General advantages, limitations, and clinical applications of comprehensive genomic methods
| Technique . | CG . | FISH . | CMA . | OGM . | Targeted . | Exome . | WGS . | RNA-seq . |
|---|---|---|---|---|---|---|---|---|
| Viable cells | Yes | No | No | No | No | No | No | No |
| Resolution | ∼5 Mb | 100-200 kb | 20-100 kb | 5-50 kb | 1 bp | 1 bp | 1 bp | 1 bp |
| Coverage | Genome | Targeted | Genome | Genome | Targeted | Exome | Genome | Genome, Targeted |
| Alterations | CNV, SV | CNV, SV | CNV, LOH | CNV, SV | ← SNV, Indel, CNV, SV, LOH → | Gene expression, SV | ||
| Sensitivity (VAF) | 5%-10% | 1%-5% | 30% | 5% | 2% | 5%-10% | 10% | 5% |
| TAT (days)∗ | 2-21 | 1-3 | 3-14 | 4-7 | 5-14 | 5-14 | 3-14 | 5-14 |
| Cost∗ | $ | $ | $$ | $$$ | $$-$$$ | $$$ | $$$$ | $$-$$$ |
| Worldwide use∗ | High | High | Low | Low | Medium | Low | Low | Low |
| Used in | ||||||||
| MDS and MDS/MPN | D, FU | D, FU | D, R | D, R | D, MRD† | D | D, ND | |
| MPN | D | D | D | D | D, MRD† | D | D | ND |
| AML | D, R | D | D | D, R | D, MRD† | D | D | D |
| ALL | D, R | D | D, R | D, R | D | D | D | D |
| Technique . | CG . | FISH . | CMA . | OGM . | Targeted . | Exome . | WGS . | RNA-seq . |
|---|---|---|---|---|---|---|---|---|
| Viable cells | Yes | No | No | No | No | No | No | No |
| Resolution | ∼5 Mb | 100-200 kb | 20-100 kb | 5-50 kb | 1 bp | 1 bp | 1 bp | 1 bp |
| Coverage | Genome | Targeted | Genome | Genome | Targeted | Exome | Genome | Genome, Targeted |
| Alterations | CNV, SV | CNV, SV | CNV, LOH | CNV, SV | ← SNV, Indel, CNV, SV, LOH → | Gene expression, SV | ||
| Sensitivity (VAF) | 5%-10% | 1%-5% | 30% | 5% | 2% | 5%-10% | 10% | 5% |
| TAT (days)∗ | 2-21 | 1-3 | 3-14 | 4-7 | 5-14 | 5-14 | 3-14 | 5-14 |
| Cost∗ | $ | $ | $$ | $$$ | $$-$$$ | $$$ | $$$$ | $$-$$$ |
| Worldwide use∗ | High | High | Low | Low | Medium | Low | Low | Low |
| Used in | ||||||||
| MDS and MDS/MPN | D, FU | D, FU | D, R | D, R | D, MRD† | D | D, ND | |
| MPN | D | D | D | D | D, MRD† | D | D | ND |
| AML | D, R | D | D | D, R | D, MRD† | D | D | D |
| ALL | D, R | D | D, R | D, R | D | D | D | D |
ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; CG, cytogenetics; CMA, chromosomal microarray; CNV, copy number variations; D, diagnosis; ES, exome sequencing; FISH, fluorescence in situ hybridization; FU, follow-up; Indel, small insertion/deletions; LOH, loss-of-heterozygosity; MPN, myeloproliferative neoplasm; ND, not done; OGM, optical genome mapping; R, relapse; SNV, single nucleotide variant; SV, structural variant; TAT, turnaround time.
TATs, cost, and use approximated. Actual TATs, cost, and use vary significantly by region and laboratory.
When used in conjunction with high coverage sequencing and error correction methods for increased sensitivity/specificity for low-abundance mutations.