Conceptual models and databases for searching the genome

Genomics is an extremely complex domain, in terms of concepts, their relations, and their representations in data. This tutorial introduces the use of ER models in the context of genomic systems: conceptual models are of great help for simplifying this domain and making it actionable. We carry out a review of successful models presented in the literature for representing biologically relevant entities and grounding them in databases. We draw a difference between conceptual models that aim to explain the domain and conceptual models that aim to support database design and heterogeneous data integration. Genomic experiments and/or sequences are described by several metadata, specifying information on the sampled organism, the used technology, and the organizational process behind the experiment. Instead, we call data the actual regions of the genome that have been read by sequencing technologies and encoded into a machiner readable representation. First, we show how data and metadata can be modeled, then we exploit the proposed models for designing search systems, visualizers, and analysis environments. Both domains of human genomics and viral genomics are addressed, surveying several use cases and applications of broader public interest. The tutorial is relevant to the EDBT community because it demonstrates the usefulness of conceptual models’ principles within very current domains; in addition, it offers a concrete example of conceptual models’ use, setting the premises for interdisciplinary collaboration with a greater public (possibly including life science researchers)

VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants

With the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can 'hunt' novel emerging variants of SARS-CoV-2 as early as possible, and then monitor their evolution and spread. We designed VariantHunter, a highly flexible and user-friendly tool for systematically monitoring the evolution of SARS-CoV-2 at global and regional levels. In VariantHunter, amino acid changes are analyzed over an interval of 4 weeks in an arbitrary geographical area (continent, country, or region); for every week in the interval, the prevalence is computed and changes are ranked based on their increase or decrease in prevalence. VariantHunter supports two main types of analysis: lineage-independent and lineage-specific. The former considers all the available data and aims to discover new viral variants. The latter evaluates specific lineages/viral variants to identify novel candidate designations (sub-lineages and sub-variants). Both analyses use simple statistics and visual representations (diffusion charts and heatmaps) to track viral evolution. A dataset explorer allows users to visualize available data and refine their selection. VariantHunter is a web application free to all users. The two types of supported analysis (lineage-independent and lineage-specific) allow user-friendly monitoring of the viral evolution, empowering genomic surveillance without requiring any computational background. Database URL http://gmql.eu/variant_hunter/

Gilbert Syndrome and the Development of Antiretroviral Therapy-Associated Hyperbilirubinemia

BackgroundUnconjugated hyperbilirubinemia results from Gilbert syndrome and from antiretroviral therapy (ART) containing protease inhibitors. An understanding of the interaction between genetic predisposition and ART may help to identify individuals at highest risk for developing jaundice MethodsWe quantified the contribution of UGT1A1*28 and ART to hyperbilirubinemia by longitudinally modeling 1386 total bilirubin levels in 96 human immunodeficiency virus (HIV)-infected individuals during a median of 6 years ResultsThe estimated average bilirubin level was 8.8 μmol/L (0.51 mg/dL). Atazanavir increased bilirubin levels by 15 μmol/L (0.87 mg/dL), and indinavir increased bilirubin levels by 8 μmol/L (0.46 mg/dL). Ritonavir, lopinavir, saquinavir, and nelfinavir had no or minimal effect on bilirubin levels. Homozygous UGT1A1*28 increased bilirubin levels by 5.2 μmol/L (0.3 mg/dL). As a consequence, 67% of individuals homozygous for UGT1A1*28 and receiving atazanavir or indinavir had ⩾2 episodes of hyperbilirubinemia in the jaundice range (>43 μmol/L [>2.5 mg/dL]), versus 7% of those with the common allele and not receiving either of those protease inhibitors (P<.001). Efavirenz resulted in decreased bilirubin levels, which is consistent with the induction of UDP-glucuronosyltransferase 1A1 ConclusionsGenotyping for UGT1A1*28 before initiation of ART would identify HIV-infected individuals at risk for hyperbilirubinemia and decrease episodes of jaundic

CD4+ T Cell Count Recovery in HIV Type 1-Infected Patients Is Independent of Class of Antiretroviral Therapy

