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Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013 Journal of Computational Biology  
Our method then leverages the inferred phylogeny to improve the accuracy of SNV discovery.  ...  Experimental analyses demonstrate that our method achieves up to 32% improvement for somatic SNV calling of multiple, related samples over the accuracy of GATK's Unified Genotyper, the state-of-theart  ...  FIG. 1 . 1 Overall workflow of our method for tumor phylogeny inference and improved SNV discovery.  ... 
doi:10.1089/cmb.2013.0106 pmid:24195709 pmcid:PMC3822366 fatcat:syr7jzsxnvgftblgpkhfrfutby

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery [chapter]

Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013 Lecture Notes in Computer Science  
Our method then leverages the inferred phylogeny to improve the accuracy of SNV discovery.  ...  Experimental analyses demonstrate that our method achieves up to 32% improvement for somatic SNV calling of multiple, related samples over the accuracy of GATK's Unified Genotyper, the state-of-theart  ...  FIG. 1 . 1 Overall workflow of our method for tumor phylogeny inference and improved SNV discovery.  ... 
doi:10.1007/978-3-642-37195-0_21 fatcat:2ajs67wvpjdhzah2gduodactqq

Inferring Clonal Composition From Multiple Tumor Biopsies

Matteo Manica, Philippe Chouvarine, Roland Mathis, Ulrich Wagner, Kathrin Oehl, Karim Saba, Laura De Vargas Roditi, Arati N Pati, Maria Rodriguez Martinez, Peter Wild, Pavel Sumazin
2017 Zenodo  
Knowledge about the clonal evolution of each tumor can inform driver-alteration discovery by pointing out initiating genetic events as well as events that contribute to the selective advantage of proliferative  ...  A necessary building block to the reconstruction of clonal evolution from tumor profiles is the estimation of the cellular composition of each tumor subclone (cellularity), and these, in turn, are based  ...  Supplementary Materials Tables S1 and S2, which include phylogenies and cellularity matrices used in simulations, and mutations and inferences from CRPC profiles are available from GitHub, project Chimaera  ... 
doi:10.5281/zenodo.841110 fatcat:t2qtfwjqmvdlvlmy3luvvk56s4

Inferring clonal composition from multiple tumor biopsies [article]

Matteo Manica, Hyunjae Ryan Kim, Roland Mathis, Philippe Chouvarine, Dorothea Rutishauser, Laura De Vargas Roditi, Bence Szalai, Ulrich Wagner, Kathrin Oehl, Karim Saba, Arati Pati, Julio Saez-Rodriguez, Angshumoy Roy, Donald W. Parsons, Peter J. Wild (+2 others)
2019 arXiv   pre-print
Explicit accounting for copy number alterations can dramatically improve mutation frequency estimates, leading to more accurate phylogeny reconstructions and subclone characterizations.  ...  CONCLUSIONS We reported on methodology to improve the accuracy of tumor phylogeny reconstruction by improving mutation-frequency estimates from DNA profiles of multiple same-tumor biopsies.  ...  Simulation of DNA profiling data We used phylogeny models-with sizes ranging from three to twelve tumor subclones, twenty to fifty somatic mutations per subclone, and varying degrees of genetic instability-to  ... 
arXiv:1701.07940v2 fatcat:4iqer3k7tbhx7ecxckojt5q2eu

Genetic Evidence for Early Peritoneal Spreading in Pelvic High-Grade Serous Cancer

Jeremy Chien, Lisa Neums, Alexis F. L. A. Powell, Michelle Torres, Kimberly R. Kalli, Francesco Multinu, Viji Shridhar, Andrea Mariani
2018 Frontiers in Oncology  
Somatic SNVs from each tumor sample were used to reconstruct phylogenies of samples from each patient.  ...  Variant allele frequencies were used to reconstruct subclone phylogenies in each tumor sample. results: We show that pelvic HGS carcinomas are highly heterogeneous, only sharing less than 4% of somatic  ...  Tumor subclones in each sample We next used Clonal Inference of Tumors Using Phylogeny (CITUP) bioinformatic program which analyzes somatic variant allele frequencies (VAFs) to infer cancer subclones in  ... 
doi:10.3389/fonc.2018.00058 pmid:29594039 pmcid:PMC5858520 fatcat:zzk2ulqtyncmnjdpz3vtqqfko4

The Evolutionary Origins of Recurrent Pancreatic Cancer

Hitomi Sakamoto, Marc A Attiyeh, Jeffrey M Gerold, Alvin P Makohon-Moore, Akimasa Hayashi, Jungeui Hong, Rajya Kappagantula, Lance Zhang, Jerry P Melchor, Johannes G Reiter, Alexander Heyde, Craig M. Bielski (+10 others)
2020 Cancer Discovery  
In one patient what was believed to be recurrent disease was an independent (second) primary tumor.  ...  We identified that recurrent disease after adjuvant or first-line platinum therapy corresponds to an increased mutational burden.  ...  To understand the evolutionary origins of recurrent disease in each patient, we inferred phylogenies based on high confidence mutations in each patient (Methods).  ... 
doi:10.1158/2159-8290.cd-19-1508 pmid:32193223 pmcid:PMC7323937 fatcat:hvc7jw4wnbfdray7jqw74ava44

Computational Cancer Biology: An Evolutionary Perspective

Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren, Ruth Nussinov
2016 PLoS Computational Biology  
Cancer cells expand because of the accumulation of selectively advantageous mutations, and expanding clones give rise to new cell subpopulations with increasingly higher somatic fitness (Fig 1) .  ...  Cancer is a leading cause of death worldwide and represents one of the biggest biomedical research challenges of our time. Tumor progression is caused by somatic evolution of cell populations.  ...  The meeting served as a starting point and source of inspiration for this work.  ... 
doi:10.1371/journal.pcbi.1004717 pmid:26845763 pmcid:PMC4742235 fatcat:zspm3avnovekflm5b5vmokgfjq

Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability

Franck Raynaud, Marco Mina, Daniele Tavernari, Giovanni Ciriello, Marcel Kool
2018 PLoS Genetics  
Here, we algorithmically inferred the clonal phylogenies of~6,000 human tumors from 32 tumor types to explore how intra-tumor heterogeneity depends on different implementations of genomic instability.  ...  Independently of the type of instability, tumors with high number of clones invariably evolved through branching phylogenies that could be stratified based on the extent of clonal (early) and subclonal  ...  of somatic mutations and copy number alterations.  ... 
doi:10.1371/journal.pgen.1007669 pmid:30212491 pmcid:PMC6155543 fatcat:de37xjvmxrgerojn7etkgkfhuu

Molecular and clonal evolution in recurrent metastatic gliosarcoma

Kevin J Anderson, Aaron C Tan, Jonathan Parkinson, Michael Back, Marina Kastelan, Allison Newey, Janice Brewer, Helen Wheeler, Amanda L Hudson, Samirkumar B Amin, Kevin C Johnson, Floris P Barthel (+2 others)
2020 Molecular Case Studies  
We compared their mutational and copy-number profiles and inferred the clonal phylogeny.  ...  The tumors harbored shared alterations in GBM driver genes, including mutations in TP53, NF1, and RB1, and CDKN2A deletion.  ...  Acknowledgments K.C.J. is the recipient of an American Cancer Society Fellowship (130984-PF-17-141-01-DMC).  ... 
doi:10.1101/mcs.a004671 pmid:31896544 pmcid:PMC6996521 fatcat:7sfvpxicufb3ljwgvqozwun7pi

