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Distance Measures for Tumor Evolutionary Trees [article]

Zach DiNardo, Kiran Tomlinson, Anna Ritz, Layla Oesper
2019 bioRxiv   pre-print
We apply CASet and DISC to two simulated and two breast cancer datasets and show that our distance measures allow for more nuanced and accurate delineation between tumor evolutionary trees than existing  ...  inheritance patterns characteristic of tumor evolutionary trees.  ...  There is then a critical need for specially calibrated distance methods that account for the intricacies of tumor evolutionary trees.  ... 
doi:10.1101/591107 fatcat:ajev6u3ihjdpxgjdypyj5xass4

Distance Measures for Tumor Evolutionary Trees

Zach DiNardo, Kiran Tomlinson, Anna Ritz, Layla Oesper, Yann Ponty
2019 Bioinformatics  
We apply CASet and DISC to multiple simulated datasets and two breast cancer datasets and show that our distance measures allow for more nuanced and accurate delineation between tumor evolutionary trees  ...  mutation inheritance patterns characteristic of tumor evolutionary trees.  ...  Acknowledgements We thank Jack Kupiers for useful conversations related to this work.  ... 
doi:10.1093/bioinformatics/btz869 pmid:31750900 pmcid:PMC7141873 fatcat:l2kiwyirirdjzjungkhhodya3a

A Consensus Approach to Infer Tumor Evolutionary Histories

Kiya Govek, Camden Sikes, Layla Oesper
2018 Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '18  
We find a minimum weight spanning arborescence in this graph and prove that the resulting tree minimizes the total distance to all input trees for one of our presented distance measures.  ...  We describe several distance measures between these tumor trees and present an algorithm to solve the consensus problem called GraPhyC.  ...  We also plan to analyze these distance measures further, and perhaps to define new distance measures for computing the distance between tumor evolutionary histories.  ... 
doi:10.1145/3233547.3233584 dblp:conf/bcb/GovekSO18 fatcat:cmrpktnhuzalhh3zdpt7wpbjs4

GraPhyC: Using Consensus to Infer Tumor Evolution

Kiya Govek, Camden Sikes, Yangqiaoyu Zhou, Layla Oesper
2020 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We describe several distance measures between these tumor trees.  ...  We find a minimum weight spanning arborescence in this graph and prove that it minimizes the total distance to all input trees for one of our distance measures.  ...  Distance Between Trees The m-TTCP relies upon having a distance measure between m-tumor trees. Several related distance measures have been proposed.  ... 
doi:10.1109/tcbb.2020.3029689 pmid:33031032 fatcat:7yqkzxo3fjewfm5yygvi5446oi

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Ke Yuan, Thomas Sakoparnig, Florian Markowetz, Niko Beerenwinkel
2015 Genome Biology  
Here, we present BitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways.  ...  Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive.  ...  The authors would like to acknowledge Wei Liu for preparing the Sankey plot script, Edith Ross for converting SNV profiles to binary data, Andrea Sottoriva for helpful discussions and providing the processed  ... 
doi:10.1186/s13059-015-0592-6 pmid:25786108 pmcid:PMC4359483 fatcat:kspn5r667fhf3geq66r7g2jigy

P-203Assessing intratumor heterogeneity and evolutionary distance in exome sequencing of colon cancer

U. Popper
2016 Annals of Oncology  
We found that our distance measure in copy number space is superior to a distance measure in SNV space for colon cancer.  ...  Using our distance measure in copy number space, phylogenetic analysis grouped together the five loci of one tumor and showed their evolutionary branching.  ... 
doi:10.1093/annonc/mdw199.195 fatcat:ynnyi73eyje2jcbcw4p2zm3glm

Scelestial: fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm [article]

Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice Carolyn McHardy
2021 bioRxiv   pre-print
Lineage trees may enable a better understanding of tumor formation and growth, as well as of organ development for healthy body cells.  ...  The objective of cell lineage tree reconstruction is to infer the evolutionary process that generated a set of observed cell genomes.  ...  Sample distance measure between trees We define the sample distance measure between two trees based on the shortest-path matrix idea proposed by [5] .  ... 
doi:10.1101/2021.05.24.445405 fatcat:m4bzniqq75cr7f2ykx5qqxrqg4

Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution [article]