Background. In recent years, treatment options for human immunodeficiency virus type 1 (HIV-1) infection have changed from nonboosted protease inhibitors (PIs) to nonnucleoside reverse-transcriptase inhibitors (NNRTIs) and boosted PI-based antiretroviral drug regimens, but the impact on immunological recovery remains uncertain. Methods. During January 1996 through May 2007, all patients in the Swiss HIV Cohort were included if they received the first combination antiretroviral therapy (cART) and had known baseline CD4+ T cell counts and HIV-1 RNA values (n=3293). The mean (±SD) duration of follow-up was 26.8±20.5 months. The follow-up time was limited to the duration of the first cART. CD4+ T cell recovery was analyzed in 3 different treatment groups: nonboosted PI, NNRTI, or boosted PI. The end point was the absolute increase of CD4+ T cell count in the 3 treatment groups after the initiation of cART. Results. Two thousand five hundred ninety individuals (78.7%) initiated a nonboosted-PI regimen, 452 (13.7%) initiated an NNRTI regimen, and 251 (7.6%) initiated a boosted-PI regimen. Absolute CD4+ T cell count increases at 48 months were as follows: in the nonboosted-PI group, from 210 to 520 cells/µL; in the NNRTI group, from 220 to 475 cells/µL; and in the boosted-PI group, from 168 to 511 cells/µL. In a multivariate analysis, the treatment group did not affect the response of CD4+ T cells; however, increased age, pretreatment with nucleoside reverse-transcriptase inhibitors, serological tests positive for hepatitis C virus, Centers for Disease Control and Prevention stage C infection, lower baseline CD4+ T cell count, and lower baseline HIV-1 RNA level were risk factors for smaller increases in CD4+ T cell count. Conclusion. CD4+ T cell recovery was similar in patients receiving nonboosted PI-, NNRTI-, and boosted PI-based cAR

Durability and Outcome of Initial Antiretroviral Treatments Received during 2000-2005 by Patients in the Swiss HIV Cohort Study

Background. Little is known about time trends, predictors, and consequences of changes made to antiretroviral therapy (ART) regimens early after patients initially start treatment. Methods. We compared the incidence of, reasons for, and predictors of treatment change within 1 year after starting combination ART (cART), as well as virological and immunological outcomes at 1 year, among 1866 patients from the Swiss HIV Cohort Study who initiated cART during 2000-2001, 2002-2003, or 2004-2005. Results. The durability of initial regimens did not improve over time (P = .15): 48.8% of 625 patients during 2000-2001, 43.8% of 607 during 2002-2003, and 44.3% of 634 during 2004-2005 changed cART within 1 year; reasons for change included intolerance (51.1% of all patients), patient wish (15.4%), physician decision (14.8%), and virological failure (7.1%). An increased probability of treatment change was associated with larger CD4+ cell counts, larger human immunodeficiency virus type 1 (HIV-1) RNA loads, and receipt of regimens that contained stavudine or indinavir/ritonavir, but a decreased probability was associated with receipt of regimens that contained tenofovir. Treatment discontinuation was associated with larger CD4+ cell counts, current use of injection drugs, and receipt of regimens that contained nevirapine. One-year outcomes improved between 2000-2001 and 2004-2005: 84.5% and 92.7% of patients, respectively, reached HIV-1 RNA loads of <50 copies/mL and achieved median increases in CD4+ cell counts of 157.5 and 197.5 cells/µL, respectively (P < .001 for all comparisons). Conclusions. Virological and immunological outcomes of initial treatments improved between 2000-2001 and 2004-2005, irrespective of uniformly high rates of early changes in treatment across the 3 study interval

Incidence and Risk Factors for Chronic Elevation of Alanine Aminotransferase Levels in HIV-Infected Persons without Hepatitis B or C Virus Co-Infection

