Using long-read sequencing to detect imprinted DNA methylation

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of ∼10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs

PITER-HCV cohort study as part of the Italian platform for the study of viral hepatitis therapies

L’Italia è uno dei Paesi in Europa con il più alto tasso di prevalenza di infezione dal virus dell’epatite C (Hepatitis C Virus, HCV), causa principale di cirrosi, epatocarcinoma e mortalità correlata a malattie del fegato. Alla luce di questo, i farmaci antivirali “direct acting” (Direct Acting Antiviral Agents, DAA) potrebbero avere un enorme impatto sulla salute pubblica in Italia. Dalla collaborazione tra Istituto Superiore di Sanità, Associazione Italiana per lo Studio del Fegato, Società Italiana per le Malattie Infettive e più di 100 tra i Centri Clinici affiliati, è nato lo studio di coorte longitudinale prospettico PITER-HCV (Piattaforma Italiana per lo studio della Terapia delle Epatiti ViRali). La coorte consisterà di un campione rappresentativo di circa 10.000 pazienti consecutivi con infezione cronica da HCV con un follow-up atteso di almeno 10 anni. La prima finestra di arruolamento è iniziata nel maggio 2014; l’arruolamento sarà riaperto per periodi di tre mesi negli anni seguenti per cogliere l’introduzione dei nuovi DAA.Italy has one of the highest prevalence rates of Hepatitis C Virus (HCV) infection in Europe, and HCV infection is the leading cause of cirrhosis, hepatocellular carcinoma, and liver-related death. In light of this, Direct Acting Antiviral Agents (DAAs) would have a huge public health impact in Italy. A longitudinal prospective HCV cohort study known as PITER (Piattaforma Italiana per lo studio della Terapia delle Epatiti viRali: Italian Platform for the Study of Viral Hepatitis Therapies) has been developed as a collaboration among the Istituto Superiore di Sanità (the National Institute of Public Health in Italy), the Italian Society for the Study of the Liver, the Italian Society for Infectious Diseases, and their more than 100 affiliated Clinical Centres. The cohort will consist of a representative sample of approximately 10,000 consecutive patients with chronic HCV liver disease with an expected follow-up of at least 10 years. The first round of enrolment began in May 2014; enrolment will be re-opened for three-month periods during subsequent years to catch the introduction of new DAAs

La Piattaforma Italiana per lo studio della Terapia delle Epatiti Virali (PITER): il primo grande studio nazionale sull'infezione cronica da virus dell'epatite C

(The Italian Platform for the study of Viral Hepatitis Therapies (PITER): the first national study on chronic HCV infection) - In order to address challenges and unanswered questions in the field of HCV therapy, the Italian Platform for the study of Viral Hepatitis Therapies (PITER), which is a strong collaboration among the Italian National Institute of Health (ISS), the Italian Association for the Study of the Liver (AISF) and the Italian Society of Infective and Tropical Diseases (SIMIT), launched as the first activity the PITER-HCV observational cohort study. Its main goal is to evaluate the direct acting antivirals (DAAs) short and long term outcomes in the patients’ real life, in order to optimize treatment protocols and to ensure the cure equity. The results of 6,058 first enrolled patients represent the first Italian snapshot of patients with chronic hepatitis C in care

Virological failure at one year in triple-class experienced patients switching to raltegravir-based regimens is not predicted by baseline factors

We evaluated rates and determinants of virological failure in triple-class experienced patients receiving raltegravir-based regimens from a national observational study over 48 weeks, defined by any one of the following: (1) no HIV-RNA suppression to undetectable levels (<50 copies/mL) during follow-up; (2) detectable viral load after obtaining undetectable levels; and (3) leaving the study before 48 weeks. Among 101 eligible patients, 26 (25.7%; 95% CI 17.2–34.2) had virological failure. No significant differences between patients with and without virological failure were observed for gender, age, route of transmission, baseline CD4/HIV-RNA, CDC group, hepatitis B or C co-infections, resistance (based on the last genotype available), type and number of concomitant drug classes, concomitant use of darunavir, atazanavir, etravirine, enfuvirtide or maraviroc, and health-related quality-of-life measures. A high rate of treatment response was observed. The analyses did not identify any baseline factor associated with failure, including resistance status. Even if we cannot exclude the presence of pre-existing minority resistant variants not captured by genotypic tests, the lack of baseline predictors of failure suggests the need to monitor patients closely during follow up for other factors, such as potential drug interactions and reduced levels of adherence, which may favour virological failure