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SubClonal Hierarchy Inference from Somatic Mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing [article]

Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q Naiman, Rachel Karchin
2014 bioRxiv   pre-print
Using data from three published multi-region tumor sequencing studies of (murine) small cell lung cancer, acute myeloid leukemia, and chronic lymphocytic leukemia, in which the authors reconstructed subclonal  ...  Recent improvements in deep next-generation sequencing of tumor samples and the ability to identify somatic mutations at low allelic fractions have opened the way for new approaches to model the evolution  ...  Modeling of subclone evolution often involves estimating the fraction of cancer cells harboring each somatic mutation i.e., somatic mutation cellularity, which can be inferred from next generation sequencing  ... 
doi:10.1101/011833 fatcat:mlsklhbzanazzljwpw7ff6feqm

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing

Noushin Niknafs, Violeta Beleva-Guthrie, Daniel Q. Naiman, Rachel Karchin, Quaid Morris
2015 PLoS Computational Biology  
Using data from three published multi-region tumor sequencing studies of (murine) small cell lung cancer, acute myeloid leukemia, and chronic lymphocytic leukemia, in which the authors reconstructed subclonal  ...  Recent improvements in deep next-generation sequencing of tumor samples and the ability to identify somatic mutations at low allelic fractions have opened the way for new approaches to model the evolution  ...  Modeling of subclone evolution often involves estimating the fraction of cancer cells harboring each somatic mutation i.e., somatic mutation cellularity, which can be inferred from next generation sequencing  ... 
doi:10.1371/journal.pcbi.1004416 pmid:26436540 pmcid:PMC4593588 fatcat:iz3niy7xvva47ib3jlv5zr53te

Fast and scalable inference of multi-sample cancer lineages

Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef-Haghighi, Robert B West, Serafim Batzoglou
2015 Genome Biology  
LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples  ...  We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.  ...  This work was funded by a grant from KAUST to SB.  ... 
doi:10.1186/s13059-015-0647-8 pmid:25944252 pmcid:PMC4501097 fatcat:dpaz75mcobd5lj2oq3yaarkqdq

Fast and Scalable Inference of Multi-Sample Cancer Lineages [article]

Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef-Haghighi, Robert B. West, Serafim Batzoglou
2014 arXiv   pre-print
LICHeE uses variant allele frequencies of SSNVs obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples.  ...  We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples.  ...  This work was funded by a grant from KAUST to SB.  ... 
arXiv:1412.8574v1 fatcat:2asalqikt5fe3poijhswzmkanq

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  
SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. PLoS Comput Biol 11, e1004416 (2015). 40.  ...  Inferring evolutionary trees From the identified mutation patterns, Treeomics inferred an evolutionary tree rooted at the germline DNA sequence of the pancreatic cancer patient Pam03 (Fig. 2c) .  ...  If there is su cient evidence, Treeomics generates additional subclones to better explain the given data and reconstructs the evolutionary history of a subject by separating the evolutionary trajectories  ... 
doi:10.1038/ncomms14114 pmid:28139641 pmcid:PMC5290319 fatcat:25avxzcat5ddro6tysdkknom2u

Detecting repeated cancer evolution from multi-region tumor sequencing data

Giulio Caravagna, Ylenia Giarratano, Daniele Ramazzotti, Ian Tomlinson, Trevor A. Graham, Guido Sanguinetti, Andrea Sottoriva
2018 Nature Methods  
When applied to multi-region sequencing datasets from lung, breast, renal, and colorectal cancer (768 samples from 178 patients), our method detected repeated evolutionary trajectories in subgroups of  ...  Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge.  ...  In every test, we generated a number of random phylogenetic trees and simulated consistent CCF values from multi-region bulk profiling.  ... 
doi:10.1038/s41592-018-0108-x pmid:30171232 pmcid:PMC6380470 fatcat:mb2rgecifjb7pfts7gytyhhckq

Joint Alignment of Multiple Protein–Protein Interaction Networks via Convex Optimization

Somaye Hashemifar, Qixing Huang, Jinbo Xu
2016 Journal of Computational Biology  
Here, we present HSA, a novel approach to reconstruct 3D chromatin structures at the genome-scale by modeling multi-track Hi-C data.  ...  HSA models chromatin as a Markov chain under a generalized linear model framework, and uses simulated annealing to globally search for the latent structure underlying the cleavage footprints of different  ...  Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type.  ... 
doi:10.1089/cmb.2016.0025 pmid:27428933 fatcat:tr4e3u3hqjaoziavhhsklxkkmi

Reconstruction of Cell Lineage Trees in Mice

Adam Wasserstrom, Rivka Adar, Gabi Shefer, Dan Frumkin, Shalev Itzkovitz, Tomer Stern, Irena Shur, Lior Zangi, Shai Kaplan, Alon Harmelin, Yair Reisner, Dafna Benayahu (+4 others)
2008 PLoS ONE  
A new method for high-resolution reconstruction of parts of such cell lineage trees was recently developed based on phylogenetic analysis of somatic mutations accumulated during normal development of an  ...  Lineage analysis based on somatic mutations enables performing high resolution reconstruction of lineage trees in mice and humans, which can provide fundamental insights to many aspects of their development  ...  Acknowledgments We thank Lea Eisenbach for giving us RMA cells, Keren Katzav and Amit Mishali for the design and preparation of the figures, and Yuval Dor for critical reading of the manuscript.  ... 
doi:10.1371/journal.pone.0001939 pmid:18398465 pmcid:PMC2276688 fatcat:dzbmlqbt4zb4nezfu5ahsxzpaa

