Stability of nocturnal wake and sleep stages defines central nervous system disorders of hypersomnolence

STUDY OBJECTIVES

We determine if young people with narcolepsy type 1 (NT1), narcolepsy type 2 (NT2), and idiopathic hypersomnia (IH) have distinct nocturnal sleep stability phenotypes compared to subjectively sleepy controls.

METHODS

Participants were 5- to 21-year old and drug-naïve or drug free: NT1 (n = 46), NT2 (n = 12), IH (n = 18), and subjectively sleepy controls (n = 48). We compared the following sleep stability measures from polysomnogram recording between each hypersomnolence disorder to subjectively sleepy controls: number of wake and sleep stage bouts, Kaplan-Meier survival curves for wake and sleep stages, and median bout durations.

RESULTS

Compared to the subjectively sleepy control group, NT1 participants had more bouts of wake and all sleep stages (p ≤ .005) except stage N3. NT1 participants had worse survival of nocturnal wake, stage N2, and rapid eye movement (REM) bouts (p < .005). In the first 8 hours of sleep, NT1 participants had longer stage N1 bouts but shorter REM (all ps < .004). IH participants had a similar number of bouts but better survival of stage N2 bouts (p = .001), and shorter stage N3 bouts in the first 8 hours of sleep (p = .003). In contrast, NT2 participants showed better stage N1 bout survival (p = .006) and longer stage N1 bouts (p = .02).

CONCLUSIONS

NT1, NT2, and IH have unique sleep physiology compared to subjectively sleepy controls, with only NT1 demonstrating clear nocturnal wake and sleep instability. Overall, sleep stability measures may aid in diagnoses and management of these central nervous system disorders of hypersomnolence.

Demystifying Fisher Information: What Observation Data Reveal about Our Models

Information theory is the basis for understanding how information is transmitted as observations. Observation data can be used to compare uncertainty on parameter estimates and predictions between models. Jacobian Information (JI) is quantified as the determinant of the weighted Jacobian (sensitivity) matrix. Fisher Information (FI) is quantified as the determinant of the weighted FI matrix. FI measures the relative disorder of a model (entropy) in a set of models. One-dimensional models are used to demonstrate the relationship between JI and FI, and the resulting uncertainty on estimated parameter values and model predictions for increasing model complexity, different model structures, different boundary conditions, and over-fitted models. Greater model complexity results in increased JI accompanied by an increase in parameter and prediction uncertainty. FI generally increases with increasing model complexity unless model error is large. Models with lower FI have a higher level of disorder (increase in entropy) which results in greater uncertainty of parameter estimates and model predictions. A constant-head boundary constrains the heads in the area near the boundary, reducing sensitivity of simulated equivalents to estimated parameters. JI and FI are lower for this boundary condition as compared to a constant-outflow boundary in which the heads in the area of the boundary can adjust freely. Complex, over-fitted models, in which the structure of the model is not supported by the observation dataset, result in lower JI and FI because there is insufficient information to estimate all parameters in the model.

Developmental Changes in Ultradian Sleep Cycles across Early Childhood

Nocturnal human sleep is composed of cycles between rapid eye movement (REM) sleep and non-REM (NREM) sleep. In adults, the structure of ultradian cycles between NREM and REM sleep is well characterized; however, less is known about the developmental trajectories of ultradian sleep cycles across early childhood. Cross-sectional studies indicate that the rapid ultradian cycling of active-quiet sleep in infancy shifts to a more adult-like pattern of NREM-REM sleep cycling by the school-age years, yet longitudinal studies elucidating the details of this transition are scarce. To address this gap, we examined ultradian cycling during nocturnal sleep following 13 h of prior wakefulness in 8 healthy children at 3 longitudinal points: 2Y (2.5-3.0 years of age), 3Y (3.5-4.0 years of age), and 5Y (5.5-6.0 years of age). We found that the length of ultradian cycles increased with age as a result of increased NREM sleep episode duration. In addition, we observed a significant decrease in the number of NREM sleep episodes as well as a nonsignificant trend for a decrease in the number of cycles with increasing age. Together, these findings suggest a concurrent change in which cycle duration increases and the number of cycles decreases across development. We also found that, consistent with data from adolescents and adults, the duration of NREM sleep episodes decreased with time since lights-off whereas the duration of REM sleep episodes increased over this time period. These results indicate the presence of circadian modulation of nocturnal sleep in preschool children. In addition to characterizing changes in ultradian cycling in healthy children ages 2 to 5 years, this work describes a developmental model that may provide insights into the emergence of normal adult REM sleep regulatory circuitry as well as potential trajectories of dysregulated ultradian cycles such as those associated with affective disorders.

