Coupled-Clone Nonnegative Matrix Factorization (CCNMF) is a method for joint inference of clonal structure using paired Single-cell DNA-Seq and RNA-Seq data. The framework is based on optimizing an objective function that maximizes clone structure coherence between single-cell gene expression and copy number profiles, in which the two profiles are copuled by the dosage effect. The coupling dosage effect can be estimated a prior either by a linear regression model using publicly aviable paired RNA and DNA bulk sequencing data (TCGA), or by using an uninformative prior. The workflow in CCNMF is illustrated in the figure below.

install.packages('devtools')
devtools::install_github("XQBai/CCNMF")

• Download NCI-N87 single-cell RNA-seq data from Gene Expression Omnibus, (GEO accession number GSE142750).

• Download NCI-N87 single-cell DNA-seq FASTQ files from National Institute of Health’s SRA repository, accession number PRJNA498809. Then we utilized Cellranger-DNA pipeline to convert raw FASTQ files to copy number variants matrix with small non-overlaping bins times cells on the reference genome (GRCh38). The processed scDNA-seq data is available at CCNMF/data/NCI_N87/scDNA.

• The pipeline using CCNMF to analyzed paired single-cell NCI-N87 cell line datasets is aviailable at CCNMF/example/NCI_N87_pipeline.R.

• Gastric cancer NCI-N87 cell line data was referenced from:

• Noemi Andor, Billy T Lau, Claudia Catalanotti, Anuja Sathe, Matthew Kubit, Jiamin Chen, Cristina Blaj, Athena Cherry, Charles D Bangs, Susan M Grimes, Carlos J Suarez, Hanlee P Ji, Joint single cell DNA-seq and RNA-seq of gastric cancer cell lines reveals rules of in vitro evolution, NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa016, https://doi.org/10.1093/nargab/lqaa016

https://nbviewer.jupyter.org/github/XQBai/CCNMF/blob/master/notebooks/SimulationProcedures.ipynb

https://nbviewer.jupyter.org/github/XQBai/CCNMF/blob/master/notebooks/CCNMF_analyze_simulated_data.ipynb

https://nbviewer.jupyter.org/github/XQBai/CCNMF/blob/master/notebooks/Real_data_analysis.ipynb

Xiangqi Bai, Zhana Duren, Lin Wan and Li C. Xia. Joint Inference of Clonal Structure using Single-cell Genome and Transcriptome Sequencing Data, bioRxiv