Table 2.
Summary of methodology, advantages, and disadvantages of four major approaches for the detection of HBV pre-S gene deletions and pre-S deleted proteins.
| Sanger DNA Sequencing-Based Approach | Pre-S Gene Chip-Based Approach |
NGS-Based Approach | IHC Staining-Based Approach |
|
|---|---|---|---|---|
| Sample Source | Serum, plasma, or liver tissues | Serum, plasma, or liver tissues | Serum, plasma, or liver tissues | Liver tissues |
| Sample Type | DNA | DNA | DNA | Protein |
| Detection Method | Sanger DNA sequencing | Pre-S gene chip | NGS | IHC staining |
| Detection Target | Pre-S gene deletions | Pre-S gene deletions | Pre-S gene deletions | Pre-S deleted proteins |
| Need of Agarose Gel Electrophoresis | Yes | Yes | No | No |
| Need of TA Cloning | Yes | Yes | No | No |
| Time of Each Assay | 2 to 4 days | 1 to 3 days | 1 to 2 days | 2 days |
| Cost of Each Assay | USD~20 (for single PCR band) | USD~80 (for single PCR band) | USD~700 | USD~30 |
| Advantages | a. Easy to operate b. Provides sequence information |
a. Easy to operate b. A little more time-efficient than the Sanger DNA sequencing-based approach |
a. Much more efficient, sensitive, and accurate than the other approaches b. Provides sequence information c. Provides not only qualitative but also quantitative results |
Provides information on the expression patterns of pre-S deleted proteins in the liver tissues |
| Disadvantages | a. Time-consuming b. Has limitations for analysis of the PCR bands with too-low intensities or too-close sizes c. Provides only qualitative or semiquantitative results |
a. Has limitations for analysis of the PCR bands with too-low intensities or too-close sizes b. Cannot provide sequence information c. Provides only qualitative or semiquantitative results |
a. Requires support from skilled instrument technicians and bioinformatics analysts b. More expensive than the other approaches |
a. Provides results from partial but not whole liver tissues b. Has limitations for detection of proteins at too-low levels c. Provides only qualitative or semiquantitative results |
Abbreviations: HBV, hepatitis B virus; NGS, next-generation sequencing; IHC, immunohistochemistry; TA, thymine–adenine; USD, United States dollar; PCR, polymerase chain reaction.