Simple methods for assessing haplotype-environment interactions in case-only and case-control studies.

For investigating haplotype-environment interactions in case-control studies, one can implement statistical methods based either on a retrospective likelihood (modeling the probability of haplotype and environment conditional on disease status) or a prospective likelihood (modeling the probability of disease status conditional on haplotype and environment). Retrospective approaches are generally more powerful than prospective approaches, but require an explicit model of the joint distribution of haplotype and environmental factors in the sample with the latter being particularly unattractive to specify. To resolve this issue, we propose a number of simple retrospective procedures for haplotype-environment interaction analysis that do not require explicit modeling of environmental covariates in the sample. We first consider a cases-only procedure, followed by a simple likelihood for case-control data that is proportional to the full-retrospective likelihood. Finally, we consider a retrospective procedure for inference on haplotype-environment interaction effects in matched or finely-stratified case-control studies. Our methods are based on the assumptions that haplotypes and environmental covariates are independent in the target population and that disease is rare. We illustrate our approaches using case-control data from the Finland-United States Investigation of Non-Insulin Dependent Diabetes Mellitus (FUSION) genetic study and simulated data.

Effect of interventions to control sexually transmitted disease on the incidence of HIV infection in female sex workers.

OBJECTIVE: To compare the seroincidence of HIV infection among female sex workers in Abidjan, Côte d'Ivoire before and during an intervention study to control sexually transmitted diseases (STD) and to study the effect of two STD diagnosis and treatment strategies on the prevalence of STD and on the seroincidence of HIV infection. METHOD: A screening facility for STD and HIV had been available since October 1992 for female sex workers. From June 1994, women who were HIV seronegative or HIV-2 positive during the screening could enroll in the intervention study in which participants reported once a month to a confidential clinic where they received health education, condoms and STD treatment if indicated. Women in the study were randomized either to a basic STD diagnosis and treatment strategy, which included a gynecologic examination when symptomatic, or to an intensive strategy that included a gynecologic examination regardless of symptoms. An outcome assessment every 6 months included a gynecologic examination, HIV serology and laboratory tests for STD. RESULTS: Of 542 women enrolled in the study, 225 (42%) had at least one outcome assessment. The HIV-1 seroincidence rate during the intervention study was significantly lower than before the study (6.5 versus 16.3 per 100 person-years; P = 0.02). During the study, the HIV-1 seroincidence rate was slightly lower in the intensive than in the basic strategy (5.3 versus 7.6 per 100 person-years; P = 0.5). CONCLUSION: National AIDS control programs should consider adopting as policy the type of integrated approach used in this intervention study for HIV prevention in female sex workers.

Analysis of dynamic cohort data.

Left-truncated and interval-censored data, termed dynamic cohort data, arise in longitudinal studies with rolling admissions and only occasional follow-up. The authors compared four approaches for analyzing such data: a constant hazard model; maximum likelihood estimation with flexible parametric models; the midpoint method, in which the midpoint of the last negative and first positive test result is used in a Cox proportional hazards model that accounts for left truncation; and a semiparametric method that uses imputed failure times in the Cox model. By using a simulation study, they assessed the performance of these approaches under conditions that can arise in observational studies: changes in disease incidence and changes in the underlying population. The simulation results indicated that the constant hazard model and midpoint method were inadequate and that the flexible parametric model was useful when enough parameters were used in modeling the baseline hazard. The semiparametric method ensured correct parameter (odds ratio) estimation when the baseline hazard was misspecified, but the trade-off increased computational complexity. In this paper, a study of the incidence of human immunodeficiency virus in patients repeatedly tested for the virus at a sexually transmitted disease clinic in New Orleans, Louisiana, illustrates the methods used.

Evaluation of a sensitive/less-sensitive testing algorithm using the 3A11-LS assay for detecting recent HIV seroconversion among individuals with HIV-1 subtype B or E infection in Thailand.

