Probability that a two-stage genome-wide association study will detect a disease-associated snp and implications for multistage designs.

Large two-stage genome-wide association studies (GWASs) have been shown to reduce required genotyping with little loss of power, compared to a one-stage design, provided a substantial fraction of cases and controls, pi(sample), is included in stage 1. However, a number of recent GWASs have used pi(sample) < 0.2. Moreover, standard power calculations are not applicable because SNPs are selected in stage 1 by ranking their p-values, rather than comparing each SNP's statistic to a fixed critical value. We define the detection probability (DP) of a two-stage design as the probability that a given disease-associated SNP will have a p-value among the lowest ranks of p-values at stage 1, and, among those SNPs selected at stage 1, at stage 2. For 8000 cases and 8000 controls available for study and for odds ratios per allele in the range 1.1-1.3, we show that DP is substantially reduced for designs with pi(sample)

Validation studies for models projecting the risk of invasive and total breast cancer incidence.

BACKGROUND: In 1989, Gail and colleagues developed a model for estimating the risk of breast cancer in women participating in a program of annual mammographic screening (designated herein as model 1). A modification of this model to project the absolute risk of developing only invasive breast cancer is referred to herein as model 2. We assessed the validity of both models by employing data from women enrolled in the Breast Cancer Prevention Trial. METHODS: We used data from 5969 white women who were at least 35 years of age and without a history of breast cancer. These women were in the placebo arm of the trial and were screened annually. The average follow-up period was 48.4 months. We compared the observed number of breast cancers with the predicted numbers from the models. RESULTS: In terms of absolute risk, the ratios of total expected to observed numbers of cancers (95% confidence intervals [CIs]) were 0.84 (0. 73-0.97) for model 1 and 1.03 (0.88-1.21) for model 2, respectively. Within the age groups of 49 years or less, 50-59 years, and 60 years or more, the ratios of expected to observed numbers of breast cancers (95% CIs) for model 1 were 0.91 (0.73-1.14), 0.96 (0.73-1. 28), and 0.66 (0.52-0.86), respectively. Thus, model 1 underestimated breast cancer risk in women more than 59 years of age. For model 2, the risk ratios (95% CIs) were 0.93 (0.72-1.22), 1.13 (0.83-1.55), and 1.05 (0.80-1.41), respectively. Both models exhibited a tendency to overestimate risk for women classified in the higher quintiles of predicted 5-year risk and to underestimate risk for those in the lower quintiles of the same. CONCLUSION: Despite some limitations, these methods provide useful information on breast cancer risk for women who plan to participate in an annual mammographic screening program.

Survival after breast cancer in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers.

BACKGROUND: Studies of survival following breast and ovarian cancers in BRCA1 and/or BRCA2 mutation carriers have yielded conflicting results. We undertook an analysis of a community-based study of Ashkenazi Jews to investigate the effect of three founder mutations in BRCA1 and BRCA2 on survival among patients with breast or ovarian cancer. METHODS: We collected blood samples and questionnaire data from 5318 Ashkenazi Jewish volunteers. The blood samples were tested for 185delAG (two nucleotide deletion) and 5382insC (single nucleotide insertion) mutations in BRCA1 and the 6174delT (single nucleotide deletion) mutation in BRCA2. To estimate survival differences in the affected relatives according to their BRCA1 and/or BRCA2 mutation carrier status, we devised and applied a novel extension of the kin-cohort method. RESULTS: Fifty mutation carriers reported that 58 of their first-degree relatives had been diagnosed with breast cancer and 10 with ovarian cancer; 907 noncarriers reported 979 first-degree relatives with breast cancer and 116 with ovarian cancer. Kaplan-Meier estimates of median survival after breast cancer were 16 years (95% confidence interval [CI] = 11-40) in the relatives of carriers and 18 years (95% CI = 15-22) in the relatives of noncarriers, a difference that was not statistically significant (two-sided P = .87). There was also no difference in survival times among the 126 first-degree relatives with ovarian cancer. We found no survival difference between patients with breast or ovarian cancer who were inferred carriers of BRCA1 and/or BRCA2 mutations and noncarriers. CONCLUSIONS: Carriers of BRCA1 and BRCA2 mutations appeared to have neither better nor worse survival prognosis.

Effects of intravenous hyperalimentation during treatment in patients with small-cell lung cancer.