Human colorectal pre-cancer atlas identifies distinct molecular programs underlying two major subclasses of pre-malignant tumors [article]

Bob Chen, Eliot T. McKinley, Alan J. Simmons, Marisol A. Ramirez-Solano, Xiangzhu Zhu, Austin N. Southard-Smith, Nicholas O. Markham, Quanhu Sheng, Julia L. Drewes, Yanwen Xu, Cody N. Heiser, Yuan Zhou (+16 others)
2021 bioRxiv   pre-print
We also examined separate sets of 66 and 274 polyps for RNA and targeted gene sequencing, respectively.  ...  AbstractMost colorectal cancers (CRCs) develop from either adenomas (ADs) or sessile serrated lesions (SSLs).  ...  All primer development and next-generation sequencing were conducted by Covance. Sequencing depth was 500X.  ... 
doi:10.1101/2021.01.11.426044 fatcat:les2wnziizcwhknfvaiicyw54a

Mitochondrial Import [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Mutational hazard for humans is generally inferred from mouse data, which include induced mutations.  ...  ▶cancer, ▶methylation of DNA, ▶methyl-Metree: A computer program package for inferring and testing minimum evolutionary trees; designed by the Institute of Molecular Evolution, Pennsylvania State University  ...  Restriction fragment length polymorphism carried out on the mtDNA of 147 people, representing African, Asian, Australian, Caucasian, and New Guinean populations indicated an evolutionary tree by the maximal  ... 
doi:10.1007/978-1-4020-6754-9_10535 fatcat:kablmiledvdx3lxxk4j3tsicca

MITE (mariner insect transposon-like element, miniature inverted-repeat transposable element) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Mutational hazard for humans is generally inferred from mouse data, which include induced mutations.  ...  ▶cancer, ▶methylation of DNA, ▶methyl-Metree: A computer program package for inferring and testing minimum evolutionary trees; designed by the Institute of Molecular Evolution, Pennsylvania State University  ...  Restriction fragment length polymorphism carried out on the mtDNA of 147 people, representing African, Asian, Australian, Caucasian, and New Guinean populations indicated an evolutionary tree by the maximal  ... 
doi:10.1007/978-1-4020-6754-9_10520 fatcat:tj67vdv34vc63hlfupk6xahu24

Inferring tumour evolution from single-cell and multi-sample data

Edith Ross, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Florian Markowetz
2018
This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data.  ...  In the second part of the dissertation, a comprehensive collection of existing multi-sample approaches is used to infer the phylogenies of metastatic breast cancers from ten patients.  ...  Thank you also to past and present members of the Markowetz lab for their friendship and for stimulating discussions.  ... 
doi:10.17863/cam.21747 fatcat:63e6vpdaqvgphmcznvuthcav2q

Survival from cancer of the pancreas in England and Wales up to 2001

N Starling, D Cunningham
2008 British Journal of Cancer  
Skoudy) 108 | 3.2 The cell biology of pancreatic cancer: 5 questions for the next 5 years (F.X. Real, A. Rodolosse and A.  ...  Klöppel) 134 | 3.4 Molecular mechanisms transforming the tumor suppressor TGFβ to a promoter of pancreatic cancer (K.  ...  ., Yokohama, Japan) for his generous gift of epimorphin antibodies.  ... 
doi:10.1038/sj.bjc.6604577 pmid:18813250 pmcid:PMC2557510 fatcat:6n26q7r2qbatnnsgawhc5nxvt4

Intertumoral heterogeneity in patient-specific drug sensitivities in treatment-naïve glioblastoma

Erlend Skaga, Evgeny Kulesskiy, Artem Fayzullin, Cecilie J. Sandberg, Swapnil Potdar, Aija Kyttälä, Iver A. Langmoen, Aki Laakso, Emília Gaál-Paavola, Markus Perola, Krister Wennerberg, Einar O. Vik-Mo
2019 BMC Cancer  
Print production: Reprosentralen, University of Oslo. 3 Vilhelm Magnus demonstrating operative technique for colleagues. From Fodstad et al. J.  ...  Neurosurgery (1990) "As soon as the diagnosis of a brain tumor is established one has to consider if the tumor is operable. (...)  ...  Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention.Science 355, 1330-1334 (2017). 125. Wakimoto, H. et al.  ... 
doi:10.1186/s12885-019-5861-4 fatcat:vf47zncv7bb2fjs4avo5hclioe

17th International Mouse Genome Conference

Ian Smyth, Tom Van Agtmael, Ian J. Jackson
2004 Mammalian Genome  
in the preparation of the abstract booklet, management of workshop finances and general support services they have rendered.  ...  Special acknowledgements to Health Reseach, Inc. of Roswell Park Cancer Institute, New York State Department of Health and the Roswell Park Cancer Institute Office of Scientific Communications for assistance  ...  One of our next targets is between the Cfs and Dmd loa. It is relatively gene poor and crosses an evolutionary breakpoint.  ... 
doi:10.1007/s00335-004-4001-9 pmid:15366370 fatcat:qiobzqwnjbgw7c6c2i4u7ezna4
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