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

Kristiana Grigoriadis, Ariana Huebner, Abigail Bunkum, Emma Colliver, Alexander M. Frankell, Mark S. Hill, Kerstin Thol, Nicolai J. Birkbak, Charles Swanton, Simone Zaccaria, Nicholas McGranahan

Published: 2023-11-28 DOI: 10.1038/s41596-023-00913-9

CONIPHER

Phylogenetic Reconstruction

Subclonal Structure

Tumor Sequencing

Error Correction

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306–313 (2012).
Jamal-Hanjani, M. et al. Tracking the evolution of non-small-cell lung cancer. N. Engl. J. Med. 376, 2109–2121 (2017).
Maley, C. C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).
Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).
Frankell, A. M. et al. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 616, 525–533 (2023).
Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254.e39 (2021).
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396–398 (2014).
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).
Satas, G. & Raphael, B. J. Tumor phylogeny inference using tree-constrained importance sampling. Bioinformatics 33, i152–i160 (2017).
Deshwar, A. G. et al. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol. 16, 35 (2015).
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).
Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144–155 (2021).
Malikic, S., McPherson, A. W., Donmez, N. & Sahinalp, C. S. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics 31, 1349–1356 (2015).
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).
Popic, V. et al. Fast and scalable inference of multi-sample cancer lineages. Genome Biol. 16, 91 (2015).
Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).
Al Bakir, M. et al. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 616, 534–542 (2023).
Martínez-Ruiz, C. et al. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 616, 543–552 (2023).
Abbosh, C. et al. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 616, 553–562 (2023).
Karasaki, T. et al. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nat. Med. 29, 833–845 (2023).
Benjamin, D. et al. Calling somatic SNVs and indels with Mutect2. Preprint at http://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).
Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010).
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).
Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64–70 (2015).
Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).
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).
Myers, M. A., Satas, G. & Raphael, B. J. CALDER: inferring phylogenetic trees from longitudinal tumor samples. Cell Syst. 8, 514–522.e5 (2019).
Wintersinger, J. A. et al. Reconstructing complex cancer evolutionary histories from multiple bulk DNA samples using Pairtree. Blood Cancer Discov. 3, 208–219 (2022).

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

Supplementary information

Supplementary Information

推荐阅读