One hundred nineteen patients were entered onto a randomized trial of the role of intravenous hyperalimentation (IVH) in patients with small-cell lung cancer. IVH was given during the first 30 days of induction chemotherapy to 54 patients. IVH did not effect any improvement in response or survival from therapy. In view of the lack of benefits from IVH, an analysis was made of the toxicities suffered by the 54 patients receiving IVH as well as any effects IVH might have made on chemotherapy-induced toxicity. Toxicities observed included mechanical difficulties with the catheter leading to temporary or permanent discontinuation of the IVH (11 patients), subclavian vein thrombosis (one patient), sepsis in nine patients v none of the 62 control patients, fluid overload (27 patients), hyponatremia (25 patients), and hyperglycemia requiring insulin (13 patients). Patients receiving IVH had higher granulocyte counts on days 14 and 21 of the first cycle of chemotherapy. Analysis shows that this difference is likely caused by fever and infection associated with IVH rather than any nutritional effect on granulopoiesis. In this population of patients, IVH had significant complications but did not ameliorate chemotherapy-induced toxicity and it did not effect any clinical benefit. Future studies of adjunctive nutritional therapy must consider the significant risk in this older population and must limit IVH volume or exclude patients with even mild compromise in cardiovascular functions. Further, any new trial must have a significant rationale for adjunctive use to justify the potential risks.

Radiation-induced thyroid neoplasms: evidence for familial susceptibility factors.

To determine if there is a familial component to susceptibility to radiation-induced thyroid neoplasms, we studied 572 individuals who were members of 286 sibpairs who received childhood radiation treatment and for whom follow-up information was obtained. Of these 572 individuals, 240 (42.0%) had thyroid neoplasms (benign and malignant), and 75 (13.1%) had surgically confirmed thyroid cancer. To test the null hypothesis, that neoplasm occurred without regard to family membership, it was necessary to take into account each individual's years at risk and known risk factors. These risk factors, analyzed by the proportional hazards model of Cox, were sex, age at time of radiation treatment, and treatment dose. For each individual, we calculated the cumulative hazard that a neoplasm would occur from that individual's specific risk factors and years at risk. Each individual was also assigned an indicator, D = 1 or 0, according to whether a neoplasm had occurred. Finally, for each individual we computed a residual, D minus the cumulative hazard. In the absence of familial effects, positive and negative residuals would be distributed without regard to family membership, whereas residuals would tend to have concordant signs and magnitudes within families if familial effects were present. Permutational methods, therefore, were used to determine whether the sum among families of the products of residuals within sibpairs was too large, compared to random pairing. For all thyroid neoplasms (both benign and malignant), within-family concordance was significant (P = 0.05, the observed sum among families of the products of residuals was larger than 9468 of 9999 permutations). For thyroid cancer considered alone, the same analysis did not demonstrate familial concordance conclusively, but the results were suggestive (P = 0.18). We conclude that in addition to the previously described risk factors of female sex, younger age at radiation exposure, and higher dose, it is likely that there are independent familial risk factors for developing thyroid neoplasms. Whether these are genetic or environmental factors remains to be determined.

Kin-cohort designs for gene characterization.

BACKGROUND: In the kin-cohort design, a volunteer with or without disease (the proband) agrees to be genotyped, and one obtains information on the history of a disease in first-degree relatives of the proband. From these data, one can estimate the penetrance of an autosomal dominant gene, and this technique has been used to estimate the probability that Ashkenazi Jewish women with specific mutations of BRCA1 or BRCA2 will develop breast cancer. METHODS: We review the advantages and disadvantages of the kin-cohort design and focus on dichotomous outcomes, although a few results on time-to-disease onset are presented. We also examine the effects of violations of assumptions on estimates of penetrance. We consider selection bias from preferential sampling of probands with heavily affected families, misclassification of the disease status of relatives, violation of Hardy-Weinberg equilibrium, violation of the assumption that family members' phenotypes are conditionally independent given their genotypes, and samples that are too small to ensure validity of asymptotic methods. RESULTS AND CONCLUSIONS: The kin-cohort design has several practical advantages, including comparatively rapid execution, modest reductions in required sample sizes compared with cohort or case-control designs, and the ability to study the effects of an autosomal dominant mutation on several disease outcomes. The design is, however, subject to several biases, including the following: selection bias that arises if a proband's tendency to participate depends on the disease status of relatives, information bias from inability of the proband to recall the disease histories of relatives accurately, and biases that arise in the analysis if the conditional independence assumption is invalid or if samples are too small to justify standard asymptotic approaches.

