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Clonality inference in multiple tumor samples using phylogeny

Salem Malikic, Andrew W. McPherson, Nilgun Donmez, Cenk S. Sahinalp
2015 Computer applications in the biosciences : CABIOS  
Tumors Using Phylogeny).  ...  Using extensive simulations and real datasets comprising tumor samples from two leukemia drugresponse studies, we show that CITUP can infer the evolutionary trajectory of human tumors with high accuracy  ...  In this work we present a combinatorial algorithm, named CITUP (Clonality Inference in Tumors Using Phylogeny), that can exploit data obtained from multiple loci from a single patient to infer the tumor  ... 
doi:10.1093/bioinformatics/btv003 pmid:25568283 fatcat:35rpbac3ibeajeph6diznre2du

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer

Andrew W. McPherson, Fong Chun Chan, Sohrab P. Shah
2017 Cold Spring Harbor Perspectives in Medicine  
We next describe results from a spatial sampling study of highgrade serous (HGS) ovarian cancer, propose mechanisms of disease spread based on the observed clonal mixtures, and provide examples of diversification  ...  As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution.  ...  Inference of clonal genotypes, and measurement of their abundance in bulk tumor samples have been used to great effect in observing clonal dynamics in human cancers.  ... 
doi:10.1101/cshperspect.a029603 pmid:28630229 fatcat:3qmxueqe7vfb5errsxkoi5d5eq

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.  ...  Vice versa, mutations of chromatin remodeling genes often characterized tumors with few subclonal but multiple clonal mutations.  ...  PhyloWGS provides in output detailed phylogenies representing the clonal evolution, thus inferring the clonal architecture and not only the clonal composition of each tumor.  ... 
doi:10.1371/journal.pgen.1007669 pmid:30212491 pmcid:PMC6155543 fatcat:de37xjvmxrgerojn7etkgkfhuu

Evolutionary dynamics and molecular features of intra-tumor heterogeneity [article]

Franck Raynaud, Marco Mina, Giovanni Ciriello
2017 bioRxiv   pre-print
Here, we addressed this challenge by integrating mathematical modeling of cancer evolution with algorithmic inference of clonal phylogenies in 2,600 human tumors from 15 tumor types.  ...  In silico investigations of large tumor cohorts can be used to decipher how multiple clones emerge and organize into complex architectures.  ...  Using the phylogenies inferred by PhyloWGS, we could repeat the same analysis in human tumors.  ... 
doi:10.1101/214791 fatcat:34go64q2bje4lpv3v3i6tygtwa

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data [article]

Sayaka Miura, Tracy Vu, Jiamin Deng, Tiffany Buturla, Jiyeong Choi, Sudhir Kumar
2019 bioRxiv   pre-print
These clone phylogenies are used to infer mutation order and clone origin times during tumor progression, rendering the selection of the appropriate clonal deconvolution method quite critical.  ...  Many computational methods produce clone phylogenies from population bulk sequencing data collected from multiple tumor samples.  ...  (multiple 278 seeding). 279 Lastly, we suggest using multiple methods to infer clone phylogenies and examining the 280 consistency among the results.  ... 
doi:10.1101/697318 fatcat:qblnvlwpejhwblzoogt76p2t3m

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.  ...  AncesTree characterizes the clonal evolution of tumors based on the probabilistic model for errors in observed read fractions and infers phylogeny matrices using integer linear programming.  ...  Phylogeny inference in prostate tumors To further test Chimaera's predictive ability, we studied ultra-deep profiles of multiple regions of a select set of prostate cancers at multiple time points.  ... 
arXiv:1701.07940v2 fatcat:4iqer3k7tbhx7ecxckojt5q2eu

Inferring clonal evolution of tumors from single nucleotide somatic mutations [article]

Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
2013 arXiv   pre-print
When multiple phylogenies are consistent with a given set of SNV frequencies, PhyloSub represents the uncertainty in the tumor phylogeny using a partial order plot.  ...  model, PhyloSub, that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells.  ...  details of the PyClone observation model in their user manual.  ... 
arXiv:1210.3384v4 fatcat:xiqwrfdczbe33ofhbv4ga5ytny

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

Sayaka Miura, Tracy Vu, Jiamin Deng, Tiffany Buturla, Olumide Oladeinde, Jiyeong Choi, Sudhir Kumar
2020 Scientific Reports  
These clone phylogenies are used to infer mutation order and clone origins during tumor progression, rendering the selection of the appropriate clonal deconvolution method critical.  ...  Many computational methods produce clone phylogenies from population bulk sequencing data collected from multiple tumor samples from a patient.  ...  Also, we suggest using multiple methods to infer clone phylogenies and examining the consistency among the results.  ... 
doi:10.1038/s41598-020-59006-2 pmid:32103044 pmcid:PMC7044161 fatcat:yeuznnxnqvdnhe5qlf3igszrxe