The development of a serologic algorithm to determine recent HIV seroconversion, using sensitive/less-sensitive testing strategies, has generated widespread interest in applying this approach to estimate HIV-1 incidence in various populations around the world. To evaluate this approach in non-B subtypes, longitudinal specimens (n = 522) collected from 90 incident infections among injecting drug users in Bangkok (subtype B infection, n = 18; subtype E infection, n = 72) were tested by the 3A11-LS assay. Standardized optical density (SOD) was calculated, using median values, and the window period between seroconversion as determined by sensitive and less sensitive tests was estimated by a maximum-likelihood model described previously. Our results show that the mean window period of the 3A11-LS assay was 155 days (95% CI, 128-189 days) for subtype B but was 270 days (95% CI, 187-349 days) for subtype E specimens from Thailand. About 4% of individuals with incident subtype E infections remained below the threshold (SOD of 0.75), even 2 years after seroconversion. Among the patients with clinical AIDS and declining antibodies, none of the 7 individuals with subtype B, but 10 (8.7%) of 115 with subtype E infections, were misclassified as recent infections. Lowering the cutoff to an SOD of 0.45 for subtype E specimens resulted in a mean window period of 185 days (95% CI, 154-211 days), with all individuals seroconverting, and reduced the number of subtype E-infected patients with AIDS who were misclassified as having recent infection to 2.6%. Our results demonstrate that the 3A11-LS assay has different performance characteristics in detecting recent infections among individuals infected with subtypes B or E. Determining appropriate cutoffs and mean window periods for other HIV-1 subtypes will be necessary before this approach can be reliably implemented in settings where non-B subtypes are common.

Nonparametric maximum likelihood estimation for competing risks survival data subject to interval censoring and truncation.

We derive the nonparametric maximum likelihood estimate (NPMLE) of the cumulative incidence functions for competing risks survival data subject to interval censoring and truncation. Since the cumulative incidence function NPMLEs give rise to an estimate of the survival distribution which can be undefined over a potentially larger set of regions than the NPMLE of the survival function obtained ignoring failure type, we consider an alternative pseudolikelihood estimator. The methods are then applied to data from a cohort of injecting drug users in Thailand susceptible to infection from HIV-1 subtypes B and E.

Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model.

We propose a novel latent-class approach to detect and account for population stratification in a case-control study of association between a candidate gene and a disease. In our approach, population substructure is detected and accounted for using data on additional loci that are in linkage equilibrium within subpopulations but have alleles that vary in frequency between subpopulations. We have tested our approach using simulated data based on allele frequencies in 12 short tandem repeat (STR) loci in four populations in Argentina.

Nonparametric estimation for the three-stage irreversible illness-death model.

In this paper, we present new nonparametric estimators of the stage-occupation probabilities in the three-stage irreversible illness-death model. These estimators use a fractional risk set and a reweighting approach and are valid under stage-dependent censoring. Using a simulated data set, we compare the behavior of our estimators with previously proposed estimators. We also apply our estimators to data on time to Pneumocystis pneumonia and death obtained from an AIDS cohort study.

Conditional and unconditional categorical regression models with missing covariates.

We consider methods for analyzing categorical regression models when some covariates (Z) are completely observed but other covariates (X) are missing for some subjects. When data on X are missing at random (i.e., when the probability that X is observed does not depend on the value of X itself), we present a likelihood approach for the observed data that allows the same nuisance parameters to be eliminated in a conditional analysis as when data are complete. An example of a matched case-control study is used to demonstrate our approach.

Repeat screening for HIV: when to test and why.

This paper presents models for repeat HIV screening under conditions of constant low HIV incidence. The models reveal a direct link between the prevalence of undetected HIV infection and the screening interval between repeat HIV tests. We show how to select screening intervals that either achieve a given HIV prevalence level, or optimally balance the cost of repeat HIV testing against the cost of HIV infection. Alternatively, given an existing repeat screening program, the model implies that cost of infection for which the given screening interval is optimal. The method also suggests how to select an HIV testing technology. The models are applied to existing repeat testing programs in the U.S. Army and among legal commercial sex workers in the state of Nevada in the Far West of the United States.

Hold everything! Holding policies for protecting plasma supplies.

In spite of advances in testing technologies for detecting infections such as human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV), occasionally blood or plasma is collected that is potentially infectious, but is not detected as such by existing screening tests. We consider the effect of a holding policy for further reducing the number of potentially infectious units that are released for fractionation. The policy dictates a holding period during which all donated units are stored. If a donor tests positive for the infection in question at a subsequent donation, then all of that donor's units currently in storage are discarded. Otherwise, donated units are released at the end of the holding period. In the case of a single disease, we determine optimal holding periods as well as policies that are as effective as the best screening tests currently available.

Validating marker-based incidence estimates in repeatedly screened populations.

