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CD4+ lymphocytes and tuberculin skin test as survival predictors in pulmonary tuberculosis HIV-infected patients.

BACKGROUND: We analyse whether the tuberculin skin test is a good survival marker in a cohort of pulmonary tuberculosis patients with HIV infection (PTB/HIV). In all, 494 PTB/HIV patients were enrolled in Barcelona (Spain) between January 1992 and December 1994 in the Tuberculosis Program of Barcelona. The main data problem was the large proportion of missing values in the covariates percentage of T CD4+ lymphocytes and the tuberculin test results: only 157 patients (31.8%) had both covariates recorded. METHODS: Patients were dichotomized into two groups according to their level of immunosuppression (< or = 14 and >14% T CD4+ cells). First, we carried out the semiparametric and parametric complete case analysis. After this, we analysed the data assuming a missing at random non-response pattern. We developed a bootstrap approach where missing data in the markers are imputed via a two-way linear model. Using Weibull regression estimation, we used a multiple imputation scheme to estimate the parameters of interest. RESULTS: We found significative differences for the most immunosuppressed group when comparing positive tuberculin patients with those who were tuberculin negative. From a complete case approach and through a multivariate Cox analysis, we obtained a significant relative hazard of 0.3657 (95% CI: 0.13-1.02; P = 0.054). When a Weibull model was fitted, we estimated a constant relative percentile value of pR = 4.1329 (95% CI: 0.97-17.59). From a missing data approach, we obtain a higher constant relative percentile 5.48 (P = 0.079). CONCLUSIONS: The imputation method allows us to assess the protective character of positivity for the tuberculin test for the lowest CD4+ level. These findings strongly suggest the value of the tuberculin skin test as a qualitative measure of the immunological response and its interest for developing countries where specific laboratory tests are not affordable.

Adult↗

Systolic blood pressure trends in US adults between 1960 and 1980: influence of antihypertensive drug therapy.

Recent blood pressure trends reflect progress in hypertension control, but prevalent drug therapy precludes direct estimation of the component due to primary prevention. In data gathered on persons aged 35-74 years in three successive US health examination surveys (1960-1980), systolic blood pressure levels assuming no drug therapy were imputed by reassigning blood pressure to the upper end of the distribution for respondents reporting use of antihypertensive medication. Blood pressure was partitioned into four ordinal categories based on weighted percentiles of the 1960-1962 distributions for 35- to 44-year-old males and females who reported no use of antihypertensive medication. Cumulative logit models (alpha = 0.01) were used to estimate age- and sex-specific trends for blacks and whites within two strata (<25 or > or =25) of body mass index (BMI) (weight (kg)/height (m)2). Before imputation, systolic blood pressure decreased between 1960 and 1980; after imputation, significant decreases remained only in 35- to 44-year-olds. Strong associations of black race and BMI > or =25 with higher blood pressures were present in models with and without drug therapy. Thus, according to the models, there has been little progress in decreasing racial or BMI-related blood pressure differentials. Above the age of 44 years, blood pressure trends were largely attributable to medication use. In contrast, data for 35- to 44-year-olds suggest progress in primary prevention.

Adult↗

Statistical methods and strategies for working with large data bases.

This article describes the statistical methods and strategies to be used in establishing the linkages between processes and structures of care with risk-adjusted outcomes in a large multicenter Veterans Affairs cooperative study in health services of patients undergoing cardiac surgery. The statistical analyses consist of test involving nine specific hypotheses related to the effect of processes and structures of care on risk-adjusted outcomes. From the statistical point of view, the major obstacles of this study are the need for data reduction and imputation of missing data. The former obstacle is addressed through the use of data-reduction techniques, such as principal components and cluster of variables. The latter is addressed through the use of classic and new techniques for imputation of missing data, such as MISSGEN, principal components for qualitative data, and the expectation and maximization algorithm. Data reduction and imputation of missing data are done with clinically derived variable groups called "dimensions" or "subdimensions." The effect of processes and structures of care is assessed by a two-step process. First, outcomes are modeled using only patient risk factors. The selection of risk factors in the modeling process is discussed in detail. Second, these risk-adjusted outcomes are modeled using one of the nine process or structure subhypotheses. The relationship of the processes and structures of care dimensions and/or subdimensions that are linked to risk-adjusted outcomes are identified.

