TABLE 1.
Differences between whole genome amplification methods
| PEP‐PCR | DOP‐PCR | LM‐PCR | T‐PCR | MDA | MALBAC | LIANTI | |
|---|---|---|---|---|---|---|---|
|
Principle |
Completely random priming method |
Partial random priming method |
Adaptor ligation‐mediated PCR |
Two‐step PCR method using tagged random primer |
Multiple displacement amplification |
Multiple annealing and looping‐based amplification cycles | Using Tn5 transponson to achieve amplification without the non‐specific primers |
| Primer | Random primers containing 15 bases | Degenerate primers containing six random primers | Universal primer and an adaptor primer | Tagged random primers containing a 9 to 15 bp arbitrary 3' tail that can bind to any DNA sequence | Six random primers | Twenty‐seven universal primers and eight random primers | / |
| Enzyme | DNA polymerase | DNA polymerase | Taq DNA polymerase | Taq DNA polymerase | Phi29 DNA polymerase | Bst enzyme; Phi29 DNA polymerase | T7 RNA polymerase |
| Coverage | ∼40% | ∼50% | ∼96% | ∼37% | ∼70% | ∼90% | ∼97% |
| Uniformity | Low | Medium | Low | Medium | Low | High | High |
| Coefficient of variation | Medium | High | High | High | Medium | Medium | Low |
| GC preference | High | High | High | High | Medium | Low | Low |
| Advantages | The operation is simple, the quality of template DNA is low, the minimum starting template quantity is up to 5 pg | Simple to operate, minimum starting template up to 50 pg | The yield is high, the fragment is long, and the quality of template DNA is low | High amplification efficiency and product specificity | High yield, minimum initial amount up to 10 pg, good fidelity | Simple operation, high output, minimum starting template of several pocks, reliable and repeatable results | Small amplification deviation and high gene coverage |
| Disadvantages | Low output and poor fidelity | The amplification deviation is large when the initial template is very low | The operation is tedious, and the template DNA is easy to be lost by multi‐step operation | Low gene coverage | Large amplification deviation | It is more difficult to amplify when the initial template is very low, and it is easy to appear false positive | Prone to false positives |
| Application | LOH analysis, STR analysis, and so forth | FISH, SNP analysis, SSCP analysis, and so forth | CGH, SNP, STR analysis, Library establishment, Gene detection, and so forth | STR analysis, Forensic Medicine, DNA identification, and so forth | SNV detection, NGS, STR analysis, single‐cell sequencing, and so forth | Chromosome analysis, CNV detection, SNV detection, CGH, single‐cell sequencing, and so forth | CNV detection, SNV detection, single‐cell sequencing, haploid typing, and so forth |
| Reference | 86 | 9 , 87 , 88 | 44 , 89 , 90 , 91 | 44 | 17 , 28 | 4 , 83 , 92 | 93 , 94 |
Abbreviations: CGH, comparative genomic hybridization; DOP‐PCR, degenerate oligonucleotide primer PCR; FISH, fluorescence in situ hybridization; LIANTI, linear amplification via transposon insertion; LM‐PCR, ligation‐mediated PCR; LOH, loss of heterozygosity; MALBAC, multiple annealing and looping‐based amplification cycles; MDA, multiple displacement amplification; PCR, polymerase chain reaction; PEP‐PCR, primer extension preamplification PCR; SSCP, single‐strand conformation polymorphism; STR, short tandem repeat; T‐PCR, tagged random primer PCR; SNP, single nucleotide polymorphism; SNV, single nucleotide variant; CNV, copy number variation; NGS, next‐generation sequencing.