Literature DB >> 23749958

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.

Nicholas B Larson1, Brooke L Fridley.   

Abstract

SUMMARY: We have developed a novel Bayesian method, PurBayes, to estimate tumor purity and detect intratumor heterogeneity based on next-generation sequencing data of paired tumor-normal tissue samples, which uses finite mixture modeling methods. We demonstrate our approach using simulated data and discuss its performance under varying conditions. AVAILABILITY: PurBayes is implemented as an R package, and source code is available for download through CRAN at http://cran.r-project.org/package=PurBayes. CONTACT: larson.nicholas@mayo.edu SUPPLEMENTARY INFORMATION: Supplementary data are available online at Bioinformatics online.

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Mesh：

Year:  2013        PMID： 23749958      PMCID： PMC3712213          DOI： 10.1093/bioinformatics/btt293

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

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7.  qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.

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Journal:  PLoS One       Date:  2012-09-25       Impact factor: 3.240
  7 in total
  43 in total

1.  MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling.

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Review 2.  An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples.

Authors:  Vinod Kumar Yadav; Subhajyoti De
Journal:  Brief Bioinform       Date:  2014-02-20       Impact factor: 11.622

Review 3.  Evolutionary scalpels for dissecting tumor ecosystems.

Authors:  Daniel I S Rosenbloom; Pablo G Camara; Tim Chu; Raul Rabadan
Journal:  Biochim Biophys Acta Rev Cancer       Date:  2016-12-05       Impact factor: 10.680

Review 4.  A population genetics perspective on the determinants of intra-tumor heterogeneity.

Authors:  Zheng Hu; Ruping Sun; Christina Curtis
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5.  Quantification of Multiple Tumor Clones Using Gene Array and Sequencing Data.

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6.  Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data.

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7.  Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer.

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Journal:  Nat Genet       Date:  2022-06-30       Impact factor: 41.307

8.  SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Authors:  Yi Qiao; Aaron R Quinlan; Amir A Jazaeri; Roeland Gw Verhaak; David A Wheeler; Gabor T Marth
Journal:  Genome Biol       Date:  2014-08-26       Impact factor: 13.583

9.  Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.

Authors:  Mark R Zucker; Lynne V Abruzzo; Carmen D Herling; Lynn L Barron; Michael J Keating; Zachary B Abrams; Nyla Heerema; Kevin R Coombes
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

10.  Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Authors:  Yi Li; Xiaohui Xie
Journal:  Bioinformatics       Date:  2014-04-02       Impact factor: 6.937
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