Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry.

The VISAGE Enhanced Tool for Appearance and Ancestry (ET) has been designed to combine markers for the prediction of bio-geographical ancestry plus a range of externally visible characteristics into a single massively parallel sequencing (MPS) assay. We describe the development of the ancestry panel markers used in ET, and the enhanced analyses they provide compared to previous MPS-based forensic ancestry assays. As well as established autosomal single nucleotide polymorphisms (SNPs) that differentiate sub-Saharan African, European, East Asian, South Asian, Native American, and Oceanian populations, ET includes autosomal SNPs able to efficiently differentiate populations from Middle East regions. The ability of the ET autosomal ancestry SNPs to distinguish Middle East populations from other continentally defined population groups is such that characteristic patterns for this region can be discerned in genetic cluster analysis using STRUCTURE. Joint cluster membership estimates showing individual co-ancestry that signals North African or East African origins were detected, or cluster patterns were seen that indicate origins from central and Eastern regions of the Middle East. In addition to an augmented panel of autosomal SNPs, ET includes panels of 85 Y-SNPs, 16 X-SNPs and 21 autosomal Microhaplotypes. The Y- and X-SNPs provide a distinct method for obtaining extra detail about co-ancestry patterns identified in males with admixed backgrounds. This study used the 1000 Genomes admixed African and admixed American sample sets to fully explore these enhancements to the analysis of individual co-ancestry. Samples from urban and rural Brazil with contrasting distributions of African, European, and Native American co-ancestry were also studied to gauge the efficiency of combining Y- and X-SNP data for this purpose. The small panel of Microhaplotypes incorporated in ET were selected because they showed the highest levels of haplotype diversity amongst the seven population groups we sought to differentiate. Microhaplotype data was not formally combined with single-site SNP genotypes to analyse ancestry. However, the haplotype sequence reads obtained with ET from these loci creates an effective system for de-convoluting two-contributor mixed DNA. We made simple mixture experiments to demonstrate that when the contributors have different ancestries and the mixture ratios are imbalanced (i.e., not 1:1 mixtures) the ET Microhaplotype panel is an informative system to infer ancestry when this differs between the contributors.

Drug addiction and alcoholism as predictors for tuberculosis treatment default in Brazil: a prospective cohort study.

This study aimed to evaluate the risk factors for tuberculosis (TB) treatment default in a priority city for disease control in Brazil. A cohort of TB cases diagnosed from 2008 to 2009 was followed up from patients' entry into three outpatient sites, in Juiz de Fora, Minas Gerais (Brazil), until the recording of the outcomes. Drug addiction, alcoholism and treatment site appeared to be independently associated with default. Current users of crack as the hardest drug (odds ratio (OR) 12·25, 95% confidence interval (CI) 3·04-49·26) were more likely to default than other hard drug users (OR 5·67, 95% CI 1·34-24·03), former users (OR 4·12, 95% CI 1·11-15·20) and those not known to use drugs (reference group). Consumers at high risk of alcoholism (OR 2·94, 95% CI 1·08-7·99) and those treated in an outpatient hospital unit (OR 8·22, 95% CI 2·79-24·21%) also were more likely to default. Our results establish that substance abuse was independently associated with default. National TB programmes might be more likely to achieve their control targets if they include interventions aimed at improving adherence and cure rates, by diagnosing and treating substance abuse concurrently with standard TB therapy.

Anxiety and depression assessment prior to initiating antiretroviral treatment in Brazil.

A cross-sectional study was carried out with 386 patients who received their first anti-retroviral prescription between May 2001 and May 2002 in public AIDS referral centers in Belo Horizonte (Brazil). The main objective was to assess the prevalence and factors associated with anxiety and depression among HIV-infected patients initiating antiretroviral treatment using the Hospital Anxiety and Depression Scale. Clinical, behavioural and demographic data were collected from interviews and medical charts. Multivariate analysis was carried out by logistic regression. Prevalence of moderate to severe anxiety and depression were 35.8% and 21.8%, respectively. Female gender, low schooling, lack of health insurance, attendance to psychotherapy, difficulty in accessing health services and exposure category were independently associated with anxiety. On the other hand, female gender, lack of health insurance, low income, living alone, and lacking a sexual partner in the last month were independently associated with depression. This study highlights the importance of detecting psychological distress by simple screening methods in the HIV/AIDS setting, where the prevalence of anxiety and depression is considerably high, so proper intervention can be established soon in the treatment course.

High incidence of adverse reactions to initial antiretroviral therapy in Brazil.

