Viral integration detection strategies and a technical update on Virus-Clip

Oncovirus infection is crucial in human malignancies.Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration,which can contribute to tumorigenesis.Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon.We discuss about major procedures in performing viral integration detection.More importantly,we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds(hg19 and hg38)and the adoption of multi-thread mode for faster initial read alignment.By comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients,we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time,while there is negligible difference in memory usage.Taken together,with the current update of Virus-Clip,it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.

Single cell analysis informing therapy response in hepatocellular carcinoma and intrahepatic cholangiocarcinoma

Liver cancer is known to have significant degree of intra-tumoral heterogeneity(ITH)(1).Hepatocellular carcinoma(HCC)and intrahepatic cholangiocarcinoma(ICC)are major forms of primary liver cancer,accounting for>95%of cases.ITH is linked,as least in part,to the aggressiveness and refractoriness of liver cancer,rendering its high lethality among human malignancies(2).The complex tumor microenvironment promotes tumor progression and contributes to poor treatment response.Hence,it is vital to address the biological mechanisms underlying liver cancer progression and treatment response analyzing the cells in high resolution rather than the mixture of many cell types.Recent advances in single-cell RNA sequencing(scRNA-seq)provide an avenue to dissect liver cancer in an unprecedented degree of high resolution to characterize the underlying pathogenesis and heterogeneity.