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

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-12-18 DOI:10.1186/s13059-024-03450-0

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

引用次数: 0

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.

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HIPSD&R-seq实现可扩展的基因组拷贝数和转录组分析

单细胞DNA测序（scDNA-seq）能够解码体细胞癌变异。现有的方法受到低通量或不能在同一细胞中与转录组测序相结合的限制。我们提出HIPSD&R-seq（高通量单细胞Dna和RNA -seq），这是一种可扩展且简单易懂的分析方法，可同时分析数千个细胞中的低覆盖率Dna和RNA。我们的方法建立在对10X Genomics平台的修改之上，用于scATAC和多组分析。在人类细胞模型和原代组织的应用中，我们证明了检测稀有克隆的可行性，并将该分析与组合索引相结合，以分析超过17,000个细胞。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.