A concurrent prospective study was conducted from 2001 to 2003 to assess factors associated with adverse reactions among individuals initiating antiretroviral therapy at two public referral HIV/AIDS centers in Belo Horizonte, MG, Brazil. Adverse reactions were obtained from medical charts reviewed up to 12 months after the first antiretroviral prescription. Cox proportional hazard model was used to perform univariate and multivariate analyses. Relative hazards (RH) were estimated with 95% confidence intervals (CI). Among 397 charts reviewed, 377 (95.0%) had precise information on adverse reactions and initial antiretroviral treatment. Most patients received triple combination regimens including nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and protease inhibitors. At least one adverse reaction was recorded on 34.5% (N = 130) of the medical charts (0.17 adverse reactions/100 person-day), while nausea (14.5%) and vomiting (13.1%) were the most common ones. Variables independently associated with adverse reactions were: regimens with nevirapine (RH = 1.78; 95% CI = 1.07-2.96), indinavir or indinavir/ritonavir combinations (RH = 2.05; 95% CI = 1.15-3.64), female patients (RH = 1.93; 95% CI = 1.31-2.83), 5 or more outpatient visits (RH = 1.94; 95% CI = 1.25-3.01), non-adherence to antiretroviral therapy (RH = 2.38; 95% CI = 1.62-3.51), and a CD4+ count of 200 to 500 cells/mm3 (RH = 2.66; 95% CI = 1.19-5.90). An independent and negative association was also found for alcohol use (RH = 0.55; 95% CI = 0.33-0.90). Adverse reactions were substantial among participants initiating antiretroviral therapy. Specially elaborated protocols in HIV/AIDS referral centers may improve the diagnosis, management and prevention of adverse reactions, thus contributing to improving adherence to antiretroviral therapy among HIV-infected patients.

High incidence of adverse reactions to initial antiretroviral therapy in Brazil

A concurrent prospective study was conducted from 2001 to 2003 to assess factors associated with adverse reactions among individuals initiating antiretroviral therapy at two public referral HIV/AIDS centers in Belo Horizonte, MG, Brazil. Adverse reactions were obtained from medical charts reviewed up to 12 months after the first antiretroviral prescription. Cox proportional hazard model was used to perform univariate and multivariate analyses. Relative hazards (RH) were estimated with 95 percent confidence intervals (CI). Among 397 charts reviewed, 377 (95.0 percent) had precise information on adverse reactions and initial antiretroviral treatment. Most patients received triple combination regimens including nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and protease inhibitors. At least one adverse reaction was recorded on 34.5 percent (N = 130) of the medical charts (0.17 adverse reactions/100 person-day), while nausea (14.5 percent) and vomiting (13.1 percent) were the most common ones. Variables independently associated with adverse reactions were: regimens with nevirapine (RH = 1.78; 95 percent CI = 1.07-2.96), indinavir or indinavir/ritonavir combinations (RH = 2.05; 95 percent CI = 1.15-3.64), female patients (RH = 1.93; 95 percent CI = 1.31-2.83), 5 or more outpatient visits (RH = 1.94; 95 percent CI = 1.25-3.01), non-adherence to antiretroviral therapy (RH = 2.38; 95 percent CI = 1.62-3.51), and a CD4+ count of 200 to 500 cells/mm³ (RH = 2.66; 95 percent CI = 1.19-5.90). An independent and negative association was also found for alcohol use (RH = 0.55; 95 percent CI = 0.33-0.90). Adverse reactions were substantial among participants initiating antiretroviral therapy. Specially elaborated protocols in HIV/AIDS referral centers may improve the diagnosis, management and prevention of adverse reactions, thus contributing to improving adherence to antiretroviral therapy among HIV-infected patients.

Hepatitis C virus infection among Brazilian hemophiliacs: a virological, clinical and epidemiological study.