Background. Chronic liver disease in human immunodeficiency virus (HIV)-infected patients is mostly caused by hepatitis virus co-infection. Other reasons for chronic alanine aminotransferase (ALT) elevation are more difficult to diagnose. Methods. We studied the incidence of and risk factors for chronic elevation of ALT levels (greater than the upper limit of normal at ⩾2 consecutive semi-annual visits) in participants of the Swiss HIV Cohort Study without hepatitis B virus (HBV) or hepatitis C virus (HCV) infection who were seen during the period 2002-2008. Poisson regression analysis was used. Results. A total of 2365 participants were followed up for 9972 person-years (median age, 38 years; male sex, 66%; median CD4+ cell count, 426/µL; receipt of antiretroviral therapy [ART], 56%). A total of 385 participants (16%) developed chronic elevated ALT levels, with an incidence of 3.9 cases per 100 person-years (95% confidence interval [CI], 3.5-4.3 cases per 100 person-years). In multivariable analysis, chronic elevated ALT levels were associated with HIV RNA level >100,000 copies/mL (incidence rate ratio [IRR], 2.23; 95% CI, 1.45-3.43), increased body mass index (BMI, defined as weight in kilograms divided by the square of height in meters) (BMI of 25-29.9 was associated with an IRR of 1.56 [95% CI, 1.24-1.96]; a BMI ⩾30 was associated with an IRR of 1.70 [95% CI, 1.16-2.51]), severe alcohol use (1.83 [1.19-2.80]), exposure to stavudine (IRR per year exposure, 1.12 [95% CI, 1.07-1.17]) and zidovudine (IRR per years of exposure, 1.04 [95% CI, 1.00-1.08]). Associations with cumulative exposure to combination ART, nucleoside reverse-transcriptase inhibitors, and unboosted protease inhibitors did not remain statistically significant after adjustment for exposure to stavudine. Black ethnicity was inversely correlated (IRR, 0.52 [95% CI, 0.33-0.82]). Treatment outcome and mortality did not differ between groups with and groups without elevated ALT levels. Conclusions. Among patients without hepatitis virus co-infection, the incidence of chronic elevated ALT levels was 3.9 cases per 100 person-years, which was associated with high HIV RNA levels, increased BMI, severe alcohol use, and prolonged stavudine and zidovudine exposure. Long-term follow-up is needed to assess whether chronic elevation of ALT levels will result in increased morbidity or mortalit

Adverse events of raltegravir and dolutegravir.

To compare the frequency and risk factors of toxicity-related treatment discontinuations between raltegravir and dolutegravir. Prospective cohort study. All antiretroviral therapy (ART)-naïve and ART-experienced HIV-infected individuals from the Swiss HIV Cohort Study who initiated raltegravir or dolutegravir between 2006 and 2015 were investigated concerning treatment modification within the first year. Of 4041 patients initiating ART containing raltegravir (n = 2091) or dolutegravir (n = 1950), 568 patients discontinued ART during the first year, corresponding to a rate of 15.5 [95% confidence interval (CI) 14.5-16.9] discontinuations per 100 patient-years. Only 10 patients on raltegravir (0.5%) and two patients on dolutegravir (0.1%) demonstrated virologic failure. The main reason for ART discontinuation was convenience expressed as patient's wish, physician's decision, or treatment simplification (n = 302). Toxicity occurred in 4.3% of patients treated with raltegravir and 3.6% with dolutegravir, respectively. In multivariable analysis, the only independent risk factor for discontinuing ART because of toxicity was female sex (hazard ratio 1.98, 95% CI 1.45-2.71, P &lt; 0.001).Neuropsychiatric complaints were the most commonly reported toxic adverse events and more frequent in the dolutegravir (n = 33, 1.7%) compared with the raltegravir group (n = 13, 0.6%). Risk of discontinuation for neurotoxicity was lower for raltegravir than for dolutegravir in multivariable analysis (hazard ratio 0.46, 95% CI 0.22-0.96, P = 0.037). In this, large cohort raltegravir and dolutegravir-containing regimen demonstrated a high virologic efficacy. Drug toxicity was infrequent and discontinuation because of neuropsychiatric events within the first year of treatment was only marginal higher with dolutegravir compared with raltegravir. However, monitoring of neurotoxic side-effects of dolutegravir is important