Cardiac Surgical Procedures↗

Differences in susceptibility to AIDS development: a cohort study of Danish and American homosexual-bisexual men, 1981 to 1995.

We estimated the annual hazard rate for progression to AIDS as defined by the 1987 case definition in HIV-infected members of a cohort of Danish and American homosexual-bisexual men who were observed from 1981 to 1995. Furthermore, we extrapolated the hazard to 25 years based on imputed future time to AIDS. Of 201 HIV-positive subjects, 112 developed AIDS before the end of follow-up. The hazard increased rapidly during the first years following infection, attained a peak of about 15% per year at year 7, and was moderately lower during years 8 through 10. In subsequent analysis, we imputed future time to AIDS in 89 subjects who had not progressed by the end of follow-up by extrapolation from subject-specific CD4 trend lines. A CD4 count of < or = 100 cells/microl was the best surrogate for clinical AIDS. Under this model, the imputed AIDS hazard stabilized at around 8% per year after 10 years. We projected that 13% (95% confidence interval [CI], 8%-19%) of the infected men may remain free from AIDS 25 years after seroconversion. Our direct data suggest that incubation times reflect a mixture of a population that is susceptible to disease progression and has short incubation periods with a group that is relatively resistant. Based on an extrapolation model, > 10% of HIV-infected persons may survive for up to 25 years without developing AIDS.

Acquired Immunodeficiency Syndrome↗

Estimating the dose response relationship for occupational radiation exposure measured with minimum detection level.

Occupational exposures are often recorded as zero when the exposure is below the minimum detection level (BMDL). This can lead to an underestimation of the doses received by individuals and can lead to biased estimates of risk in occupational epidemiologic studies. The extent of the exposure underestimation is increased with the magnitude of the minimum detection level (MDL) and the frequency of monitoring. This paper uses multiple imputation methods to impute values for the missing doses due to BMDL. A Gibbs sampling algorithm is developed to implement the method, which is applied to two distinct scenarios: when dose information is available for each measurement (but BMDL is recorded as zero or some other arbitrary value), or when the dose information available represents the summation of a series of measurements (e.g., only yearly cumulative exposure is available but based on, say, weekly measurements). Then the average of the multiple imputed exposure realizations for each individual is used to obtain an unbiased estimate of the relative risk associated with exposure. Simulation studies are used to evaluate the performance of the estimators. As an illustration, the method is applied to a sample of historical occupational radiation exposure data from the Oak Ridge National Laboratory.

Algorithms↗

Acute transfusion reactions in the pediatric intensive care unit.

BACKGROUND: Acute transfusion reactions (ATRs) are probably underdiagnosed in critically ill children because associated symptoms can frequently be attributed to the patient's underlying disease. This study was undertaken to determine the incidence, type, imputability, and severity of ATRs observed in a tertiary care pediatric intensive care unit (PICU). STUDY DESIGN AND METHODS: All transfusions of labile blood product administered to consecutive patients admitted to our PICU, between February 2002 and February 2004, were prospectively recorded. For each transfusion, the bedside nurse recorded the patient's status before, during, and up to 4 hours after the transfusion, as well as the presence of any new sign or symptom suggesting an ATR. Three independent experts retrospectively reviewed all transfusion event reports and hospital charts. The presence, type, imputability, and severity of ATRs were adjudicated by consensus of two of three experts (Delphi method), with predefined criteria. RESULTS: A total of 2509 transfusions were administered to 305 patients during the study. Forty transfusion events (1.6%) were confirmed to be ATRs by expert consensus: 24 febrile nonhemolytic, 6 minor allergic, 4 isolated hypotension, 3 bacterial contamination, 1 major allergic (anaphylactic shock), 1 TRALI, and 1 hemolytic reaction. Imputability of ATRs was probable or possible in 35 cases (88%). ATRs led to an immediate vital threat in 15 percent of cases. CONCLUSION: Improved surveillance of transfusions given to PICU patients and better knowledge of these reactions by health care professionals should improve the safety of transfusions in the PICU.

Acute Disease↗

Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals.

