Table 1.
Summary of Hepatitis B Virus (HBV) DNA integration site detection methods.
Technique | Biases | Drawbacks | Advantages | Suitable Uses | Ref. |
---|---|---|---|---|---|
Southern blot |
|
|
|
Detecting presence of integrated HBV DNA in highly clonal samples | [39,40,42,43,44,45,46] |
Direct cloning and Sanger sequencing |
|
|
|
Determining structure of integrated HBV genome in highly clonal samples | [45,47] |
Alu PCR |
|
|
|
Detecting and sequencing integrated HBV DNA in clonal samples | [48,49,50] |
invPCR |
|
|
|
Detecting and quantifying rare HBV DNA integrations | [16,26,28,29,31,32,33] |
WGS |
|
|
|
Integration site detection in highly clonal samples | [18,19,20,21,22,23] |
WES |
|
|
|
Integration site detection in coding regions | [51,52] |
RNA-Seq |
|
|
|
Virus-fusion transcripts | [19,22,53,54,55] |
invPCR, inverse-nested PCR; WGS, Whole Genome Sequencing; WES, Whole Exome Sequencing; RNA-Seq, RNA Sequencing.