Single-cell DNA sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD&R-seq (HIgh-throughPut Single-cell Dna and Rna-seq), a scalable yet simple and accessible assay to profile low-coverage DNA and RNA in thousands of cells in parallel. Our approach builds on a modification of the 10X Genomics platform for scATAC and multiome profiling. In applications to human cell models and primary tissue, we demonstrate the feasibility to detect rare clones and we combine the assay with combinatorial indexing to profile over 17,000 cells.
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http://dx.doi.org/10.1186/s13059-024-03450-0 | DOI Listing |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657747 | PMC |
STAR Protoc
December 2024
Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands. Electronic address:
The study of somatic mutations in single cells provides insights into aging and carcinogenesis, which is complicated by the dependency on whole-genome amplification (WGA). Here, we describe a detailed workflow starting from single-cell isolation to WGA by primary template-directed amplification (PTA), sequencing, quality control, and downstream analyses. A machine learning approach, the PTA Analysis Toolkit (PTATO), is used to filter the hundreds to thousands of artificial variants induced by WGA from true mutations at high sensitivity and accuracy.
View Article and Find Full Text PDFClin Epigenetics
December 2024
Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
Background: Pancreatic adenocarcinoma (PDAC) exhibits a complex microenvironment with diverse cell populations influencing patient prognosis. Single-cell RNA sequencing (scRNA-seq) was used to identify prognosis-related cell types, and DNA methylation (DNAm)-based models were developed to predict outcomes based on their cellular characteristics.
Methods: We integrated scRNA-seq, bulk data, and clinical information to identify key cell populations associated with prognosis.
Br J Cancer
December 2024
Institute of Clinical Sciences, Imperial College London, London, UK.
Background: Quiescence is reversible proliferative arrest. Multiple mechanisms regulate quiescence that are not fully understood. High expression of the CDK inhibitor p21 correlates with a poor prognosis in non-small cell lung cancer (NSCLC) and, in non-transformed cells, p21 promotes quiescence after replication stress.
View Article and Find Full Text PDFmBio
December 2024
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Unique for a eukaryote, protein-coding genes in trypanosomes are arranged in polycistronic transcription units (PTUs). This genome arrangement has led to a model where Pol II transcription of PTUs is unregulated and changes in gene expression are entirely post-transcriptional. is unable to infect humans because of its susceptibility to an innate immune complex, trypanosome lytic factor (TLF) in the circulation of humans.
View Article and Find Full Text PDFNAR Genom Bioinform
December 2024
Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, 225 North Avenue NW, Atlanta, GA, 30332, USA.
Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g.
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