Progressive Loss of the Orexin Neurons Reveals Dual Effects on Wakefulness

STUDY OBJECTIVES

Narcolepsy is caused by loss of the orexin (also known as hypocretin) neurons. In addition to the orexin peptides, these neurons release additional neurotransmitters, which may produce complex effects on sleep/wake behavior. Currently, it remains unknown whether the orexin neurons promote the initiation as well as the maintenance of wakefulness, and whether the orexin neurons influence initiation or maintenance of sleep. To determine the effects of the orexin neurons on the dynamics of sleep/wake behavior, we analyzed sleep/wake architecture in a novel mouse model of acute orexin neuron loss.

METHODS

We used survival analysis and other statistical methods to analyze sleep/wake architecture in orexin-tTA ; TetO diphtheria toxin A mice at different stages of orexin neuron degeneration.

RESULTS

Progressive loss of the orexin neurons dramatically reduced survival of long wake bouts, but it also improved survival of brief wake bouts. In addition, with loss of the orexin neurons, mice were more likely to wake during the first 30 sec of nonrapid eye movement sleep and then less likely to return to sleep during the first 60 sec of wakefulness.

CONCLUSIONS

These findings help explain the sleepiness and fragmented sleep that are characteristic of narcolepsy. Orexin neuron loss impairs survival of long wake bouts resulting in poor maintenance of wakefulness, but this neuronal loss also fragments sleep by increasing the risk of awakening at the beginning of sleep and then reducing the likelihood of quickly returning to sleep.

Errors in coarse particulate matter mass concentrations and spatiotemporal characteristics when using subtraction estimation methods

In studies of coarse particulate matter (PM10-2.5), mass concentrations are often estimated through the subtraction of PM2.5 from collocated PM10 tapered element oscillating microbalance (TEOM) measurements. Though all field instruments have yet to be updated, the Filter Dynamic Measurement System (FDMS) was introduced to account for the loss of semivolatile material from heated TEOM filters. To assess errors in PM10-2.5 estimation when using the possible combinations of PM10 and PM2.5 TEOM units with and without FDMS, data from three monitoring sites of the Colorado Coarse Rural-Urban Sources and Health (CCRUSH) study were used to simulate four possible subtraction methods for estimating PM10-2.5 mass concentrations. Assuming all mass is accounted for using collocated TEOMs with FDMS, the three other subtraction methods were assessed for biases in absolute mass concentration, temporal variability, spatial correlation, and homogeneity. Results show collocated units without FDMS closely estimate actual PM10-2.5 mass and spatial characteristics due to the very low semivolatile PM10-2.5 concentrations in Colorado. Estimation using either a PM2.5 or PM10 monitor without FDMS introduced absolute biases of 2.4 microg/m3 (25%) to -2.3 microg/m3 (-24%), respectively. Such errors are directly related to the unmeasured semivolatile mass and alter measures of spatiotemporal variability and homogeneity, all of which have implications for the regulatory and epidemiology communities concerned about PM10-2.5. Two monitoring sites operated by the state of Colorado were considered for inclusion in the CCRUSH acute health effects study, but concentrations were biased due to sampling with an FDMS-equipped PM2.5 TEOM and PM10 TEOM not corrected for semivolatile mass loss. A regression-based model was developed for removing the error in these measurements by estimating the semivolatile concentration of PM2.5 from total PM2.5 concentrations. By estimating nonvolatile PM2.5 concentrations from this relationship, PM10-2.5 was calculated as the difference between nonvolatile PM10 and PM2.5 concentrations.

Residential indoor PM2.5 in wood stove homes: follow-up of the Libby changeout program

In 2005 through 2008, a small rural mountain valley community engaged in a woodstove changeout program to address concerns of poor ambient air quality. During this program, we assessed changes to indoor air quality before and after the introduction of a new, lower emission woodstove. We previously reported a >70% reduction in indoor PM(2.5) concentrations in homes following the installation of a new Environmental Protection Agency's-certified stove within the home. We report here on follow-up of the experiences in these and other homes over three winters of sample collection. In 21 homes, we compared pre-changeout PM(2.5) concentrations [mean (s.d.) = 45.0 (33.0) μg/m(3)] to multiple post-changeout measures of PM(2.5) concentrations using a DustTrak. The mean reduction (and 95% confidence interval) from pre-changeout to post-changeout was -18.5 μg/m(3) (-31.9, -5.2), adjusting for ambient PM(2.5) , ambient temperature, and other factors. Findings across homes and across years were highly variable, and a subset of homes did not experience a reduction in PM(2.5) following changeout. Reductions were also observed for organic carbon, elemental carbon, and levoglucosan, but increases were observed for dehydroabietic acid and abietic acid. Despite overall improvements in indoor air quality, the varied response across homes may be due to factors other than the introduction of a new woodstove.

PRACTICAL IMPLICATIONS

Biomass combustion is a common source of ambient PM(2.5) in many cold-climate communities. The replacement of older model woodstoves with newer technology woodstoves is a potential intervention strategy to improve air quality in these communities. In addition to ambient air, woodstove changeouts should improve residential indoor air quality. We present results from a multi-winter study to evaluate the efficacy of woodstove changeouts on improving indoor air quality. Reductions in indoor PM(2.5) were evident, but this observation was not consistent across all homes. These findings suggest that other factors beyond the introduction of an improved wood burning device are relevant to improving indoor air quality in wood burning homes.

A rural community intervention targeting biomass combustion sources: effects on air quality and reporting of children's respiratory outcomes

OBJECTIVE

Improvements in urban air quality are largely driven by controls on industrial and mobile source emissions, but such factors may have limited influence on many rural environments where biomass combustion (eg, wood stoves) serves as the primary source of fine particulate matter (PM(2.5)). The authors tracked changes in children's respiratory health during a wood stove intervention in a rural mountain valley community heavily impacted by wood smoke-derived PM(2.5).

METHODS

Community-wide impacts on children's health were assessed by prospectively collecting surveys from parents of school children during four winter periods in Libby, Montana. Generalised estimating equations with a logit link were used to estimate the effect of reduction in ambient PM(2.5) on wheeze prevalence and other reported symptoms and infections.

RESULTS

Over 1100 wood stoves were replaced with new lower emission wood stoves or other heating sources. Ambient PM(2.5) was 27.6% lower in the winters following the changeout programme compared with baseline winters. There was a 26.7% (95% CI 3.0% to 44.6%) reduced odds of reported wheeze for a 5 μg/m(3) decrease in average winter PM(2.5). Lower ambient PM(2.5) was also associated with reduced odds for reported respiratory infections, including cold (25.4% (95% CI 7.6% to 39.7%)), bronchitis (54.6% (95% CI 24.2% to 72.8%)), influenza (52.3% (95% CI 42.5% to 60.5%)) and throat infection (45.1% (95% CI 29.0% to 57.6%)).

CONCLUSION

This wood stove intervention provided a unique opportunity to prospectively observe health benefits resulting from a targeted air pollution reduction strategy in a rural community.