We determined and analyzed risk factors of hepatitis C virus (HCV)-infected Brazilian hemophiliacs according to their virological, clinical and epidemiological characteristics. A cross-sectional and retrospective study of 469 hemophiliacs was carried out at a Brazilian blood center starting in October 1997. The prevalence of HCV infection, HCV genotypes and factors associated with HCV RNA detection was determined. The seroprevalence of anti-HCV antibodies (ELISA-3.0) was 44.6% (209/469). Virological, clinical and epidemiological assessments were completed for 162 positive patients. There were seven (4.3%) anti-HCV seroconversions between October 1992 and October 1997. During the same period, 40.8% of the positive anti-HCV hemophiliacs had abnormal alanine transaminase (ALT) levels. Plasma HCV RNA was detected by nested-RT-PCR in 116 patients (71.6%). RFLP analysis showed the following genotype distribution: HCV-1 in 98 hemophiliacs (84.5%), HCV-3 in ten (8.6%), HCV-4 in three (2.6%), HCV-2 in one (0.9%), and not typeable in four cases (3.4%). Univariate analysis indicated that older age (P = 0.017) and abnormal ALT levels (P = 0.010) were associated with HCV viremia, while the presence of inhibitor antibodies (P = 0.024) and HBsAg (P = 0.007) represented a protective factor against the presence of HCV RNA. These findings may contribute to a better understanding of the relationship between HCV infection and hemophilia.

Hepatitis C virus infection among Brazilian hemophiliacs: a virological, clinical and epidemiological study

We determined and analyzed risk factors of hepatitis C virus (HCV)-infected Brazilian hemophiliacs according to their virological, clinical and epidemiological characteristics. A cross-sectional and retrospective study of 469 hemophiliacs was carried out at a Brazilian blood center starting in October 1997. The prevalence of HCV infection, HCV genotypes and factors associated with HCV RNA detection was determined. The seroprevalence of anti-HCV antibodies (ELISA-3.0) was 44.6 percent (209/469). Virological, clinical and epidemiological assessments were completed for 162 positive patients. There were seven (4.3 percent) anti-HCV seroconversions between October 1992 and October 1997. During the same period, 40.8 percent of the positive anti-HCV hemophiliacs had abnormal alanine transaminase (ALT) levels. Plasma HCV RNA was detected by nested-RT-PCR in 116 patients (71.6 percent). RFLP analysis showed the following genotype distribution: HCV-1 in 98 hemophiliacs (84.5 percent), HCV-3 in ten (8.6 percent), HCV-4 in three (2.6 percent), HCV-2 in one (0.9 percent), and not typeable in four cases (3.4 percent). Univariate analysis indicated that older age (P = 0.017) and abnormal ALT levels (P = 0.010) were associated with HCV viremia, while the presence of inhibitor antibodies (P = 0.024) and HBsAg (P = 0.007) represented a protective factor against the presence of HCV RNA. These findings may contribute to a better understanding of the relationship between HCV infection and hemophilia

Risk factors for breast cancer among pre- or post-menopausal women in Belo Horizonte, Brazil.

BACKGROUND: Much controversy has been generated about pre- and post-menopausal breast cancer patients and investigators have sought to identify whether risk factors differ between these two groups. In Brazil, breast cancer is an important cause of death among women and there are few analytical studies concerning pre- or post-menopausal comparisons. METHODS: A case-control study was carried out at the Federal University Hospital, Belo Horizonte, Brazil, to determine if selected socio-economic and reproductive risk factors for breast cancer differed between pre-menopausal and post-menopausal women. Cases were 300 women with breast carcinoma and controls were 600 women with other benign diseases matched for age and date of diagnosis, admitted to the same hospital during the same period (1978-1987). Univariate and multivariate conditional logistic regression analyses were performed. RESULTS: Multivariate analysis showed no differences in breast cancer risk in pre- and post-menopausal women (risk factors were similar in direction and magnitude). Occupation, irregular menstrual cycles, parity, history of breast cancer in at least one first-degree female relative, and oral contraceptive use had similar associations in both groups. CONCLUSIONS: The present study indicates that breast cancer diagnosed before and after menopause has a similar risk profile.

Safe sexual behaviour among female partners of HIV-infected men in Rio de Janeiro, Brazil.

A cross-sectional study was designed to assess safe sexual behaviour among heterosexual couples after the woman learned of her partner's infection with HIV. Female partners who had known their partners' serostatus for at least 4 weeks were eligible for participation. Couples were interviewed separately and independent predictors of safe sexual behaviour were identified using multiple logistic regression. Safe sexual behaviour was defined as no unprotected vaginal, oral, or anal intercourse. Of 328 women, 197 (60%) reported safe sexual behaviour since learning of their partners' infection. Significant independent predictors of safe sexual behaviour included older women (>30 years old) (odds ratio [OR]=1.89; 95% confidence intervals [CI]=1.01-3.51), current negative HIV serostatus (OR=2.72; 95% CI=1.50-4.94), advanced clinical stage of the index case (OR=1.96; 95% CI=1.07-3.59), longer duration of relationship (10+ years) (OR= 2.35; 95% CI=1.15-4.82), fewer sex contacts (<100) (OR=2.01; 95% CI=1.14-3.56), only one lifetime partner (OR=2.29; 95% CI=1.26-4.17), non-smoking (OR=2.67; 95% CI=1.43-4.99), not practising oral sex (OR=3.35; 95% CI=1.82-6.19) and previous HIV testing (OR=2.11; 95% CI=1.09-4.07). In addition, women who had known their partner's infection for longer were less likely to report safe sexual behaviour (P < 0.001). Our results indicate that among female partners of HIV-positive Brazilian men, learning of their partner's infection does not uniformly result in safe sexual behaviour. Counselling must emphasize disclosure of serostatus to female partners and target couples with short-term relationships, as well as those where the woman has known about her male partner's infection for a long time, because these are the least likely to maintain safe sexual behaviour.

