MEDALT: single-cell copy number lineage tracing enabling gene discovery

被引：0
作者：
Fang Wang
Qihan Wang
Vakul Mohanty
Shaoheng Liang
Jinzhuang Dou
Jincheng Han
Darlan Conterno Minussi
Ruli Gao
Li Ding
Nicholas Navin
Ken Chen
机构：
[1] The University of Texas MD Anderson Cancer Center,Department of Bioinformatics and Computational Biology
[2] Sun Yat-sen University,Present Address: Precision Medicine Institute, The First Affiliated Hospital
[3] Rice University,Department of Computer Science
[4] The University of Texas MD Anderson Cancer Center,Department of Cancer Biology
[5] The University of Texas MD Anderson Cancer Center,Department of Genetics
[6] Houston Methodist Research Institute,Department of Cardiovascular Sciences, Center for Bioinformatics and Computational Biology
[7] McDonnell Genome Institute Washington University School of Medicine,Department of Medicine
来源：
Genome Biology | / 22卷
关键词：
Single-cell; scDNA-seq; scRNA-seq; Copy number alteration; Tumor evolution; Lineage tracing; Driver discovery;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees. MEDALT appears more accurate than phylogenetics approaches in reconstructing copy number lineage. From data from 20 triple-negative breast cancer patients, our approaches effectively prioritize genes that are essential for breast cancer cell fitness and predict patient survival, including those implicating convergent evolution.
引用
收藏
相关论文
共 50 条
[21]   CONET: copy number event tree model of evolutionary tumor history for single-cell data [J].
Magda Markowska ;
Tomasz Cąkała ;
BłaŻej Miasojedow ;
Bogac Aybey ;
Dilafruz Juraeva ;
Johanna Mazur ;
Edith Ross ;
Eike Staub ;
Ewa Szczurek .
Genome Biology, 23
[22]   Methods for copy number aberration detection from single-cell DNA-sequencing data [J].
Mallory, Xian F. ;
Edrisi, Mohammadamin ;
Navin, Nicholas ;
Nakhleh, Luay .
GENOME BIOLOGY, 2020, 21 (01)
[23]   CONET: copy number event tree model of evolutionary tumor history for single-cell data [J].
Markowska, Magda ;
Cakala, Tomasz ;
Miasojedow, Blazej ;
Aybey, Bogac ;
Juraeva, Dilafruz ;
Mazur, Johanna ;
Ross, Edith ;
Staub, Eike ;
Szczurek, Ewa .
GENOME BIOLOGY, 2022, 23 (01)
[24]   Methods for copy number aberration detection from single-cell DNA-sequencing data [J].
Xian F. Mallory ;
Mohammadamin Edrisi ;
Nicholas Navin ;
Luay Nakhleh .
Genome Biology, 21
[25]   DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies [J].
Weiner, Samson ;
Bansal, Mukul S. .
LIFE SCIENCE ALLIANCE, 2024, 8 (03)
[26]   Detection of Copy Number Alterations Using Single Cell Sequencing [J].
Knouse, Kristin A. ;
Wu, Jie ;
Hendricks, Austin .
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, 2017, (120)
[27]   A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites [J].
Zwaans, A. ;
Seidel, S. ;
Manceau, M. ;
Stadler, T. .
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2025, 380 (1919)
[28]   The role of single-cell analyses in understanding cell lineage commitment [J].
Gibson, Tyler M. ;
Gersbach, Charles A. .
BIOTECHNOLOGY JOURNAL, 2013, 8 (04) :397-+
[29]   Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics [J].
Kelly Street ;
Davide Risso ;
Russell B. Fletcher ;
Diya Das ;
John Ngai ;
Nir Yosef ;
Elizabeth Purdom ;
Sandrine Dudoit .
BMC Genomics, 19
[30]   Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics [J].
Street, Kelly ;
Risso, Davide ;
Fletcher, Russell B. ;
Das, Diya ;
Ngai, John ;
Yosef, Nir ;
Purdom, Elizabeth ;
Dudoit, Sandrine .
BMC GENOMICS, 2018, 19
12345