CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction

Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306–313 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jamal-Hanjani, M. et al. Tracking the evolution of non-small-cell lung cancer. N. Engl. J. Med. 376, 2109–2121 (2017).

Article  CAS  PubMed  Google Scholar 

Maley, C. C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).

Article  CAS  PubMed  Google Scholar 

Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Frankell, A. M. et al. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 616, 525–533 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254.e39 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396–398 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Satas, G., Zaccaria, S., El-Kebir, M. & Raphael, B. J. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Syst. 12, 1004–1018.e10 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Satas, G. & Raphael, B. J. Tumor phylogeny inference using tree-constrained importance sampling. Bioinformatics 33, i152–i160 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Deshwar, A. G. et al. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol. 16, 35 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Dentro, S. C., Wedge, D. C. & Van Loo, P. Principles of reconstructing the subclonal architecture of cancers. Cold Spring Harb. Perspect. Med. 7, a026625 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144–155 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Malikic, S., McPherson, A. W., Donmez, N. & Sahinalp, C. S. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics 31, 1349–1356 (2015).

Article  CAS  PubMed  Google Scholar 

El-Kebir, M., Oesper, L., Acheson-Field, H. & Raphael, B. J. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics 31, i62–i70 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Popic, V. et al. Fast and scalable inference of multi-sample cancer lineages. Genome Biol. 16, 91 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Al Bakir, M. et al. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 616, 534–542 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Martínez-Ruiz, C. et al. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 616, 543–552 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Abbosh, C. et al. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 616, 553–562 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karasaki, T. et al. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nat. Med. 29, 833–845 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benjamin, D. et al. Calling somatic SNVs and indels with Mutect2. Preprint at https://www.biorxiv.org/content/10.1101/861054v1 (2019).

Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Zaccaria, S. & Raphael, B. J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nat. Commun. 11, 4301 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64–70 (2015).

Article  CAS  PubMed  Google Scholar 

Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

McGranahan, N. et al. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci. Transl. Med. 7, 283ra54 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Myers, M. A., Satas, G. & Raphael, B. J. CALDER: inferring phylogenetic trees from longitudinal tumor samples. Cell Syst. 8, 514–522.e5 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wintersinger, J. A. et al. Reconstructing complex cancer evolutionary histories from multiple bulk DNA samples using Pairtree. Blood Cancer Discov. 3, 208–219 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

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