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Native single molecule sequencing and de novo assembly of Hepatitis B Virus to detect 5mCpG

ABSTRACT: Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences

ORGANISM(S): Homo sapiens

PROVIDER: GSE162518 | GEO | 2021/01/05

REPOSITORIES: GEO

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Project description:Only 59% of Alaska Native people have been adequately screened for colorectal cancer (CRC) despite having the highest reported incidence of CRC in the world. A new at-home multi-target stool DNA screening test (MT-sDNA; Cologuard) with high sensitivity for pre-cancerous polyps and CRC is now available. MT-sDNA has not been tested for feasibility or acceptability within the Alaska tribal health care delivery system, and it is unknown whether use of this new test will increase Alaska Native CRC screening rates. The long-term study goal is to improve screening and reduce CRC-attributable mortality. The objective of this application is to test the effectiveness of MT-sDNA for increasing CRC screening in Alaska Native communities using a mixed methods, community-based participatory research (CBPR) approach. The study will be conducted in collaboration with regional Tribal health organizations responsible for providing health care to geographically remote Alaska Native communities. Although the proposed implementation strategy is evidence-informed and promising, it is novel in that MT-sDNA has not been evaluated in the tribal health setting or among rural/remote populations. Using the Social Ecological Model, the research will be multi-level, examining influence on patients, providers, and tribal health organizations (THOs). This research study will pursue two specific aims: (1) Identify patient-, provider-, and system-level factors associated with CRC screening preferences, uptake, and follow-up; and (2) test the effectiveness of graded intensity MT-sDNA intervention in the Alaska Native community setting. For the first aim, focus groups with Alaska Native people who are not adherent to CRC screening guidelines and interviews with healthcare providers will be used to identify factors for future intervention. For the second aim, a three-arm cluster randomized controlled trial (high intensity with patient navigation, medium intensity with mailed reminders, usual care) will provide evidence on the MT-sDNA usefulness (MT-sDNA sample quality and neoplastic yield) as well as the first data on MT-sDNA follow up adherence rates in the Alaska Native population, which will inform plans to scale-up the intervention model. This research has the potential to sustainably improve public health by increasing CRC screening rates among a rural/remote tribal population as well as provide a model for other integrated health systems that provide care to high-risk or underserved populations in the U.S. and worldwide.

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Native single molecule sequencing and de novo assembly of Hepatitis B Virus to detect 5mCpG

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