Disease incidence (new cases of disease per person per year) is usually measured by using longitudinal data. However, several recent proposals for measuring the incidence of human immunodeficiency virus (HIV) rely on cross-sectional data only. These methods assume each person is only sampled once; however, in some instances, it is necessary to consider these cross-sectional methods when individuals are represented more than once in the survey sample. We derive an extension of the cross-sectional incidence estimator that is valid for data from repeatedly screened populations and show under what conditions our new estimator reduces to the old estimator. An example involving estimation of HIV incidence among repeat blood donors is presented.

Estimating the extent of tracking in interval-censored chain-of-events data.

This paper describes a method for determining whether the times between a chain of successive events (which all individuals experience in the same order) are correlated, for data in which the exact event times are not observed. Such data arise when individuals are only observed occasionally to determine which events have occurred. In such data, the (unknown) event times are interval censored. In addition, some individuals may have experienced some of the events before their first observation and may be lost to follow-up before experiencing the last event. Using a frailty model proposed by Aalen (1988, Mathematical Scientist 13, 90-103) but which has never been used to analyze real data, we examine whether individuals who develop early markers of HIV infection can also be expected to develop antibody and other indicators of HIV infection more rapidly.

Fitting semi-Markov models to interval-censored data with unknown initiation times.

In a semi-Markov model, the hazard of making a transition between stages depends on the time spent in the current stage but is independent of time spent in other stages. If the initiation time (time of entry into the network) is not known for some persons and if transition time data are interval censored (i.e., if transition times are not known exactly but are known only to have occurred in some interval), then the length of time these persons spent in any stage is not known. We show how a semi-Markov model can still be fit to interval-censored data with missing initiation times. For the special case of models in which all persons enter the network at the same initial stage and proceed through the same succession of stages to a unique absorbing stage, we present discrete-time nonparametric maximum likelihood estimators of the waiting-time distributions for this type of data.

Discrete-time nonparametric estimation for semi-Markov models of chain-of-events data subject to interval censoring and truncation.

Chain-of-events data are longitudinal observations on a succession of events that can only occur in a prescribed order. One goal in an analysis of this type of data is to determine the distribution of times between the successive events. This is difficult when individuals are observed periodically rather than continuously because the event times are then interval censored. Chain-of-events data may also be subject to truncation when individuals can only be observed if a certain event in the chain (e.g., the final event) has occurred. We provide a nonparametric approach to estimate the distributions of times between successive events in discrete time for data such as these under the semi-Markov assumption that the times between events are independent. This method uses a self-consistency algorithm that extends Turnbull's algorithm (1976, Journal of the Royal Statistical Society, Series B 38, 290-295). The quantities required to carry out the algorithm can be calculated recursively for improved computational efficiency. Two examples using data from studies involving HIV disease are used to illustrate our methods.

Detection of early HIV infection and estimation of incidence using a sensitive/less-sensitive enzyme immunoassay testing strategy at anonymous counseling and testing sites in San Francisco.

Timely estimates of HIV incidence are needed to monitor the epidemic and target primary prevention but have been difficult to obtain. We applied a sensitive/ less-sensitive (S/LS) enzyme immunoassay (EIA) testing strategy to stored HIV-positive sera (N = 452) to identify early infections, estimate incidence, and characterize correlates of recent seroconversion among persons seeking anonymous HIV testing in San Francisco from 1996 to 1998 (N = 21,292). Sera positive on a sensitive EIA but negative on a less-sensitive EIA were classified as early HIV infections; sera positive on both EIA were classified as long standing. Seventy-nine sera were from people with early HIV infection. Estimated HIV incidence was 1.1% per year (95% confidence interval [CI], 0.68%-1.6%) overall and 1.9% per year (95% CI, 1.2%-3.0%) among men who have sex with men (MSM). Early HIV infection among MSM was associated with injection drug use, unprotected receptive anal sex, and multiple sex partners in the previous year. No temporal trend in HIV incidence was noted over the study period. The S/LS strategy provides a practical public health tool to identify early HIV infection and estimate HIV incidence in a variety of study designs and settings.

HIV seroincidence and risk factors among patients repeatedly tested for HIV attending sexually transmitted disease clinics in the United States, 1991 to 1996. STD Clinic HIV Seroincidence Study Group.

