Bioinform..

[10]  Michael C. Schatz,et al.  Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score , 2012, Bioinform..

[11]  S. C. Sahinalp,et al.  nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing , 2012, Genome research.

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

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

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

[15]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[16]  D. Shibata Heterogeneity and Tumor History , 2012, Science.

[17]  Benjamin J. Raphael,et al.  Reconstructing cancer genomes from paired-end sequencing data , 2012, BMC Bioinformatics.

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

[19]  Huanming Yang,et al.  Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm , 2012, Cell.

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

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

[22]  C. Greenman Estimation of Rearrangement Phylogeny in Cancer , 2012 .

[23]  N. Carter,et al.  Estimation of rearrangement phylogeny for cancer genomes. , 2012, Genome research.

[24]  Thomas LaFramboise,et al.  Calling amplified haplotypes in next generation tumor sequence data. , 2012, Genome research.

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

[26]  Henry M. Wood,et al.  Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data , 2012, Bioinform..

[27]  Mark D. Johnson,et al.  Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion , 2011, Proceedings of the National Academy of Sciences.

[28]  Yuval Kluger,et al.  Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies , 2011, BMC Genomics.

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

[30]  Christopher A. Miller,et al.  ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads , 2011, PloS one.

[31]  E. Mardis,et al.  Analysis of next-generation genomic data in cancer: accomplishments and challenges. , 2010, Human molecular genetics.

[32]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

[33]  C. Perou,et al.  Allele-specific copy number analysis of tumors , 2010, Proceedings of the National Academy of Sciences.

[34]  Oliver Sieber,et al.  A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data , 2010, Genome Biology.

[35]  Russell Schwartz,et al.  Robust unmixing of tumor states in array comparative genomic hybridization data , 2010, Bioinform..

[36]  S. Swamy,et al.  PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data , 2009, Biostatistics.

[37]  Raymond Hemmecke,et al.  Nonlinear Integer Programming , 2009, 50 Years of Integer Programming.

[38]  J. Salk Clonal evolution in cancer , 2010 .

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

[40]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[41]  Gerald T. Quon,et al.  ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing , 2009, Bioinform..

[42]  Ali Bashir,et al.  A geometric approach for classification and comparison of structural variants , 2009, Bioinform..

[43]  Marc A. Attiyeh,et al.  Erratum: Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy (Genome Research (2009) 19 (276-283)) , 2009 .

[44]  Marc A. Attiyeh,et al.  Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. , 2008, Genome research.

[45]  Derek Y. Chiang,et al.  High-resolution mapping of copy-number alterations with massively parallel sequencing , 2009, Nature Methods.

[46]  James R. Downing,et al.  Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia , 2008, Science.

[47]  Barbara L Parsons,et al.  Many different tumor types have polyclonal tumor origin: evidence and implications. , 2008, Mutation research.

[48]  Jiahua Chen,et al.  Extended Bayesian information criteria for model selection with large model spaces , 2008 .

[49]  Elmar Bucher,et al.  Genome‐wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients , 2008, Genes, chromosomes & cancer.

[50]  T. LaFramboise,et al.  SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. , 2008, American journal of human genetics.

[51]  Ali Bashir,et al.  Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer , 2008, PLoS Comput. Biol..

[52]  M. Knowles,et al.  Loss of heterozygosity analysis and DNA copy number measurement on 8p in bladder cancer reveals two mechanisms of allelic loss. , 2005, Cancer research.

[53]  Ajay N. Jain,et al.  Hidden Markov models approach to the analysis of array CGH data , 2004 .

[54]  Martin Strauch,et al.  Reconstructing Tumor Genome Architectures , 2022 .

[55]  Benjamin J. Raphael,et al.  Reconstructing tumor amplisomes , 2004, ISMB/ECCB.

[56]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[57]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[58]  J. Gusella,et al.  A region of deletion on chromosome 22q13 is common to human breast and colorectal cancers. , 2000, Cancer research.

[59]  J. Peterse,et al.  Genetic alterations on chromosome 16 and 17 are important features of ductal carcinoma in situ of the breast and are associated with histologic type , 1999, British Journal of Cancer.

[60]  R Anbazhagan,et al.  Allelic loss of chromosomal arm 8p in breast cancer progression. , 1998, The American journal of pathology.

[61]  S. Rogatto,et al.  Cytogenetic evaluation of 20 primary breast carcinomas. , 2004, Hereditas.

[62]  R. Lidereau,et al.  Loss of heterozygosity on chromosome arm 16q in breast cancer metastases , 1997, Genes, chromosomes & cancer.

[63]  A. Sahin,et al.  Deletion map of chromosome 16q in ductal carcinoma in situ of the breast: refining a putative tumor suppressor gene region. , 1996, Cancer research.

[64]  W. Recant,et al.  Loss of heterozygosity from the short arm of chromosome 8 is an early event in breast cancers , 1995, Genes, chromosomes & cancer.

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