The US National Cancer Institute has recently sponsored the formation of a Cohort Consortium (http://2002.cancer.gov/scpgenes.htm) to facilitate the pooling of data on very large numbers of people, concerning the effects of genes and environment on cancer incidence. One likely goal of these efforts will be generate a large population-based case-control series for which a number of candidate genes will be investigated using SNP haplotype as well as genotype analysis. The goal of this paper is to outline the issues involved in choosing a method of estimating haplotype-specific risk estimates for such data that is technically appropriate and yet attractive to epidemiologists who are already comfortable with odds ratios and logistic regression. Our interest is to develop and evaluate extensions of methods, based on haplotype imputation, that have been recently described (Schaid et al., Am J Hum Genet, 2002, and Zaykin et al., Hum Hered, 2002) as providing score tests of the null hypothesis of no effect of SNP haplotypes upon risk, which may be used for more complex tasks, such as providing confidence intervals, and tests of equivalence of haplotype-specific risks in two or more separate populations. In order to do so we (1) develop a cohort approach towards odds ratio analysis by expanding the E-M algorithm to provide maximum likelihood estimates of haplotype-specific odds ratios as well as genotype frequencies; (2) show how to correct the cohort approach, to give essentially unbiased estimates for population-based or nested case-control studies by incorporating the probability of selection as a case or control into the likelihood, based on a simplified model of case and control selection, and (3) finally, in an example data set (CYP17 and breast cancer, from the Multiethnic Cohort Study) we compare likelihood-based confidence interval estimates from the two methods with each other, and with the use of the single-imputation approach of Zaykin et al. applied under both null and alternative hypotheses. We conclude that so long as haplotypes are well predicted by SNP genotypes (we use the Rh2 criteria of Stram et al. [1]) the differences between the three methods are very small and in particular that the single imputation method may be expected to work extremely well.

Algorithms↗

Disability evolution in multiple sclerosis: how to deal with missing transition times in the Markov model?

Markov modeling of disability progression in multiple sclerosis requires knowledge of all times of transitions from a given level of disability to the next level, but such data are often missing. We address methodological challenges due to partly missing transition times. To estimate the effects of prognostic factors on the risk of transitions between three consecutive disability levels, two methods were used to deal with missing data. Listwise deletion limited the analysis to subjects with complete data. Multiple imputation of missing data revealed that data were missing at random (MAR mechanism) and imputed the missing transition times from the Weibull model. The results were then compared with the full data set with the actual times established through chart review. Multiple imputation estimates were systematically closer to those from the full data set than the listwise deletion estimates.

Adult↗

Genome-wide linkage analysis of the tracking of systolic blood pressure using a mixed model.

BACKGROUND: Elevated blood pressure in middle age is a major risk factor for subsequent cardiovascular complications. An important longitudinal characteristic of blood pressure is the "tracking phenomenon". Tracking is defined as the persistence of the rank of a person's blood pressure level in a group over a long period of time. In this analysis, we used the Framingham data to investigate whether there are some genes responsible for this phenomenon. RESULTS: Both two-point and multipoint linkage analyses were applied to family members with complete data only and to all family data with missing values imputed by a Gaussian model. The results of two-point linkage analysis indicated that two loci for linkage with the intercept were on chromosomes 10 and 13, and two loci for linkage with both slope and intercept were on chromosomes 1 and 3. Multipoint linkage analysis indicated only one region, 200-240 cM on chromosome 1, to be linked with both intercept and slope. For the intercept of SBP, the highest LOD (4.43) was found at 214 cM when missing data were imputed, and the highest LOD (2.81) was at 231 cM for the complete case data. For the slope of SBP, the highest multipoint LODs were 3.63 at 227 cM and 2.02 at 234 cM for the complete case data and imputation data, respectively. CONCLUSION: One or more genes in the range of 200-240 cM on chromosome 1 may be related to the tracking phenomenon of SBP.

Adult↗

Breastfeeding patterns and exposure to suboptimal breastfeeding among children in developing countries: review and analysis of nationally representative surveys.