Statistical design of calibration studies.

We investigated some design aspects of calibration studies. The specific situation addressed was one in which a large group is evaluated with a food-frequency questionnaire and a smaller calibration study is conducted through use of repeated food records or recalls, with the subjects in the calibration study constituting a random sample of those in the large group. In designing a calibration study, one may use large sample sizes and few food records per individual or smaller samples and more records per subject. Neither strategy is always preferable. Instead, the optimal method for a given study depends on the survey instrument used (24-h recalls or multiple-day food records) and the variables of interest.

Reproducibility studies and interlaboratory concordance for assays of serum hormone levels: estrone, estradiol, estrone sulfate, and progesterone.

We conducted studies to measure sources of assay variability for estrone, estradiol, estrone sulfate, and progesterone for postmenopausal women (n = 5) and for women in the mid-follicular (n = 5) and mid-luteal (n = 5) phases of the menstrual cycle. A single blood sample from each woman was divided into 2.5-ml aliquots and stored at -70 degrees C, and sets of two aliquots were sent at monthly intervals to each of three laboratories (four for progesterone). Each aliquot was analyzed in duplicate. Thus, within each menstrual category, we were able to estimate the components of variance due to variation among women, variation among aliquots, variation among duplicate measurements, and variation among the 4 analysis days. Using the logarithm of assay measurements, we estimated the percentage of variance attributable to variation among women in each menstrual category, 100 rho, is the estimated intraclass correlation. For each assay, 100 rho exceeded 90% for mid-follicular and mid-luteal women. For postmenopausal women, values of 100 rho exceed 84% for estrone in two laboratories. Values of 100 rho were lower for progesterone in postmenopausal women, although a value of 84% was estimated from one laboratory. These studies indicate that estrogen assays over a period of 3 months permit reliable comparisons among women in a given menstrual category. Progesterone measurements are likewise reliable for women in the mid-follicular and mid-luteal phases but somewhat less satisfactory for postmenopausal women. These assessments of variability pertain only to laboratory techniques and do not allow for secular variation in intra-woman hormone levels. Moreover, although these measurements tend to be reliable enough for making comparisons among women, estimates of coefficients of variation for estrogens are about 10% for mid-follicular and mid-luteal phase women and about 11-20% for postmenopausal women. Coefficients of variation for progesterone are about 10% for mid-luteal, 20% for mid-follicular, and 30% for postmenopausal women.

Effective treatment with fucoidin for perinatal hypoxic-ischemic encephalopathy in rats.

Leukocyte-endothelial adhesion is a key step to initiate post-ischemic reperfusion injury in many organs. In this study, we found that the expressions of P-selectin mRNA and protein were increased in the ipsilateral hemisphere with a peak at 8 h after hypoxia-ischemia in immature brain. Such temporal profiles of P-selectin expression followed by hypoxia-ischemia are consistent with a role in the subsequent brain injury. Because fucoidin is known to inhibit P/L-selectin mediated leukocyte adhesion, we examined whether the treatment of fucoidin attenuates hypoxia-ischemia-induced neural damages. Treatment with fucoidin exhibited a substantial neuroprotective effect in a dose-dependent manner and inhibited the leukocyte adhesion significantly, as revealed by myeloperoxidase activity. These results suggest that anti-adhesion strategy may be an effective therapeutic application for the perinatal hypoxic-ischemic encephalopathy.

Quantitative criteria for prediction of the results after displaced fracture of the ankle.

In a series of 146 displaced ankle fractures, the effects of age, sex, side of injury, mechanism of injury, severity as determined by the Lauge-Hansen classification, type of injury (open or closed), open or closed treatment, and internal fixation of one or both malleoli were analyzed using subjective, objective, and radiographic parameters. Statistically significant prognostic features were identified and a prognostic scale was developed using multiple linear-regression analysis. The significant parameters were age, adequacy of the post-reduction positions of the medial and lateral malleoli, and completeness of the restoration of the deltoid ligament and distal tibiofibular syndesmosis. Open reduction proved superior to closed reduction, and in bimalleolar fractures open reduction of both malleoli was better than fixing only the medial side. Using the data on the first 109 fractures, a multiple linear-regression equation was formulated and used to predict the outcomes of the last thirty-seven fractures in the study. The accuracy of the predictions in them was 81 per cent.