Dian Yang, Matthew G Jones, Santiago Naranjo, William M Rideout, Kyung Hoi Joseph Min, Raymond Ho, Wei Wu, Joseph M Replogle, Jennifer L Page, Jeffrey J Quinn, Felix Horns, Xiaojie Qiu (+11 others)
2021 biorxiv/medrxiv   pre-print
Finally, we showed that tumors develop through stereotypical evolutionary trajectories, and perturbing additional tumor suppressors accelerates tumor progression by creating novel evolutionary paths.  ...  Overall, our study elucidates the hierarchical nature of tumor evolution, and more broadly enables the in-depth study of tumor progression.  ...  We thank Michelle Tan, the UCSF Center for Advanced Technology and the Chan Zuckerberg Biohub for assistance with high-throughput sequencing. We thank UCSF  ... 
doi:10.1101/2021.10.12.464111 fatcat:fg6oujidnvfedi4pussstlkmwm

Phylogenetic Quantification of Intratumor Heterogeneity

Thomas B.K. Watkins, Roland F. Schwarz
2017 Cold Spring Harbor Perspectives in Medicine  
Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions  ...  We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles.  ...  To address these challenges in a unified framework, we developed MEDICC (Minimum Event Distance for Intra-tumor Copy-number Comparisons), an algorithm for computing evolutionary distances between genomes  ... 
doi:10.1101/cshperspect.a028316 pmid:28710259 fatcat:vm3fexo6dbfejpgmklo3kysngy

Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data

Leila Baghaarabani, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Seyed Peyman Shariatpanahi, Bahram Goliaei
2021 BMC Bioinformatics  
Result In this study, a new method called Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching  ...  An appropriate approach for identifying clones is determining the variant allele frequency of mutations that occurred in the tumor.  ...  Let t and f be the distance measurements between customers and the decay function, respectively. The customer assignments are drawn by distance-dependent CRP as Eq. (2).  ... 
doi:10.1186/s12859-021-04338-7 pmid:34461827 fatcat:hgrod6swxvggfftjjj6iedvh6q

Genomic data analysis in tree spaces [article]

Sakellarios Zairis, Hossein Khiabanian, Andrew J. Blumberg, Raul Rabadan
2016 arXiv   pre-print
Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces  ...  In many problem settings one encounters heavily populated phylogenetic trees, where the large number of leaves encumbers visualization and analysis in the relevant evolutionary moduli spaces.  ...  It is also essential to assess the value of genomic information measured at a particular time for predicting subsequent events in tumor progression.  ... 
arXiv:1607.07503v1 fatcat:3pbgdgnk6nhgte5uuhx3tifbju

Inference of clonal selection in cancer populations using single-cell sequencing data [article]

Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky
2018 bioRxiv   pre-print
SCIFIL allows to estimate maximum likelihood fitnesses of clone variants, measure their selective advantages and order of appearance by fitting an evolutionary model into the tumor phylogeny.  ...  Quantification of clonal selection and inference of fitness landscapes of tumors is a key step to understanding evolutionary mechanisms driving cancer.  ...  Evolutionary model. We consider tumor evolution as a branching process described by the mutation tree T .  ... 
doi:10.1101/465211 fatcat:m765mohntjcxlip5ltk5o2bp4q

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity

Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra, Gianvito Urgese
2021 BMC Bioinformatics  
Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass.  ...  Results We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated.  ...  This result verified the hypothesis that the heterogeneity measured by the SHscore captures the evolutionary distance of the cells belonging to the samples analyzed.  ... 
doi:10.1186/s12859-021-04277-3 fatcat:mus2xjaxmffvhfqxmbafwkcpjq

SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances [article]

Sandra Hui, Rasmus Nielsen
2022 bioRxiv   pre-print
We present SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data.  ...  Single cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations.  ...  In order to ensure tree B was a perfectly balanced binary tree and to be consistent between tree structures, read depths for 128 tumor cells and 100 diploid cells were simulated for each tree.  ... 
doi:10.1101/2022.05.12.491742 fatcat:vhiajqc6gnaqhp5awmldci6mpi

Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels

Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova, Arne Elofsson
2020 Bioinformatics  
Results To overcome these limitations, in this paper we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time  ...  Motivation The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster  ...  Acknowledgements The authors acknowledge Iman Hajirasouliha, Victoria Popic and Murray Patterson for many illuminating discussions on tumor phylogenies.  ... 
doi:10.1093/bioinformatics/btaa676 pmid:32730595 pmcid:PMC8055217 fatcat:zj64usox5zbp5ojv4lxup6vdbm
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