BACKGROUND: Suboptimal breastfeeding is associated with higher mortality among infants and young children in the developing world. We describe patterns in 'exclusive breastfeeding' and 'any breastfeeding' rates and quantify exposure to suboptimal breastfeeding among children aged two years or younger in developing countries. METHODS: We reviewed nationally representative surveys that collected data on breastfeeding rates in 94 developing countries. Surveys were categorized by completeness and comprehensiveness of data. Complete and comprehensive data were analysed with minimum chi-square regression. With a fitting procedure, estimated parameters were used to impute missing observations for incomplete or non-comprehensive surveys. Breastfeeding indicators were calculated and are reported for 135 developing countries by UN region. RESULTS: Amongst infants aged six months or younger in the developing world, the prevalence of exclusive breastfeeding is 39% and the prevalence of no breastfeeding is 5.6%. The prevalence of continued breastfeeding is 86% and 68% for infants and children aged 6-11 and 12-23 months, respectively, in the developing world. Imputation expands population coverage of indicators, especially for infants. Breastfeeding trends are highly linear and estimated parameters defining the age-specific attrition hazard are robust. Survey-reported rates, particularly for exclusive breastfeeding, appear to have systematic upward bias, and exposure estimates must be considered conservative. CONCLUSIONS: Compliance with breastfeeding recommendations in developing countries is low, and more attention should be given to increasing breastfeeding - especially exclusive breastfeeding - and to monitoring trends. Although the introduction of more standardized and better validated survey instruments is desirable, since data coverage, completeness and comprehensiveness are extensive, global exposure assessment is relatively robust. Moreover, the regularity of breastfeeding patterns show existing survey data capture real biological and social phenomena. Our method for the analysis of breastfeeding rates provides a potent tool for summarizing trends, validating observations, translating and extrapolating indicators (as well as projecting and imputing estimates when necessary) and should support more effective child health monitoring.

Age Factors↗

Are missing outcome data adequately handled? A review of published randomized controlled trials in major medical journals.

BACKGROUND: Randomized controlled trials almost always have some individuals with missing outcomes. Inadequate handling of these missing data in the analysis can cause substantial bias in the treatment effect estimates. We examine how missing outcome data are handled in randomized controlled trials in order to assess whether adequate steps have been taken to reduce nonresponse bias and to identify ways to improve procedures for missing data. METHODS: We reviewed all randomized trials published between July and December 2001 in BMJ, JAMA, Lancet and New England Journal of Medicine, excluding trials in which the primary outcome was described as a time-to-event. We focused on trial designs, how missing outcome data were described and the statistical methods used to deal with the missing outcome data, including sensitivity analyses. RESULTS: We identified 71 trials of which 63 (89%) reported having partly missing outcome data: 13 trials had more than 20% of patients with missing outcomes. In 26 trials that measured the outcome at a single time point, 92% performed a complete case analysis and 8% imputed the missing outcomes using baseline values or the worst case value. In 37 trials with repeated measures of the outcome, 46% performed complete case analyses, potentially excluding individuals with some follow-up data, while 14% performed a repeated measures analysis, 19% used the last observation carried forward, 11% imputed with the worst case value and 2% imputed using regression predictions. Thirteen (21%) of trials with missing data reported a sensitivity analysis. CONCLUSIONS: Our review shows that missing outcome data are a common problem in randomized controlled trials, and are often inadequately handled in the statistical analysis in the top tier medical journals. Authors should explicitly state the assumptions underlying the handling of the missing outcomes and justify them through data descriptions and sensitivity analyses.

Bias↗

Epidemiologic evaluation of measurement data in the presence of detection limits.

Quantitative measurements of environmental factors greatly improve the quality of epidemiologic studies but can pose challenges because of the presence of upper or lower detection limits or interfering compounds, which do not allow for precise measured values. We consider the regression of an environmental measurement (dependent variable) on several covariates (independent variables). Various strategies are commonly employed to impute values for interval-measured data, including assignment of one-half the detection limit to nondetected values or of "fill-in" values randomly selected from an appropriate distribution. On the basis of a limited simulation study, we found that the former approach can be biased unless the percentage of measurements below detection limits is small (5-10%). The fill-in approach generally produces unbiased parameter estimates but may produce biased variance estimates and thereby distort inference when 30% or more of the data are below detection limits. Truncated data methods (e.g., Tobit regression) and multiple imputation offer two unbiased approaches for analyzing measurement data with detection limits. If interest resides solely on regression parameters, then Tobit regression can be used. If individualized values for measurements below detection limits are needed for additional analysis, such as relative risk regression or graphical display, then multiple imputation produces unbiased estimates and nominal confidence intervals unless the proportion of missing data is extreme. We illustrate various approaches using measurements of pesticide residues in carpet dust in control subjects from a case-control study of non-Hodgkin lymphoma.

