HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

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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Publication Details

Journal
Genome biology
Published
2024-12-18
DOI
https://doi.org/10.1186/s13059-024-03450-0
Citations
5
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
1.17

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HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

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HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

Aurélie Ernst, Olga Lazareva, Urja Parekh, Judith B. Zaugg, Mikael Marttinen, Jan Otoničar, Pooja Sant, Jan‐Philipp Mallm, Linda Hammann, Umut Yildiz, George Philippos, Kyung‐Min Noh, Oliver Stegle, Milena Simovic-Lorenz, Albert P. Li
article en
5 citations

Abstract

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.

Genome biologyVol. 25(1)
German Cancer Research Center (DE), Heidelberg University (DE), Wellcome Sanger Institute (GB), European Molecular Biology Laboratory (DE), European Molecular Biology Laboratory (DE), Deutsches Konsortium für Translationale Krebsforschung (DE)
Deutsches Krebsforschungszentrum, Deutsche Krebshilfe
Good health and well-being
Openalex Percentile: Top 21%
Single-cell and spatial transcriptomics
1.17
DOIOpen Access PDFOpenAlex
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