Table 1.
Summary of techniques for SV detection
| TECHNIQUE | Detectable SV types | Resolution | Key features |
|---|---|---|---|
| Karyotyping | Large CNV, TRA, aneuploidies | >3 Mbp | Staining |
| FISH | CNV, TRA, CGR | 10 kbp | Fluorescent probes |
| aCGH | CNV, CGR | 5–10 kbp | hybridization |
| SNP Array | CNV, LOH, CGR | 100 bp | SNP probes |
| Illumina short-read Sequencing | Simple SVs, CGR | bp | Paired-end reads |
| WES | Simple SVs | >50 bp (generally more than 3 exons) | Protein coding region |
| 10X genomics | Simple SVs | bp | Gel-bead in Emulsion |
| PacBio SMRT Sequencing | Simple SVs, CGR | bp | CCS and CLR |
| Oxford Nanopore Sequencing | Simple SVs, CGR | bp | Ultra-long reads |
| Bionano Optical mapping | Simple SVs, CGR | >500 bp | Long contigs |
| Strand-seq | INV, SCE | bp | Template strand |
| Transcriptome Sequencing | TRA; Fusion genes | bp | RNA |