Bias↗

Global and local ancestry estimation in a captive baboon colony.

The last couple of decades have highlighted the importance of studying hybridization, particularly among primate species, as it allows us to better understand our own evolutionary trajectory. Here, we report on genetic ancestry estimates using dense, full genome data from 881 olive (Papio anubus), yellow (Papio cynocephalus), or olive-yellow crossed captive baboons from the Southwest National Primate Research Center. We calculated global and local ancestry information, imputed low coverage genomes (n = 830) to improve marker quality, and updated the genetic resources of baboons available to assist future studies. We found evidence of historical admixture in some putatively purebred animals and identified errors within the Southwest National Primate Research Center pedigree. We also compared the outputs between two different phasing and imputation pipelines along with two different global ancestry estimation software. There was good agreement between the global ancestry estimation software, with R2 > 0.88, while evidence of phase switch errors increased depending on what phasing and imputation pipeline was used. We also generated updated genetic maps and created a concise set of ancestry informative markers (n = 1,747) to accurately obtain global ancestry estimates.

Animals↗

A procedure for linking psychosocial job characteristics data to health surveys.

A system is presented for linking information about psychosocial characteristics of job situations to national health surveys. Job information can be imputed to individuals on surveys that contain three-digit US Census occupation codes. Occupational mean scores on psychosocial job characteristics-control over task situation (decision latitude), psychological work load, physical exertion, and other measures-for the linkage system are derived from US national surveys of working conditions (Quality of Employment Surveys 1969, 1972, and 1977). This paper discusses a new method for reducing the biases in multivariate analyses that are likely to arise when utilizing linkage systems based on mean scores. Such biases are reduced by modifying the linkage system to adjust imputed individual scores for demographic factors such as age, education, race, marital status and, implicitly, sex (since men and women have separate linkage data bases). Statistics on the linkage system's efficiency and reliability are reported. All dimensions have high inter-survey reproducibility. Despite their psychosocial nature, decision latitude and physical exertion can be more efficiently imputed with the linkage system than earnings (a non-psychosocial job characteristic). The linkage system presented here is a useful tool for initial epidemiological studies of the consequences of psychosocial job characteristics and constitutes the methodological basis for the subsequent paper.

Decision Making↗

Meta-analysis of over 8,000 individuals from Hawai'i and Samoa for genetic associations to cardiometabolic phenotypes.

Although genome-wide association studies (GWAS) now routinely reveal genetic associations and biological insights in millions of individuals, underrepresentation of global populations, such as those from Polynesia, continue to persist. These exclusions, often driven by logistical challenges and lack of data, prevent systematic identification of population-enriched associations, such as the association of the missense variant at the CREBRF locus to BMI and type 2 diabetes discovered commonly occurring in Polynesian populations due to its rarity in global populations. Armed with the recently updated TOPMed imputation panel that could benefit studies in diverse populations that previously had poorer imputation performance, we performed the first GWAS of Native Hawaiians and largest to date of Polynesian-ancestry populations (combined N up to 8,461) to identify population-enriched associations for 13 adiposity and cardiometabolic traits available across both cohorts: BMI, fasting glucose, fasting insulin, HDL, height, hip circumference, HOMA-IR, LDL, T2D, total cholesterol, triglycerides, waist circumference, and waist-hip ratio. We found 25 trait-loci associations that met genome-wide significance: 20 previously reported or known associations and 5 associations newly confirmed via meta-analysis. In particular, with improved statistical power, we were able to confirm the suspected association between the missense CREBRF variant with fasting glucose levels. The remaining 4 potentially novel loci-trait associations for BMI, LDL, and waist-hip ratio, however, were not replicated in multi-ethnic datasets from All-of-Us despite having reasonable power to replicate. The lack of Polynesian-enriched findings outside of the CREBRF locus informs the bounds of the effect sizes or frequency of any enriched variants, and suggests that further expansion of cohort sizes from this region of the world and improved imputation references specific to these populations are needed to identify more population-enriched associations.

