SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform

• Published in: Genome Biology Vol. 22; no. 1; p. 195
• Main Authors: Fan, Xiaoying, Yang, Cheng, Li, Wen, Bai, Xiuzhen, Zhou, Xin, Xie, Haoling, Wen, Lu, Tang, Fuchou
• Format: Journal Article
• Language: English
• Published: England BioMed Central 30.06.2021; BMC
• Subjects: Base Sequence; Chromosome Mapping - methods; Chromosomes; Cloning; Colorectal cancer; Colorectal carcinoma; colorectal neoplasms; Colorectal Neoplasms - genetics; Colorectal Neoplasms - pathology; DNA Copy Number Variations; DNA polymerase; DNA Transposable Elements; DNA, Circular - genetics; Extra-chromosomal circular DNAs; genome; Genome, Human; Genomes; HEK293 Cells; High-Throughput Nucleotide Sequencing - methods; Humans; K562 Cells; Metastasis; Method; neoplasm cells; Polymorphism, Single Nucleotide; Single-Cell Analysis - methods; Single-cell genome sequencing; Single-molecule sequencing; Structure variants; Third-generation sequencing platform; transposons; Tumor cell lines; Tumorigenesis; Whole genome sequencing; Whole Genome Sequencing - methods; Single-molecule sequencing; Structure variants; Extra-chromosomal circular DNAs; Third-generation sequencing platform; Single-cell genome sequencing
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-021-02406-y

There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based single-cell whole-genome sequencing (scWGS) method named SMOOTH-seq (single-molecule real-time sequencing of long fragments amplified through transposon insertion). We evaluate the method for detecting CNVs, SVs, and SNVs in human cancer cell lines and a colorectal cancer sample and show that SMOOTH-seq reliably and effectively detects SVs and ecDNAs in individual cells, but shows relatively limited accuracy in detection of CNVs and SNVs. SMOOTH-seq opens a new chapter in scWGS as it generates high fidelity reads of kilobases long.