[Association between socioeconomic factors and infant deaths due to diarrhea, pneumonia, and malnutrition in a metropolitan area of Southeast Brazil: a case-control study]. / Associação entre fatores sócio-econômicos e mortalidade infantil por diarréia, pneumonia e desnutrição em região metropolitana do Sudeste do Brasil: um estudo caso-controle.

A population-based case-control study was carried out to identify determinant factors for post-neonatal infant deaths due to diarrhea, pneumonia, and malnutrition in Greater Metropolitan Belo Horizonte, Southeast Brazil. From May 1, 1991, to April 30, 1992, 511 post-neonatal deaths due to diarrhea, pneumonia, and malnutrition were selected after investigation of medical records to validate cause of death. Of this total, 396 deaths were compared to a neighborhood control group, matched for age. The study was carried out in a low-income area with a high proportion of families living in shantytowns. The article discusses the methodology and selected socioeconomic factors. Logistic regression analysis indicated that number of household appliances, mother's and father's education, and mother's marital and work status were significantly associated with risk of infant death, i.e., they were determinants of infant deaths due to avoidable causes.

Tatuajes ayer y hoy / Tattoos, yesterday and today

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[Temporal study in AIDS-associated disease in Brazil, 1980-1999]. / Estudo temporal das doenças associadas à AIDS no Brasil, 1980-1999.

Trends in annual incidence of reported AIDS-associated opportunistic infections (OI/100 adults > 12 years old) among AIDS cases were estimated at the national level in Brazil from 1980 through May 1999. The analysis included chi-square and linear regression modeling. The opportunistic infections included: candidiasis (CD), tuberculosis (TB), Pneumocystis carinii pneumonia (PCP), neurotoxoplasmosis (NT), Kaposi sarcoma (KS), cryptococcal meningitis (CM), and protozoa infections (PI). The overall cumulative incidence rates/100 reported AIDS cases were: CD = 59, TB = 26, PCP = 23, NT = 15, KS = 5, CM = 4, and PI = 4. Annual trends indicated a statistically significant decline in all OIs. However, in the Northeast and Central-West regions there were increases in TB (b = 0.39) and NT (b = 0.20), respectively. TB showed a higher incidence among individuals with less schooling (< 8 years), while PCP and KS had higher incidence rates among those with 8 or more years of schooling, despite similar downward trends. Access to antiretroviral therapy and OI prophylaxis may partially explain these results. However, data reliability, delay in reporting, OI incidence after AIDS, and reporting and diagnostic criteria are factors that also need to be carefully assessed.

Prognostic aspects of cystic fibrosis in Brazil.

Selected prognostic factors were assessed in a cohort of 111 Brazilian children with cystic fibrosis diagnosed between 1 June 1970 and 31 December 1994 and followed in the Pediatric Pulmonology Unit of the Federal University of Minas Gerais Hospital. A standardized protocol was used to collect information retrospectively from medical charts which included date of birth, age at diagnosis, gender, ethnic group, predominant mode of presentation, duration of follow-up, status on 31 December 1994, date of death or date of the last clinical evaluation. The risk of death (univariate and multivariate) was assessed using Cox's proportional hazard model. Mean age at death was higher in males (5.10 years), when the diagnosis was made before the age of 12 months (3.10 years), when clinical presentation was other than respiratory (4.01 years old) and in 'non-whites' (4.86 years old). Age at diagnosis was the only factor associated with death in this population, with both Cox's univariate (RH: 19.4) and multivariate analyses (RH: 17.6; 95% CI: 4.8-64.1). The increased risk of dying in children diagnosed before 12 months of age found in our analysis indicates that they should receive differentiated and intensive multi-professional care.