Journal Article↗

Major gene segregation of actinic prurigo among North American Indians in Saskatchewan.

Actinic prurigo is an idiopathic, familial photodermatosis seen especially in American Indians. Segregation analysis was performed on 12 Saskatchewan pedigrees with American Indian ancestry, comprising a total of 1,148 individuals, ascertained via probands diagnosed with actinic prurigo. Although a high degree of familial aggregation has been noted in the past and dominant inheritance has been suggested, no formal segregation analysis has been attempted. Actinic prurigo has a variable age of onset and, therefore, age at the time of censoring must be taken into account in the analysis. However, as these ages of 57% of the unaffected individuals were missing, an algorithm was devised to impute the missing ages from known birth years in the family based on the age differences among relatives and spouses. Using these imputed ages, simple dominant inheritance with incomplete penetrance and a single age of onset distribution was found. The method for imputing the ages at examination was evaluated, as was the correction for ascertainment, by using alternative methods and comparing the results. Regardless of the method used, a dominant mode of inheritance without any multifactorial component remained the best hypothesis.

Adolescent↗

[Photodermatosis induced by hydroxychloroquine: 4 cases].

BACKGROUND: Hydroxychloroquine is an antimalarial drug often used in dermatology for its photo-protective effects. Four cases of photodermatosis induced by hydroxychloroquine are reported. CASE REPORTS: Four patients, aged from 21 to 68 years, developed a photolocalized eruption from 6 days to 10 weeks after starting hydroxychloroquine. The minimal erythemal dose was decreased in the total spectra and UVA at the onset of the eruption and became normal after stopping hydroxychloroquine in the 2 patients that were controlled. In 3 cases, hydroxychloroquine was the only single drug imputable; chronological imputability was plausible. In the last case, both hydroxychloroquine, carbamazepine and fluvoxamine had a common imputability which was plausible. In the 4 cases, a favourable outcome was observed after stopping hydroxychloroquine, and no recurrence occurred with a mean follow-up of 3.8 years (1-4 years). In one case, a photodistributed eruption occurred during treatment with a related molecule: chloroquine. DISCUSSION: Photodermatosis with hydroxychloroquine have rarely been described in the literature, while quinine from which hydroxychloroquine is derived, is well known for its risk of photosensibilization. The main differential diagnosis of these drug eruptions is an eruption caused by the photodermatosis that initially required treatment with hydroxychloroquine.

Adult↗

[Lyell syndrome in Senegal: responsibility of thiacetazone].

INTRODUCTION: Toxic epidermal necrolysis is a severe disease often leading to death or to mucosal, particularly ocular, after effects. The principle drugs responsible are antibacterial sulfonamides, anti-epileptics, non-steroid anti-inflammatories, allopurinol and chlormezanone. We report a series of 38 cases of toxic epidermal necrolysis, observed in Dakar, imputable to thiacetazone and lethal in 60 percent of cases. PATIENTS AND METHODS: Our study was retrospective. Diagnosis of toxic epidermal necrolysis was made in patients presenting more than 30 p. 100 of the epidermis of their total body surface stripped off, multi-orificial mucosal damage and epidermal necrosis revealed on histological examination. Drug imputability was established on classical criteria. Treatment was composed of reanimation and antibiotics. RESULTS: Among the 38 cases of toxic epidermal necrolysis counted, 24 were imputable to thiacetazone. All the patients presented typical clinical features, confirmed histologically. Evolution was lethal in 60 p. 100 of cases. The causes of death were frequently hypovolemic shock during the first week and septic shock during the second. The deceased were generally aged over 50, had more than 50 p. 100 of total epidermis stripped off, presented evolving tuberculosis at the time of the accident and HIV infection at the AIDS stage. After effects were vaginal synechia and 2 cases of blindness. COMMENTS: Our series is exceptional in that a) the drug responsible: thiacetazone, an economic tuberculostatic of minor efficacy, was systematically introduced after 2 months of intensive treatment with 4 major anti-tuberculosis agents; b) the 60 percent mortality rate, two-fold greater that that usually observed. Other than the known elements of poor prognosis in our patients, the treatment conditions of this dermatological emergency explain this high rate of mortality.

Adolescent↗