To assess the incidence of HIV infection and risk factors associated with HIV seroconversion among patients attending clinics for sexually transmitted diseases (STD), medical record reviews were conducted in 12 clinics in 7 U.S. cities. The records of all patients who initially tested negative for HIV from 1991 through 1996 and who received at least one additional HIV test during the study period were reviewed. In each of 7 cities, 5 to 112 patients seroconverted. Of the 286 seroconverters identified in total, 53% (152 of 286) were heterosexual men and 28% (81 of 286) were women. HIV incidence rates among men who have sex with men (MSM) ranged by city from 0.81 to 7.0 new infections/100 person-years. Rates among heterosexual men and women ranged from 0.018 to 1.2 infections/100 person-years. Multivariate analyses showed that drug use was associated with HIV seroconversion only among heterosexuals. Most new HIV infections in these clinics are being transmitted heterosexually and are associated with drug use. Nevertheless, MSM, particularly young MSM, are at greatest risk for HIV in this population: 1 of 47 seroconvert/year. The effective use of targeted prevention efforts depends upon the continued ability to monitor the incidence of HIV infection.

The incubation period to AIDS in injecting drug users estimated from prevalent cohort data, accounting for death prior to an AIDS diagnosis.

OBJECTIVE: To estimate the incubation-period distribution (time from seroconversion to AIDS) accounting for death before an AIDS diagnosis (DBAD) in a cohort of injecting drug users (IDU) in Amsterdam, The Netherlands and to compare these estimates with those previously obtained from a contemporaneous study of homosexual and bisexual men in Amsterdam carried out using the same facilities. DESIGN: Participants in a cohort study begun in Amsterdam at the end of 1985 have scheduled follow-up visits every 4 months. All participants of Dutch nationality and who had two or more follow-up visits before January 1996 from which CD4 measurements were available were included in this study. Data concerning AIDS diagnosis and death were verified through review of national and municipal registries. METHODS: Because time of seroconversion was unknown for study participants and because IDU are at substantial risk for DBAD, we used a Markov model with CD4-based stages that allows for DBAD. The parameters in this model were estimated using the method of maximum likelihood and confidence intervals were calculated using bootstrap methods. RESULTS: A total of 173 IDU (134 seroprevalent, 39 seroincident) made 1829 visits. Nearly 10% of the visits were non-consecutive. Forty-five IDU developed AIDS and 25 died without an AIDS diagnosis. We estimated that 24% [95% confidence interval (CI), 17-25%] of IDU die before an AIDS diagnosis. As a result, the median time from seroconversion to AIDS (10.5 years; 95% CI, 9.1-10.7 years) is considerably longer than the median time from seroconversion to death (8.3 years; 95% CI, 7.9-8.5 years). Conditional on survival to an AIDS diagnosis, the median time to AIDS is 8.2 years (95% CI, 7.7-8.7 years). The median survival time after a diagnosis of AIDS is estimated to be 1.0 years. CONCLUSION: The high occurrence of DBAD in IDU has a considerable influence on estimates of the incubation-period distribution. Progression from seroconversion to death was faster in the IDU cohort than in a cohort of homosexual men in Amsterdam (median, 8.3 years and 9.6 years, respectively). However, progression to AIDS conditional on survival to an AIDS diagnosis seems to be similar in both the IDU cohort and in the cohort of homosexual men (median, 8.2 years and 8.3 years, respectively).

New testing strategy to detect early HIV-1 infection for use in incidence estimates and for clinical and prevention purposes.