Assessing the impact of a wood stove replacement program on air quality and children's health

Many rural mountain valley communities experience elevated ambient levels of fine particulate matter (PM*) in the winter, because of contributions from residential wood-burning appliances and sustained temperature inversion periods during the cold season. A wood stove change-out program was implemented in a community heavily affected by wood-smoke-derived PM2.5 (PM < or = 2.5 microm in aerodynamic diameter). The objectives of this study were to evaluate the impact of this intervention program on ambient and indoor PM2.5 concentrations and to identify possible corresponding changes in the frequency of childhood respiratory symptoms and infections and illness-related school absences. Over 1100 old wood stoves were replaced with new EPA-certified wood stoves or other heating sources. Ambient PM2.5 concentrations were 30% lower in the winter after the changeout program, compared with baseline winters, which brought the community's ambient air within the PM2.5 standards of the U.S. Environmental Protection Agency (U.S. EPA). The installation of a new wood stove resulted in an overall reduction in indoor PM2.5 concentrations in a small sample of wood-burning homes, but the effects were highly variable across homes. Community-level reductions in wood-smoke-derived PM2.5 concentration were associated with decreased reports of childhood wheeze and of other childhood respiratory health conditions. The association was not limited to children living in homes with wood stoves nor does it appear to be limited to susceptible children (e.g., children with asthma). Community-level reductions in wood-smoke-derived PM2.5 concentration were also associated with lower illness-related school absences among older children, but this finding was not consistent across all age-groups. This community-level intervention provided a unique opportunity to prospectively observe exposure and outcome changes resulting from a targeted air pollution reduction strategy.

Determining bioequivalence of topical dermatological drug products by tape-stripping

The maximum level of drug in the stratum corneum (C(max)) and the area under the curve of drug level in the stratum corneum versus time (AUC) have been proposed as metrics for assessing bioequivalence of topical drugs. These metrics, which require that concentrations be measured at eight or more times, were developed for drugs that are absorbed into the bloodstream, and are less appropriate for topical drugs. Concentrations of topical drugs are measured by tape-stripping, and it is difficult to make a large number of precise measurements due to the limited amount of available skin. We present a new method (the two-time method) for assessing bioequivalence of topical drugs. The method involves some modifications to standard tape-stripping methodology, designed to reduce the variability in measured drug levels. Perhaps most importantly, drug levels are measured at only two times, one during the uptake phase and one during the clearance phase. Measuring concentrations at only two times allows replicate measurements to be made, which increases efficiency. We compared the performance of the two-time method with a standard method through a simulation study that uses a model based on real data. When two drugs are in fact bioequivalent, the two-time method requires only 20 subjects to achieve the efficiency of a standard study with 50 subjects. In a situation in which two drugs are bioinequivalent, the two-time method requires only 30 subjects to achieve the efficiency of a standard study with 100 subjects.

The observed human sperm mutation frequency cannot explain the achondroplasia paternal age effect

The lifelong spermatogonial stem cell divisions unique to male germ cell production are thought to contribute to a higher mutation frequency in males. The fact that certain de novo human genetic conditions (e.g., achondroplasia) increase in incidence with the age of the father is consistent with this idea. Although it is assumed that the paternal age effect is the result of an increasing frequency of mutant sperm as a man grows older, no direct molecular measurement of the germ-line mutation frequency has been made to confirm this hypothesis. Using sperm DNA from donors of different ages, we determined the frequency of the nucleotide substitution in the fibroblast growth factor receptor 3 (FGFR3) gene that causes achondroplasia. Surprisingly, the magnitude of the increase in mutation frequency with age appears insufficient to explain why older fathers have a greater chance of having a child with this condition. A number of alternatives may explain this discrepancy, including selection for sperm that carry the mutation or an age-dependent increase in premutagenic lesions that remain unrepaired in sperm and are inefficiently detected by the PCR assay.

