Cargando…

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors

Emerging ultra-low coverage single-cell DNA sequencing (scDNA-seq) technologies have enabled high resolution evolutionary studies of copy number aberrations (CNAs) within tumors. While these sequencing technologies are well suited for identifying CNAs due to the uniformity of sequencing coverage, th...

Descripción completa

Detalles Bibliográficos
Autores principales:	Weber, Leah L., Zhang, Chuanyi, Ochoa, Idoia, El-Kebir, Mohammed
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2023
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593221/ https://www.ncbi.nlm.nih.gov/pubmed/37819942 http://dx.doi.org/10.1371/journal.pcbi.1011544

Ejemplares similares

Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples
por: Zhang, Chuanyi, et al.
Publicado: (2021)

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data
por: El-Kebir, Mohammed, et al.
Publicado: (2015)

Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors
por: Weber, Leah L., et al.
Publicado: (2021)

doubletD: detecting doublets in single-cell DNA sequencing data
por: Weber, Leah L, et al.
Publicado: (2021)

ClonArch: visualizing the spatial clonal architecture of tumors
por: Wu, Jiaqi, et al.
Publicado: (2020)

Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses
por: Zhang, Chuanyi, et al.
Publicado: (2022)

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors
por: Weber, Leah L., et al.
Publicado: (2020)

Sampling and summarizing transmission trees with multi-strain infections
por: Sashittal, Palash, et al.
Publicado: (2020)

Ultra Low-Coverage Whole-Genome Sequencing as an Alternative to Genotyping Arrays in Genome-Wide Association Studies
por: Chat, Vylyny, et al.
Publicado: (2022)

Parsimonious Clone Tree Integration in cancer
por: Sashittal, Palash, et al.
Publicado: (2022)

Jumper enables discontinuous transcript assembly in coronaviruses
por: Sashittal, Palash, et al.
Publicado: (2021)

SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing
por: Rozhoňová, Hana, et al.
Publicado: (2022)

Summarizing the solution space in tumor phylogeny inference by multiple consensus trees
por: Aguse, Nuraini, et al.
Publicado: (2019)

Performance Comparison between Rapid Sequencing Platforms for Ultra-Low Coverage Sequencing Strategy
por: Chen, Shengpei, et al.
Publicado: (2014)

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria
por: Ekblom, Robert, et al.
Publicado: (2014)

High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage
por: Emiola, Akintunde, et al.
Publicado: (2018)

Does policy grow on trees?
por: Knoppers, Bartha M
Publicado: (2014)

Why trees grow at night
por: Zweifel, Roman, et al.
Publicado: (2021)

SaAlign: Multiple DNA/RNA sequence alignment and phylogenetic tree construction tool for ultra-large datasets and ultra-long sequences based on suffix array
por: Wang, Ziyuan, et al.
Publicado: (2022)

SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error
por: El-Kebir, Mohammed
Publicado: (2018)

Genome-wide association of multiple complex traits in outbred mice by ultra low-coverage sequencing
por: Nicod, Jérôme, et al.
Publicado: (2016)

Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data
por: Baghaarabani, Leila, et al.
Publicado: (2021)

Aging in a Long-Lived Clonal Tree
por: Ally, Dilara, et al.
Publicado: (2010)

Standardization of Sequencing Coverage Depth in NGS: Recommendation for Detection of Clonal and Subclonal Mutations in Cancer Diagnostics
por: Petrackova, Anna, et al.
Publicado: (2019)

Effect of clonal testing on the efficiency of genomic evaluation in forest tree breeding
por: Stejskal, J., et al.
Publicado: (2022)

Guide to growing stunning trees & shrubs /
Publicado: (2005)

Aspects of coverage in medical DNA sequencing
por: Wendl, Michael C, et al.
Publicado: (2008)

Intercellular adhesion promotes clonal mixing in growing bacterial populations
por: Kan, Anton, et al.
Publicado: (2018)

TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data
por: Fernandes, Daniel M., et al.
Publicado: (2021)

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data
por: Lalani, Zubair, et al.
Publicado: (2022)

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
por: Kader, Tanjina, et al.
Publicado: (2016)

Trees Grow on Money: Urban Tree Canopy Cover and Environmental Justice
por: Schwarz, Kirsten, et al.
Publicado: (2015)

A multi-labeled tree dissimilarity measure for comparing “clonal trees” of tumor progression
por: Karpov, Nikolai, et al.
Publicado: (2019)

Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors
por: Qi, Yuanyuan, et al.
Publicado: (2019)

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data
por: Zhu, Wei, et al.
Publicado: (2016)

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing
por: Staton, Margaret, et al.
Publicado: (2015)

Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes
por: Hui, Ruoyun, et al.
Publicado: (2020)

Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy
por: Hovelson, Daniel H., et al.
Publicado: (2017)

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data
por: Smolander, Johannes, et al.
Publicado: (2021)

Growing and cultivating the forest genomics database, TreeGenes
por: Falk, Taylor, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_vr0nkr7q9sd7khoe2dd5g3umpb