Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Department of General Surgery, Third Hospital, Peking University, Beijing, 100871, China.
Genome Biol. 2021 Jun 30;22(1):195. 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.
目前尚无有效的方法可在单细胞全基因组水平上检测结构变异（SV）和染色体外环状 DNA（ecDNA）。在此，我们开发了一种新型的基于第三代测序平台的单细胞全基因组测序（scWGS）方法，命名为 SMOOTH-seq（通过转座子插入扩增的长片段的单分子实时测序）。我们评估了该方法在人癌细胞系和结直肠癌样本中检测 CNV、SV 和 SNV 的性能，并表明 SMOOTH-seq 能够可靠有效地在单个细胞中检测 SV 和 ecDNA，但在检测 CNV 和 SNV 方面的准确性相对有限。SMOOTH-seq 在 scWGS 领域开辟了新篇章，因为它能够生成具有高保真度的数千碱基长的读取序列。