CONTEXT: Differentiating individuals with early human immunodeficiency virus 1 (HIV-1) infection from those infected for longer periods is difficult but important for estimating HIV incidence and for purposes of clinical care and prevention. OBJECTIVE: To develop and validate a serologic testing algorithm in which HIV-1-positive persons with reactive test results on a sensitive HIV-1 enzyme immunoassay (EIA) but nonreactive results on a less sensitive (LS) EIA are identified as having early infection. DESIGN: Diagnostic test and testing strategy development, validation, and application. Specimens were tested with both a sensitive HIV-1 EIA (3A11 assay) and a less sensitive modification of the same EIA (3A11-LS assay). SETTINGS AND PARTICIPANTS: For assay development: 104 persons seroconverting to HIV-1 comprising 38 plasma donors, 18 patients of a sexually transmitted disease clinic in Trinidad, and 48 participants in the San Francisco Men's Health Study (SFMHS); 268 men without the acquired immunodeficiency syndrome (AIDS) in the SFMHS who had been infected for at least 2.5 years; and 207 persons with clinical AIDS; for testing strategy validation: 488 men in the SFMHS from 1985 through 1990 and 1275449 repeat blood donors at 3 American Red Cross blood centers from 1993 through 1995; and for HIV-1 incidence estimates: 2717910 first-time blood donors. We retrospectively identified persons eligible for a study of early infection. MAIN OUTCOME MEASURE: Ability to identify early HIV infection. RESULTS: Estimated mean time from being 3A11 reactive/3A11-LS nonreactive to being 3A11 reactive/3A11-LS reactive was 129 days (95% confidence interval [CI], 109-149 days) [corrected]. Our testing strategy accurately diagnosed 95% of persons with early infection; however, 0.4% (1/268) of men with established infection and 2% (5/207) of persons with late-stage AIDS were misdiagnosed as having early HIV-1 infection. Average yearly incidence estimates in SFMHS subjects were 1.5% per year vs observed average incidence of 1.4 per 100 person-years. Incidence in repeat blood donors using the sensitive/less sensitive assay testing strategy was 2.95 per 100000 per year (95% CI, 1.14-6.53/100000) vs observed incidence of 2.60 per 100000 person-years (95% CI, 1.49-4.21/100000). Overall incidence in first-time blood donors was 7.18 per 100000 per year (95% CI, 4.51-11.20/100000) and did not change statistically significantly between 1993 and 1996. Use of the sensitive/less sensitive testing strategy alone would have identified all 17 persons with antibodies to HIV-1 eligible for a study of early HIV-1 infection and would have increased enrollment. CONCLUSIONS: The sensitive/less sensitive testing strategy provides accurate diagnosis of early HIV-1 infection, provides accurate estimates of HIV-1 incidence, can facilitate clinical studies of early HIV-1 infection, and provides information on HIV-1 infection duration for care planning.

Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators.

BACKGROUND AND METHODS: National surveillance data show recent, marked reductions in morbidity and mortality associated with the acquired immunodeficiency syndrome (AIDS). To evaluate these declines, we analyzed data on 1255 patients, each of whom had at least one CD4+ count below 100 cells per cubic millimeter, who were seen at nine clinics specializing in the treatment of human immunodeficiency virus (HIV) infection in eight U.S. cities from January 1994 through June 1997. RESULTS: Mortality among the patients declined from 29.4 per 100 person-years in the first quarter of 1995 to 8.8 per 100 in the second quarter of 1997. There were reductions in mortality regardless of sex, race, age, and risk factors for transmission of HIV. The incidence of any of three major opportunistic infections (Pneumocystis carinii pneumonia, Mycobacterium avium complex disease, and cytomegalovirus retinitis) declined from 21.9 per 100 person-years in 1994 to 3.7 per 100 person-years by mid-1997. In a failure-rate model, increases in the intensity of antiretroviral therapy (classified as none, monotherapy, combination therapy without a protease inhibitor, and combination therapy with a protease inhibitor) were associated with stepwise reductions in morbidity and mortality. Combination antiretroviral therapy was associated with the most benefit; the inclusion of protease inhibitors in such regimens conferred additional benefit. Patients with private insurance were more often prescribed protease inhibitors and had lower mortality rates than those insured by Medicare or Medicaid. CONCLUSIONS: The recent declines in morbidity and mortality due to AIDS are attributable to the use of more intensive antiretroviral therapies.

Time course of viremia and antibody seroconversion following human immunodeficiency virus exposure.

Rational application of diagnostic assays in the management of healthcare workers (HCWs) following occupational exposure is needed to rule out pre-existing human immunodeficiency virus (HIV) infection, detect HIV infection or seroconversion as early as possible in the small proportion individuals who become infected, and to rule out infection in the high proportion of individuals who remain uninfected following occupational exposure to HIV. An understanding of the time course of viremia and seroconversion following HIV exposure is essential in developing recommendations for management of occupational exposure among HCWs. Several data sources that address the timing and dynamics of HIV viremia and seroconversion following primary infection are reviewed. The implications of each data source for management of occupational exposure among HCWs is assessed. Although the majority of infected HCWs seroconvert within 2 months of exposure, the possibility of delayed seroconversion is well established, with approximately 5% of infected HCWs estimated to seroconvert >6 months after exposure. In contrast, the period of viremia (detectable by p24 antigen or RNA assays) preceding antibody seroconversion is consistently brief (1-3 weeks). Animal inoculation studies indicate that a variable period of localized viral replication in lymphoid tissue draining inoculation sites exists prior to systemic viremia and subsequent seroconversion.