Table 1 Techniques for identifying the position of HERV-K (HML-2)
Techniques | Need sequencing? | Target enrichment? | High throughput? | Detectable loci | Reference |
|---|---|---|---|---|---|
Mining in the reference human genome (hg19) | No | No | Yes | Proviruses and solo-LTR | Subramanian et al. [17] |
Locus-specific PCR | Yes, Sanger sequencing | Yes, PCR | No | Proviruses or solo-LTR | Otowa et al. [22] Moyes et al. [23] Wildschutte et al. [24] |
Genome-wide amplification of proviral sequences (GAPS) | Yes, Sanger sequencing | Yes, PCR | No | Proviruses | Macfarlane and Badge [25] |
Mining in whole-genome sequencing (WGS) data | Yes, WGS | No | Yes | Proviruses and solo-LTR | Wildschutte et al. [19] Wallace et al. [18] Hollway et al. [26] |
Customized target enrichment method | Yes, Miseq PE300 | Yes, probe-based enrichment | Yes | Proviruses and solo-LTR | Santander et al. [27] Karamitors et al. [16] |
Specific PCR enrichment protocol target HML-2 proviruses | Yes, Miseq | Yes, PCR-based enrichment | Yes | Proviruses | Hollway et al. [26] |
PCR-based target enrichment sequencing of HERV-K (HML-2) (PTESHK) | Yes, Hiseq X ten | Yes, PCR-based enrichment | Yes | Proviruses and solo-LTR | This study |