Table 1.
Summary of single-cell analysis methods used for CTCs.
| Method | Application | Advantages | Disadvantages | |
|---|---|---|---|---|
| Genomic | Pure PCR-based amplification | Amplifying specific sites in the genome | Better uniformity of amplification | Uneven amplification, low coverage, amplification errors, allele dropout |
| MDA-based methods in HCC | Point mutations amplifying to analyze the genome of patient-derived CTCs | Higher fidelity than PCR-based methods | Amplification bias, allele dropout |
|
| MALBAC combines MDA and PCR-based methods |
Analysis of single-nucleotide variants (SNVs) | Intermediate coverage and uniformity | Allele dropout | |
| LIANTI | Amplifies T7 promoter-tagged DNA fragments into thousands of RNA copies. | Covers 97% of the genome with a reduced false-negative rate. | ||
| GenomPlex and Ampli1 | Copy-number variation (CNV) profiling | Maintains representation of the entire genome through subsequent reamplifications. Preserves precious source material by amplifying nanogram amounts of starting genomic DNA. |
Significantly higher genomic coverage | |
| Transcriptomic | STRT-seq | An established approach to profile entire transcriptomes of individual cells from different cell types | High specificity | 5′-only end base |
| Smart-seq and Smart-seq2 | Single-cell gene expression analyses hold promise for characterizing cellular heterogeneity. | Good coverage of the transcriptome with rarer transcripts being detectable Independent of cell size |
High cost, low specificity, low number of cells |
|
| CEL-seq | Single-cell RNA-Seq using multiplexed linear amplification | Sensitive, accurate, and reproducible | 3′-only end base, low number of cells |
|
| InDrop and Drop-seq | Sequence thousands of single cells in parallel | Cost benefit, high specificity |
3′-only end base | |
| Mars-seq | Analysis to explore cellular heterogeneity by assembling an automated experimental platform that enables RNA profiling of cells | Long-term storage, cost benefit, high specificity |
3′-only end base | |
| 10x Genomics Chromium | A droplet-based scRNA-seq technology allowing genome-wide expression profiling for thousands of cells at once | Cost benefit, high sensitivity and precision |
Must process immediately | |
| Epigenomic | sci-ATAC-seq | Generation of sequencing library molecules is selective toward regions of open chromatin on the hyperactive derivative of the cut-and-paste Tn5 transposase | High throughput, independent of antibody |
Low coverage per cell |
| scChIP-seq | Enabled in-depth characterization of protein-DNA interactions of histone marks at single-cell resolution | High throughput | Low coverage per cell, dependence on antibody |
Pure PCR-based amplification (DOP-PCR), multiple displacement amplification [70], degenerate oligonucleotide-primed polymerase chain reaction, multiple annealing- and looping-based amplification cycles (MALBAC), or linear amplification via transposon insertion (LIANTI).