Hepatitis C virus genotypes in hemophiliacs in the state of Minas Gerais, Brazil.

BACKGROUND: Hepatitis C virus (HCV) is a positive-strand RNA virus composed of at least 10 genotypes and dozens of subtypes. Six major genotypes can be distinguished by restriction fragment length polymorphism (RFLP) analysis of the amplified 5' noncoding region (NCR) of the genome. The genotypes are unequally distributed throughout the world. Types 1 and 3 are most common in Europe and the United States. Although fewer studies have been performed in Brazil, the pattern seems to mirror that in the other areas. HCV infection is highly prevalent among hemophiliacs and is a major cause of chronic liver disease. STUDY DESIGN AND METHODS: This study investigated a sample of the hemophiliac population in the state of Minas Gerais, Brazil, by RFLP analysis of the 5' NCR. RESULTS: It was observed that 84.1 percent were of genotype 1 and 13.6 percent of genotype 3. Sequence analysis of nine isolates confirmed the RFLP results and determined that all of the type 1 isolates belonged to subtype 1a. Phylogenetic analysis by parsimony and distance revealed that lineages of genotypes 1, 2, and 3, and 4 could be separated. The isolates of type 3 from this study were distinct from published sequences, which possibly indicated their different geographical origin. CONCLUSION: Although the frequency of genotypes observed (types 1 and 3) among hemophiliacs in the state of Minas Gerais was higher than that in the southern part of the country, these frequencies were not different from those in other groups of patients in Brazil and other countries studied. Further investigation is needed of the evidence that the type 3 isolates observed in these studies are significantly different from other isolates previously characterized by sequence analysis.

[Utilization of prescribed drugs by HIV infected individuals: qualitative approach]. / Utilização de medicamentos por indivíduos HIV positivos: abordagem qualitativa.

OBJECTIVE: The assessment, in its qualitative dimension, of the utilization--by HIV infected individuals--of selected prescribed drugs during the process of the search for and the obtaining of care in public health services in Belo Horizonte, Brazil. METHODS: Fifty two semi-structured interviews with patients, health care workers and non-governamental organizations volunteers were carried out and 1,079 medical records were reviewed. Data were obtained on the utilization of prescribed drugs by HIV infected individuals, whose first visit to one of the public services studied occurred between January 1989 and December 1992. Problems related to the use of anti-retroviral and/or opportunistic infection medication were identified and a qualitative description of their possible causes and consequences was commented on. RESULTS: Refusal to use, difficulty in obtaining and in complying with the prescription were the main problems related to anti-retroviral drug use. Causes for such problems included: fear or occurrence of side effects, large number of daily capsules/pills, insufficient and/or irregular distribution of drugs by the public health services and the high cost of anti-retroviral therapy. Based on the reports, the main consequences are likely to be no or late use of anti-retroviral drugs, an increase in resistance and a worsening of the clinical course of the infection. Other problems identified were: self-medication, difficulty in obtaining medications for associated pathologies and in complying with sulfa prescription. CONCLUSION: A better understanding of the main obstacles and difficulties experienced by the user of the services, from the moment of the prescription and throughout the treatment, may contribute to an improvement in compliance and the availability and adequate distribution of drugs.

[Analysis of agreement between coding of underlying cause of death by traffic accidents]. / Análise da concordância da codificação de causa básica de óbito por acidentes de trânsito.

OBJECTIVE: An evaluation of information researched as to basic underlying cause of death by traffic accidents and a comparison with codings attributed on the basis of death certificates. MATERIAL AND METHOD: The official coding of underlying cause of death on Death Certificates was compared with coding based on primary data obtained from five hospitals and accident reports. Kappa statistics with 95% CI were used to assess the agreement between the two coding systems. RESULTS: The research covered 1,719 patients. 57 of whom died. Of these 57 deaths, the official coding for 50 was obtained. Data showed an underreporting of deaths by traffic accidents, since 32% of the 50 deaths were coded as non-specific accidents (E928.9) There were also 38% of deaths coded as non-specific traffic accidents (E 819.9). Using primary data, non-specific traffic accidents dropped to 4%, accidents to pedestrians (E814.7) being responsible for 48% of deaths. The Kappa coefficient (0.124), with 95% confidence interval (-.1533-0.4022) was calculated to assess the inter-rater reliability between the two codings, which was considered poor. CONCLUSION: It is concluded that coroners, who perform autopsies on casualties of traffic accidents, should dedicabe greater effort to filling out Death Certificates correctly.