Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility

Konstantin Queitsch; Travis W Moore; Brendan L O'Connell; Ruth V Nichols; John L Muschler; Dove Keith; Charles Lopez; Rosalie C Sears; Gordon B Mills; Galip Gürkan Yardımcı; Andrew C Adey

doi:10.1016/j.crmeth.2023.100625

Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility

Cell Rep Methods. 2023 Nov 20;3(11):100625. doi: 10.1016/j.crmeth.2023.100625. Epub 2023 Nov 1.

Authors

Affiliations

¹ Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
² Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
³ Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
⁴ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA; Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, Portland, OR, USA.
⁵ Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, Portland, OR, USA.
⁶ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
⁷ Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, Portland, OR, USA.
⁸ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
⁹ Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA. Electronic address: adey@ohsu.edu.

Abstract

Single-cell whole-genome sequencing (scWGS) enables the assessment of genome-level molecular differences between individual cells with particular relevance to genetically diverse systems like solid tumors. The application of scWGS was limited due to a dearth of accessible platforms capable of producing high-throughput profiles. We present a technique that leverages nucleosome disruption methodologies with the widely adopted 10× Genomics ATAC-seq workflow to produce scWGS profiles for high-throughput copy-number analysis without new equipment or custom reagents. We further demonstrate the use of commercially available indexed transposase complexes from ScaleBio for sample multiplexing, reducing the per-sample preparation costs. Finally, we demonstrate that sequential indexed tagmentation with an intervening nucleosome disruption step allows for the generation of both ATAC and WGS data from the same cell, producing comparable data to the unimodal assays. By exclusively utilizing accessible commercial reagents, we anticipate that these scWGS and scWGS+ATAC methods can be broadly adopted by the research community.

Keywords: CP: Biotechnology; CP: Genetics; cancer biology; chromatin accessibility; copy-number alterations; single-cell genomics.

MeSH terms

Chromatin* / genetics
Genome
High-Throughput Nucleotide Sequencing / methods
Nucleosomes* / genetics
Sequence Analysis, DNA / methods

Substances

Chromatin
Nucleosomes

Abstract

MeSH terms

Substances

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