Cancer genomics: one cell at a time

Table 1 Single-cell sequencing methods ^a

Approach^b	WGA method^c	Enzyme^d	Cells/nuclei^e	Applications^f	Coverage breadth^g	Commercial kits^h	References
SCS DNA-seq
SNS	DOP-PCR	Thermosequenase	Nuclei	Copy number profiling	~10%	WGA4 Sigma	[34]
MALBAC	DOP-PCR	Bst	Cells	Copy number profiling	>90%	Bst NEB	[31]
BGI MDA	MDA	Phi29	Cells	Genome/exome	>90%	Repli-G Qiagen	[30]
NUC-SEQ	MDA	Phi29	Nuclei	Genome/exome	>90%	Repli-G Qiagen	[37]
SCS RNA-seq
Tang method	PolyA priming	Reverse transcriptase	Cells	Transcriptome	3' bias	NA	[21]
Quartz-seq	PolyA priming	Reverse transcriptase	Cells	Transcriptome	3' bias	NA	[24]
CEL-seq	PolyA priming	Transcription in vitro	Cells	Transcriptome	3' bias	NA	[20]
STRT-seq	Template-switching	Reverse transcriptase	Cells	Transcriptome	Full-length	NA	[23]
Smart-seq	Template-switching	RT MMLV	Cells	Transcriptome	Full-length	Clontech	[22]
PMA	MDA	Phi29	Cells	Transcriptome	3' bias	NA	[25]

^aTable summarizes the methods for single-cell DNA sequencing and single-cell RNA sequencing. ^bName of the method; ^camplification method; ^denzyme used for amplification; ^edescription of whether the method was designed for analysis of cells or nuclei; ^fdescription of the type of molecular information that is best measured using the method; ^greference to the total number of bases that can be covered with sequencing data using the approach; ^hindication of whether any commercially available kits have been developed to perform the method. Abbreviations: BGI Beijing Genome Institute, Bst Bacillus stearothermophilus DNA polymerase, DOP-PCR degenerative-oligonucleotide PCR, MALBAC multiple annealing and looping-based amplification cycles, MDA multiple-displacement amplification, NA not applicable, PCR polymerase chain reaction, PMA Phi29 DNA-polymerase-based mRNA transcriptome amplification, RT MMLV reverse transcriptase Moloney murine leukemia virus, SNS single-nucleus sequencing, WGA whole-genome amplification.

ISSN: 1474-760X