Intratumoral Heterogeneity of the Epigenome

Tali Mazor, Aleksandr Pankov, Jun S. Song, Joseph F. Costello
2016 Cancer Cell  
At the time a patient is first diagnosed with cancer, the tumor may be composed of tens of millions of cells.  ...  The patterns of tumor evolution inferred from epigenetic ITH and genetic ITH are remarkably similar, suggesting widespread co-dependency of these disparate mechanisms.  ...  Inference of "evolutionary history" of a tumor from somatic mutations relies on the pattern of shared mutations across multiple samples of a tumor: mutations present in all samples of a tumor are inferred  ... 
doi:10.1016/j.ccell.2016.03.009 pmid:27070699 pmcid:PMC4852161 fatcat:pxgqz2h4ofbzzjpuyr7s2q3kf4

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Ke Yuan, Thomas Sakoparnig, Florian Markowetz, Niko Beerenwinkel
2015 Genome Biology  
Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive.  ...  In two case studies, we demonstrate how BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.  ...  Acknowledgements KY and FM would like to acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.  ... 
doi:10.1186/s13059-015-0592-6 pmid:25786108 pmcid:PMC4359483 fatcat:kspn5r667fhf3geq66r7g2jigy

Abstract 2374: Reconstructing the evolutionary history of metastatic cancers

Johannes G. Reiter, Alvin P. Makohon-Moore, Jeffrey M. Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine A. Iacobuzio-Donahue, Bert Vogelstein, Martin A. Nowak
2016 Cancer Research  
We have developed a tool, called Treeomics, that utilizes Bayesian inference and Integer Linear Programming to reconstruct the phylogeny of metastases.  ...  These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples.  ...  We obtained an average coverage of 69x with 97.5% of bases covered at >10x, revealing a total of 127,597 putative coding and noncoding somatic mutations, (average of 4,908 per sample).  ... 
doi:10.1158/1538-7445.am2016-2374 fatcat:kyyppa6fdbdn5hmjprwlkt4ivu

Reconstructing metastatic seeding patterns of human cancers

Johannes G. Reiter, Alvin P. Makohon-Moore, Jeffrey M. Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine A. Iacobuzio-Donahue, Bert Vogelstein, Martin A. Nowak
2017 Nature Communications  
Inference of tumor phylogenies with improved somatic mutation discovery. J. Comput. Biol. 20, 933-944 (2013). 47. Hajirasouliha, I. & Raphael, B. J.  ...  Clonality inference in multiple tumor samples using phylogeny.  ...  In the case of SNVs in copynumber-neutral regions of the genome, p LOH can be set to zero. 5 . Run through all incompatible mutation patterns ⌫ with a reliability score (Equation (8) )  ... 
doi:10.1038/ncomms14114 pmid:28139641 pmcid:PMC5290319 fatcat:25avxzcat5ddro6tysdkknom2u

Improving personalized prediction of cancer prognoses with clonal evolution models [article]

Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
2019 bioRxiv   pre-print
We develop a computational paradigm using evolutionary tree inference (tumor phylogeny) algorithms to derive features quantifying single-tumor mutational preferences, followed by a machine learning frame-work  ...  We build phylogenies tracing the evolution of subclones of cells in tumor tissues using a variety of somatic genomic alterations, including single nucleotide variations, copy number alterations, and structural  ...  phylogenies of individual tumors and then derive quantitative estimates of the evolutionary processes acting on that tumor from these phylogenies.  ... 
doi:10.1101/761510 fatcat:tovkg6sjdzeb7dvt5cyzmgtzkq

Sensitivity to sequencing depth in single-cell cancer genomics [article]

Joao M. Alves, David Posada
2017 bioRxiv   pre-print
of clonal genotypes or the estimation of phylogenies from single tumor cells.  ...  Altogether, our results suggest that, for relatively large sample sizes (25 or more cells), sequencing single tumor cells at depths >5x does not drastically improve somatic variant discovery, the characterization  ...  In addition, clonal trees were also inferred from 321 the somatic SNVs with OncoNEM [24] .  ... 
doi:10.1101/213744 fatcat:5jibl2rejrh3npwsrq6eqgyfbe
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