Letter to the editor: Low sensitivity of RT‐Alu‐PCR in detection of HBV integrated chimeric transcripts

Abstract

To the editor, We read with great interest the study by Erken et al. in which they developed Alu-PCR and RT-Alu-PCR for quantitative detection of integrated HBV DNA and their chimeric transcripts, respectively. [1] Because their detection of chimeric transcripts relied on the presence of the Alu sequence, here we demonstrate that a huge amount of chimeric transcripts would not be detected by RT-Alu-PCR. Firstly, up to 468 unique HBV integration sites were identified from two RNA-sequencing (RNA-seq) data sets (GSE94660 and SRA447498) of liver samples derived from 47 HBV-related patients with HCC, through the Viral Integration Site Database. Among them, 344 unique long chimeric transcripts were reconstructed using transcriptome F I G U R E 1 Low proportion of chimeric transcripts containing Alu elements. (A) The unique HBV integration sites in two RNA-seq data sets of liver samples from 47 HBV-related patients with HCC were identified, and the integrated long chimeric transcripts were reconstructed by trinity v2.14.0. (B) Representative screenshots of the integrative genomics viewer (IGV) showing the reconstructed chimeric transcripts in one patient with HBV-related HCC with an Alu element. (C) Representative screenshots of the IGV showing the reconstructed chimeric transcripts in the same patient with HBV-related HCC (B) without an Alu element. (D) Schematic diagram of HBV transcripts sharing the overlapping 3′ end.