Septic arthritis caused by Haemophilus influenzae associated with endocarditis.

Septic arthritis with Haemophilus influenzae is infrequent in adults and often associated with an extra-articular septic focus. We report the case of a septic arthritis caused by H. influenzae in an elderly (89-year-old) female patient in whom an transoesophageal echocardiogram showed an aortic valve endocarditis.

Metal fume fever.

Metal fume fever (MFF) is an acute self-limited, flu-like illness resulting from inhalation of metal oxides. Despite the well-documented history of MFF in the medical literature, the illness may remain unrecognized because it may mimic a viral illness. The case of a patient with MFF due to galvanized steel welding presenting to the emergency room is described.

A stratified Wilcoxon-type test for trend.

We propose an extension of Cuzick's non-parametric Wilcoxon-like trend test for situations when the observations can be grouped into strata which are thought to be related to the outcome. We illustrate its use in two examples from cancer epidemiology.

Selecting an efficient design for assessing exposure-disease relationships in an assembled cohort.

We develop approximate methods to compare the efficiencies and to compute the power of alternative potential designs for sampling from a cohort before beginning to collect exposure data. Our methods require only that the cohort be assembled, meaning that the numbers of individuals Nkj at risk at pairs of event times tk and tj greater than or equal to tk are available. To compute Nkj, one needs to know the entry, follow-up, censoring, and event history, but not the exposure, for each individual. Our methods apply to any "unbiased control sampling design," in which cases are compared to a random sample of noncases at risk at the time of an event. We apply our methods to approximate the efficiencies of the nested case-control design, the case-cohort design, and an augmented case-cohort design, compared to the full cohort design, in an assembled cohort of 17,633 members of an insurance cooperative who were followed for mortality from prostatic cancer. The assumptions underlying the approximation are that exposure is unrelated both to the hazard of an event and to the hazard for censoring. The approximations performed well in simulations when both assumptions held and when the exposure was moderately related to censoring.

Mean square error of estimates of HIV prevalence and short-term AIDS projections derived by backcalculation.

We simulated multinomial AIDS incidence counts from 27 'representative' AIDS epidemics that spanned a period corresponding to previous applications of backcalculation (1 January 1977 to 1 July 1987) and assessed mean square error for several back-calculated estimators of HIV prevalence and short-term AIDS projections. Estimators were based on flexible model selection procedures that chose the best-fitting non-negatively constrained model of the infection curve from a family of possible step-function models. Selection of the best-fitting model from a family of four-step models each with a long last step of width of 4 or 4.5 years offered a favourable tradeoff between bias and variance when compared with selection from families of models with three steps or from families with a short last step. Five-step models performed as well as four-step models. Three-step models had substantially larger mean square error in some epidemic situations. Percentage root mean square error (PRMSE) for estimates of cumulative HIV prevalence as of 1 January 1985 was less than 14 per cent over a range of hypothetical epidemics of N = 50,000 infected individuals. PRMSE for short-term projections was less than 18 per cent. Estimates of cumulative HIV prevalence as of 1 July 1987 were substantially more uncertain and had a PRMSE of 33 per cent in the unfavourable case of a rapidly rising HIV epidemic. Estimates of cumulative HIV prevalence as of 1 July 1987 were positively biased in HIV epidemics with a rapidly decreasing recent HIV incidence rate and negatively biased in rapidly increasing HIV epidemics. Despite these uncertainties, we obtained useful estimates even for HIV epidemics with as few as 5000 infected individuals.

Design aspects of calibration studies in nutrition, with analysis of missing data in linear measurement error models.

Motivated by an example in nutritional epidemiology, we investigate some design and analysis aspects of linear measurement error models with missing surrogate data. The specific problem investigated consists of an initial large sample in which the response (a food frequency questionnaire, FFQ) is observed and then a smaller calibration study in which replicates of the error prone predictor are observed (food records or recalls, FR). The difference between our analysis and most of the measurement error model literature is that, in our study, the selection into the calibration study can depend on the value of the response. Rationale for this type of design is given. Two major problems are investigated. In the design of a calibration study, one has the option of larger sample sizes and fewer replicates or smaller sample sizes and more replicates. Somewhat surprisingly, neither strategy is uniformly preferable in cases of practical interest. The answers depend on the instrument used (recalls or records) and the parameters of interest. The second problem investigated is one of analysis. In the usual linear model with no missing data, method of moments estimates and normal-theory maximum likelihood estimates are approximately equivalent, with the former method in most use because it can be calculated easily and explicitly. Both estimates are valid without any distributional assumptions. In contrast, in the missing data problem under consideration, only the moments estimate is distribution-free, but the maximum likelihood estimate has at least 50% greater precision in practical situations when normality obtains. Implications for the design of nutritional calibration studies are discussed.

