Bei Xue
Shantou University Medical College, Canada
Title: Identification of Distribution of Human Endogenous Retroviruses K (HML-2) by PCR-based Target Enrichment Sequencing
Biography
Biography: Bei Xue
Abstract
Human endogenous retroviruses (HERVs), suspected to be transposition-defective, are more likely to reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least accumulation of mutations, has been documented to be involved in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for HERV-K (HML-2), a major barrier in delineating HERV-K (HML-2) function. In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals (3 replicates each). We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified,and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since the integration polymorphism of HERV-K (HML-2) is suspected to be one of the reasons for their pathogenicity, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases.