Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02406-y
Keywords
Third-generation sequencing platform; Single-molecule sequencing; Single-cell genome sequencing; Structure variants; Extra-chromosomal circular DNAs
Funding
- Beijing Advanced Innovation Center for Genomics at Peking University
- National Natural Science Foundation of China [31625018]
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There is currently no effective method to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. However, the newly developed SMOOTH-seq method shows promise in reliably and effectively detecting SVs and ecDNAs in individual cells, while having relatively limited accuracy in detecting CNVs and SNVs. SMOOTH-seq opens up new possibilities for single-cell whole-genome sequencing by providing high fidelity reads of kilobases long.
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.
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