Incidence and Outcome of Progressive Multifocal Leukoencephalopathy over 20 Years of the Swiss HIV Cohort Study

Background. We investigated the incidence and outcome of progressive multifocal leukoencephalopathy (PML) in human immunodeficiency virus (HIV)-infected individuals before and after the introduction of combination antiretroviral therapy (cART) in 1996. Methods. From 1988 through 2007, 226 cases of PML were reported to the Swiss HIV Cohort Study. By chart review, we confirmed 186 cases and recorded all-cause and PML-attributable mortality. For the survival analysis, 25 patients with postmortem diagnosis and 2 without CD4+ T cell counts were excluded, leaving a total of 159 patients (89 before 1996 and 70 during 1996-2007). Results. The incidence rate of PML decreased from 0.24 cases per 100 patient-years (PY; 95% confidence interval [CI], 0.20-0.29 cases per 100 PY) before 1996 to 0.06 cases per 100 PY (95% CI, 0.04-0.10 cases per 100 PY) from 1996 onward. Patients who received a diagnosis before 1996 had a higher frequency of prior acquired immunodeficiency syndrome-defining conditions (P=.007) but similar CD4+ T cell counts (60 vs. 71 cells/µL; P=.25), compared with patients who received a diagnosis during 1996 or thereafter. The median time to PML-attributable death was 71 days (interquartile range, 44-140 days), compared with 90 days (interquartile range, 54-313 days) for all-cause mortality. The PML-attributable 1-year mortality rate decreased from 82.3 cases per 100 PY (95% CI, 58.8-115.1 cases per 100 PY) during the pre-cART era to 37.6 cases per 100 PY (95% CI, 23.4.-60.5 cases per 100 PY) during the cART era. In multivariate models, cART was the only factor associated with lower PML-attributable mortality (hazard ratio, 0.18; 95% CI, 0.07-0.50; P<.001), whereas all-cause mortality was associated with baseline CD4+ T cell count (hazard ratio per increase of 100 cells/µL, 0.52; 95% CI, 0.32-0.85; P=.010) and cART use (hazard ratio, 0.37; 95% CI, 0.19-0.75; P=.006). Conclusions. cART reduced the incidence and PML-attributable 1-year mortality, regardless of baseline CD4+ T cell count, whereas overall mortality was dependant on cART use and baseline CD4+ T cell coun

Characteristics, Determinants, and Clinical Relevance of CD4 T Cell Recovery to <500 Cells/µL in HIV Type 1—Infected Individuals Receiving Potent Antiretroviral Therapy

Background. The CD4 T cell count recovery in human immunodeficiency virus type 1 (HIV-1)—infected individuals receiving potent antiretroviral therapy (ART) shows high variability. We studied the determinants and the clinical relevance of incomplete CD4 T cell restoration. Methods. Longitudinal CD4 T cell count was analyzed in 293 participants of the Swiss HIV Cohort Study who had had a plasma HIV-1 RNA load .05). Older age (adjusted odds ratio [aOR], 1.71 per 10-year increase; 95% confidence interval [CI], 1.21-2.43), lower baseline CD4 T cell count (aOR, 0.37 per 100-cell increase; 95% CI, 0.28-0.49), and longer duration of HIV infection (aOR, 2.39 per 10-year increase; 95% CI, 1.19-4.81) were significantly associated with a CD4 T cell count <500 cells/µL at 5 years. The median increases in CD4 T cell count after 3-6 months of ART were smaller in incomplete responders (P < .001) and predicted, in conjunction with baseline CD4 T cell count and age, incomplete response with 80% sensitivity and 72% specificity. Conclusion. Individuals with incomplete CD4 T cell recovery to <500 cells/µL had more advanced HIV-1 infection at baseline. CD4 T cell changes during the first 3-6 months of ART already reflect the capacity of the immune system to replenish depleted CD4 T lymphocyte