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. 2020 Jun 19;15(6):e0234773. doi: 10.1371/journal.pone.0234773

Table 4. Comparison of the pre-S genotyping results by IHC- and NGS-based analyses in 30 HBV-related HCC patients.

Patient groups by pre-S genotyping McNemar’s paired proportion test Simple Kappa Coefficient
NGS (−) NGS (+) P value κ value 95% CI
Patients without (−)/with (+) any type of GGH/pre-S del (n) (%) IHC (−) 5 (17)a 6 (20)b 0.0143 0.51 0.20–0.81
IHC (+) 0 (0)c 19 (63)d
Patients without (−)/with (+) type I GGH (score 1–4) and type II GGH (score 0–4)/deletion spanning pre-S1 gene segment (n) (%) IHC (−) 12 (40) 5 (17) 0.0253 0.67 0.42–0.92
IHC (+) 0 (0) 13 (43)
Patients without (−)/with (+) type II GGH (score 1–4) and type I GGH (score 0–4)/deletion spanning pre-S2 gene segment (n) (%) IHC (−) 9 (30) 6 (20) 0.0143 0.60 0.33–0.86
IHC (+) 0 (0) 15 (50)

aThe number of patients without the indicated GGH and pre-S deletion by both IHC- and NGS-based analyses.

bThe number of patients with the indicated pre-S deletion by NGS- but not IHC-based analysis.

cThe number of patients with the indicated pre-S deletion by IHC- but not NGS-based analysis.

dThe number of patients with the indicated pre-S deletion by both IHC- and NGS-based analyses.

Abbreviations: NGS, next-generation sequencing; GGH, ground glass hepatocytes; IHC, immunohistochemistry; del, deletion; n, number.