Alveolar macrophage interleukin (IL)-10 and IL-12 production in atopic asthma.

Inflammation in asthma is characterized by a Th2 response. In many experimental systems, this response can be regulated by interleukin (IL)-10 and IL-12. IL-10 deactivates T cells, and IL-12 reorients the response toward a Th1 pattern. Alveolar macrophages (AM) can secrete both of these cytokines, and thus regulate T-cell behavior in asthma. They can enhance the Th2 response by turning off their secretion of IL-10 and IL-12, or tend to downregulate it by producing these cytokines. To elucidate that point, we assayed the AM IL-10 and IL-12 from 11 asthmatic patients and four controls. Six asthmatics were treated by inhaled corticosteroids. AM were recovered by bronchoalveolar lavage (BAL). They were isolated and cultured for 24 h without stimulation or in the presence of lipopolysaccharide (LPS). IL-10 and the p40 subunit of IL-12 were assayed in the BAL fluid and in AM culture supernatants by ELISA. Spontaneous AM IL-10 production was higher in asthmatics, particularly in the treated group. The AM IL-10 production after stimulation by LPS was also elevated in asthmatics, but was mainly so in untreated patients. IL-12 levels were higher in BAL fluids from untreated patients than from controls. The IL-12 production of LPS-stimulated-AM from these patients was increased. These results show that AM are at least primed for the production of IL-10 and IL-12 in asthma, and suggest that these cells could be involved in the resolution of the asthmatic inflammation.

Designing studies to estimate the penetrance of an identified autosomal dominant mutation: cohort, case-control, and genotyped-proband designs.

One can obtain population-based estimates of the penetrance of a measurable mutation from cohort studies, from population-based case-control studies, and from genotyped-proband designs (GPD). In a GPD, we assume that representative individuals (probands) agree to be genotyped, and one then obtains information on the phenotypes of first-degree relatives. We also consider an extension of the GPD in which a relative is genotyped (GPDR design). In this paper, we give methods and tables for determining sample sizes needed to achieve desired precision for penetrance estimates from such studies. We emphasize dichotomous phenotypes, but methods for survival data are also given. In an example based on the BRCA1 gene and parameters given by Claus et al. [(1991) Am J Hum Genet 48:232-242], we find that similar large numbers of families need to be studied using the cohort, case-control, and GPD designs if the allele frequency is known, though the GPDR design requires fewer families, and, if one can study mainly probands with disease, the GPD design also requires fewer families. If the allele frequency is not known, somewhat larger sample sizes are required. Surprisingly, studies with mixtures of families of affected and non-affected probands can sometimes be more efficient than studies based exclusively on affected probands when the allele frequency is unknown. We discuss the feasibility and validity of these designs and point out that GPD and GPDR designs are more susceptible to a bias that results when the tendency for an individual to volunteer to be a proband or to be a subject in a cohort or case-control study depends on the phenotypes of his or her relatives.

Fruit and vegetables in the American diet: data from the NHANES II survey.

Twenty-four hour dietary recall data from the Second National Health and Nutrition Examination Survey (1976-80) were used to estimate the numbers of servings of fruit and vegetables consumed by Black and White adults, to examine the types of servings (e.g., potatoes, garden vegetables, fruit, and juice), and to estimate the mean intake of calories, fat, dietary fiber, and vitamins A and C by number of servings. An estimated 45 percent of the population had no servings of fruit or juice and 22 percent had no servings of a vegetable on the recall day. Only 27 percent consumed the three or more servings of vegetables and 29 percent had the two or more servings of fruit recommended by the US Departments of Agriculture and of Health and Human Services; 9 percent had both. Consumption was lower among Blacks than Whites. The choice of vegetables lacked variety. Diets including at least three servings of vegetables and two servings of fruit contained about 17 grams of dietary fiber. Although caloric and fat intake increased with increasing servings of fruit and vegetables, the percent of calories from fat remained relatively constant. Although these data are 10 years old, more recent surveys have shown similar results. The discrepancy between dietary guidelines and the actual diet suggests a need for extensive public education.