BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

Genome Biology
Ke YuanNiko Beerenwinkel

Abstract

Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, we present BitPhylogenyBitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them. We validate our approach in the controlled setting of a simulation study and compare it against several competing methods. In two case studies, we demonstrate how BitPhylogeny BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.

References

Oct 1, 1976·Science·P C Nowell
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Vineet BafnaShibu Yooseph
Sep 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Brian P KelleyTrey Ideker
Feb 28, 2004·Bioinformatics·Eran Halperin, Eleazar Eskin
Jun 5, 2004·Journal of Theoretical Biology·Richard DesperAlejandro A Schäffer
Nov 30, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jung Yeon KimDarryl Shibata
Apr 4, 2006·Cell Cycle·Darryl Shibata, Simon Tavaré
Nov 17, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jason H BielasLawrence A Loeb
Jul 4, 2008·Statistical Applications in Genetics and Molecular Biology·Kimberly D SiegmundDarryl Shibata
May 2, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yongjin ParkRussell Schwartz
Jan 22, 2010·BMC Bioinformatics·Russell Schwartz, Stanley E Shackney
May 14, 2010·PLoS Computational Biology·Markus RiesterFranziska Michor
Jun 12, 2010·Molecular Oncology·Nicholas E Navin, James Hicks
Nov 16, 2010·Carcinogenesis·Darryl Shibata
Jan 5, 2011·Gastroenterology·Trevor A GrahamNicholas A Wright
Jan 7, 2011·PloS One·Roland F SchwarzFlorian Markowetz
Mar 15, 2011·Nature·Nicholas NavinMichael Wigler
May 3, 2011·PLoS Computational Biology·Peng QiuSylvia K Plevritis
Oct 4, 2011·Nature Biotechnology·Peng QiuSylvia K Plevritis
Mar 9, 2012·The New England Journal of Medicine·Marco GerlingerCharles Swanton
May 3, 2012·Nature Communications·Moritz GerstungNiko Beerenwinkel
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
Sep 14, 2012·Frontiers in Microbiology·Niko BeerenwinkelKarin J Metzner
Feb 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Andrea SottorivaSimon Tavaré
Mar 1, 2013·The New England Journal of Medicine·Samuel Aparicio, Carlos Caldas
Jun 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Adam HumphriesTrevor A Graham
Jul 31, 2013·Nucleic Acids Research·Francesco StrinoYuval Kluger
Jul 31, 2013·Genome Biology·Layla OesperBenjamin J Raphael
Jul 31, 2013·Nature Reviews. Genetics·Ehud ShapiroSten Linnarsson
Sep 21, 2013·Nature·Rebecca A BurrellCharles Swanton
Nov 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Raheleh SalariSerafim Batzoglou
Feb 4, 2014·BMC Bioinformatics·Wei JiaoQuaid Morris
Mar 19, 2014·Nature Methods·Andrew RothSohrab P Shah
Apr 20, 2014·PLoS Computational Biology·Roland F SchwarzFlorian Markowetz
Jul 30, 2014·Cell Reports·David BrocksUNKNOWN ICGC Early Onset Prostate Cancer Project
Aug 28, 2014·Bioinformatics·John A Capra, Dennis Kostka
Oct 9, 2014·Systematic Biology·Niko BeerenwinkelFlorian Markowetz

❮ Previous
Next ❯

Citations

Apr 17, 2016·Genome Biology·Edith M Ross, Florian Markowetz
May 7, 2016·Genome Biology·Katharina JahnNiko Beerenwinkel
May 28, 2016·Genome Biology·Alexander Davis, Nicholas E Navin
Jul 29, 2016·Cell Systems·Mohammed El-KebirBenjamin J Raphael
Aug 31, 2016·Proceedings of the National Academy of Sciences of the United States of America·Yuchao JiangNancy R Zhang
Sep 25, 2015·PLoS Computational Biology·Florian Markowetz
Feb 6, 2016·PLoS Computational Biology·Niko BeerenwinkelJens Lagergren
Feb 14, 2017·Nature Reviews. Genetics·Russell Schwartz, Alejandro A Schäffer
Feb 16, 2017·ELife·Justin D SilvermanLawrence A David
May 2, 2017·PLoS Computational Biology·Yusuke MatsuiTeppei Shimamura
Feb 1, 2017·Nature Communications·Johannes G ReiterMartin A Nowak
Jun 30, 2016·Nature Methods·Nicholas E Navin, Ken Chen
Sep 13, 2019·Bioinformatics·Nuraini AguseMohammed El-Kebir
Oct 5, 2019·Bioinformatics·Camir RickettsIman Hajirasouliha
Sep 10, 2019·Algorithms for Molecular Biology : AMB·Yuanyuan QiMohammed El-Kebir
Jul 31, 2020·Bioinformatics·Simone CiccolellaGianluca Della Vedova
Oct 2, 2020·PLoS Computational Biology·Leah L WeberMohammed El-Kebir
Nov 14, 2018·Bioinformatics·Sayaka MiuraSudhir Kumar
Jun 7, 2019·BMC Bioinformatics·Hosein ToosiIman Hajirasouliha
Oct 24, 2017·PLoS Computational Biology·Theodore RomanRussell Schwartz
Jun 23, 2019·Nature Communications·Salem MalikicNiko Beerenwinkel
Apr 18, 2020·BMC Genomics·Garance Cordonnier, Manuel Lafond
Jul 1, 2017·Frontiers in Genetics·Fabio Vandin
May 19, 2017·Algorithms for Molecular Biology : AMB·Mohammed El-KebirRon Zeira
Mar 9, 2017·Cold Spring Harbor Perspectives in Medicine·Stefan C DentroPeter Van Loo
Sep 2, 2018·Nature Methods·Giulio CaravagnaAndrea Sottoriva
Apr 28, 2018·Nature Genetics·Mohammed El-KebirBenjamin J Raphael
Feb 8, 2019·Biophysics Reviews·Christopher Yau, Kieran Campbell
Jan 27, 2019·PloS One·Oyetunji E OgundijoDimitris Anastassiou
May 21, 2020·Quantitative Biology·Wazim Mohammed IsmailHaixu Tang
Jan 7, 2019·BMC Bioinformatics·Oyetunji E Ogundijo, Xiaodong Wang
Aug 18, 2020·Bioinformatics·Simone CiccolellaGianluca Della Vedova
Jun 28, 2020·Bioinformatics·Nico BorgsmüllerNiko Beerenwinkel

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRA050202

Methods Mentioned

BETA
single-cell sequencing
exome sequencing

Software Mentioned

TrAp
BitPhylogeny
SPADE
qquad
sim
igraph
R
PhyloSub
R package
THetA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Molecular Oncology
Nicholas E Navin, James Hicks
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
E P Martins
© 2021 Meta ULC. All rights reserved