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data: Supplementary Materials [article]

Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schaeffer, Xulian Shi, Kui Wu, Guibo Li, Liquin Xu, Yong Hu, Michael Dean, Russell Schwartz
2019 bioRxiv   pre-print
We then improve on that algorithm by integrating deconvolution with clonal phylogeny inference, using a mixed integer linear programming (MILP) model to incorporate a minimum evolution phylogenetic tree  ...  Bulk DNA sequencing is the most common technology to assess ITH, but mixes many genetically distinct cells in each sample, which must then be computationally deconvolved.  ...  circles, also called true cells); in step 2, we simulatedn tumor samples from each region using the k cells; in step 3, we combined then tumor samples to get a simulated bulk tumor; in step 4, we deconvolved  ... 
doi:10.1101/519892 fatcat:radxvlu7hndk3lwepn2a22xxkq

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data [article]

Hamim Zafar, Nicholas Navin, Ken Chen, Luay Nakhleh
2018 bioRxiv   pre-print
The performance of our method on synthetic and experimental datasets suggests that joint reconstruction of tumor clones and clonal phylogeny under a finite-site model of evolution leads to more accurate  ...  inferences.  ...  Figure 3 : 3 Inference of tumor clones and clonal phylogeny using SiCloneFit on metastatic colorectal cancer patient CRC1.  ... 
doi:10.1101/394262 fatcat:6tw3em35mvcknbdwcaz2epjtla

Inferring clonal composition from multiple tumor biopsies

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 (+5 others)
2020 npj Systems Biology and Applications  
Our analyses inferred recurrent initiating mutations in hepatocellular carcinomas, resolved the clonal composition of Wilms' tumors, and characterized the acquisition of mutations in drug-resistant prostate  ...  Instead, we propose an optimization algorithm, Chimæra, to account for the effects of CNAs using profiles of multiple biopsies per tumor.  ...  .; by the Foundation for Research in Science and the Humanities at the University of Zurich to P.J.W., and by NCI R21CA223140, Texas Children's Cancer Center, and Cookies for Kids' Cancer Foundation to  ... 
doi:10.1038/s41540-020-00147-5 pmid:32843649 fatcat:vds3jjg3vzbcxgcqdymnmherqy

Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing

Yuchao Jiang, Yu Qiu, Andy J. Minn, Nancy R. Zhang
2016 Proceedings of the National Academy of Sciences of the United States of America  
Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from  ...  Canopy successfully identifies cell populations and infers phylogenies that are in concordance with existing knowledge and ground truth.  ...  Canopy's inferred phylogeny is confirmed by the SCP samples, which we use as validation.  ... 
doi:10.1073/pnas.1522203113 pmid:27573852 pmcid:PMC5027458 fatcat:wge7d574pnazvcwnhcoyrxxipe

Computational approaches for inferring tumor evolution from single-cell genomic data

Hamim Zafar, Nicholas Navin, Luay Nakhleh, Ken Chen
2018 Current Opinion in Systems Biology  
Precise knowledge about mutational heterogeneity and evolutionary trajectory of a tumor can provide useful insights into predicting cancer progression and designing personalized treatment.  ...  Genomic heterogeneity in tumors results from mutations and selection of high-fitness single cells, the operational components of evolution.  ...  The single-sample approach of bulk sequencing is augmented in multiregion sequencing through which multiple samples obtained from different geographical regions of a tumor are analyzed [25e28] .  ... 
doi:10.1016/j.coisb.2017.11.008 fatcat:ynw5xltnvndghbajgpmhnjpmhy

Inferring clonal evolution of tumors from single nucleotide somatic mutations

Wei Jiao, Shankar Vembu, Amit G Deshwar, Lincoln Stein, Quaid Morris
2014 BMC Bioinformatics  
When multiple phylogenies are consistent with a given set of SNV frequencies, PhyloSub represents the uncertainty in the tumor phylogeny using a "partial order plot".  ...  These SNV frequencies were then used to partially reconstruct the evolutionary history of tumors based on a single [10, 16] or multiple [9] samples of same tumor.  ...  details of the PyClone observation model in their user manual.  ... 
doi:10.1186/1471-2105-15-35 pmid:24484323 pmcid:PMC3922638 fatcat:mdadr3njpbanvjkbcmq4gjidxu

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  
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  ...  on estimates of the relative abundance (frequency) of subclone-specific genetic alterations in tumor biopsies.  ...  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
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