Risk set sampling for case-crossover designs

In the case-crossover design, only cases are sampled, and effect estimates are based on within-subject comparisons of exposures at failure times with exposures at control times. Sampling control times appropriately can provide some control for unmeasured confounding, but may introduce bias owing to time trends in the exposure of interest. The theory of risk set sampling (Borgan Ø, Goldstein L, Langholz B. Ann Stat 1995;23:1749-1778) can be used to develop effect estimates in these situations that are free from bias caused by time trends. Through simulation, we compared four sampling schemes: the full-stratum bidirectional design, a matched pair design, the symmetric bidirectional design of Bateson and Schwartz (Bateson T, Schwartz J. Epidemiology 1999;10:539-544), and the semi-symmetric bidirectional design. We also studied a quasi-likelihood extension of Poisson regression with overdispersion. We used daily mean particulate matter less than 10 microm in aerodynamic diameter levels in Denver as the exposure of interest, simulated confounding with linear and seasonal trends, and simulated mortality counts using a log relative risk of 1.1. Neither the matched pair, the full-stratum design, or Poisson regression with overdispersion provided control for seasonal confounding. The symmetric bidirectional design controlled for seasonal confounding but exhibited bias from time trends in exposure. The semi-symmetric bidirectional design provided control of seasonal confounding equal to that of the symmetric bidirectional design, without any time-trend bias.

Unequal exchange at the Charcot-Marie-Tooth disease type 1A recombination hot-spot is not elevated above the genome average rate

An increasing number of human diseases and syndromes are being found to result from micro-duplications or microdeletions arising from meiotic recombination between homologous repeats on the same chromosome. The first microduplication syndrome delineated, Charcot-Marie-Tooth disease type 1A (CMT1A), results from unequal crossing over between two >98% identical 24 kb repeats (CMT1A-REPs) on chromosome 17. In addition to its medical significance, the CMT1A region has features that make it a unique resource for detailed analysis of human unequal recombination. Previous studies of CMT1A patients showed that the majority of unequal crossovers occurred within a small region (<1 kb) of the REPs suggesting the presence of a recombination hot-spot. We directly measured the frequency of unequal recombination in the hot-spot region using sperm from four normal individuals. Surprisingly, unequal recombination between the REPs occurs at a rate no greater than the average rate for the male genome (approximately 1 cM/Mb) and is the same as that expected for equally aligned REPs. This conclusion extends to humans the findings in yeast that recombination between repeated sequences far apart on the same chromosome may occur at similar frequencies to allelic recombination. Finally, the CMT1A hot-spot stands in sharp contrast to the human MS32 mini-satellite-associated hot-spot that exhibits highly enhanced recombination initiation in addition to positional specificity. One possibility is that the CMT1A hot-spot may consist of a region with genome average recombination potential embedded within a recombination cold-spot.

Statistical methods for epidemiologic studies of the health effects of air pollution

We describe two statistical designs that can provide efficient estimates of the health effects of exposure to air pollutants in epidemiologic studies. We also evaluate the effects of measurement error in exposure assessment on the accuracy of estimated health effects. The bidirectional case-crossover design is a variant of a method proposed by Maclure (1991). Our version of the method takes advantage of the fact that in epidemiologic studies involving environmental exposure, accurate information about past exposure is more readily available, and that levels of exposure are generally unaffected by the response of the subject. It differs from other case-crossover methods in that control information is assessed both before and after failure, thus avoiding confounding due to time trends in exposure. The multilevel analytic design provides a method of combining estimates of health effects made on the individual level with those made at the group level. It has great potential value in situations where variations in exposure within groups may not be great enough to provide adequate power to detect health effects, as is often the case in air pollution studies where exposure levels are similar within a geographic community. Measurement errors in exposure assessment can have substantial impact on the accuracy of estimated health effects. When the microenvironmental approach is used to estimate exposure, a standard error of 30% in estimating indoor/outdoor ratios can increase the standard error of a relative risk estimate by 50%, and introduce bias as well. Similar results hold when exposure is estimated with personal samplers. When the microenvironmental approach is used, errors in estimating indoor/outdoor ratios have more influence on the accuracy of risk estimation than do errors in estimating the time spent in microenvironments.

A study of twelve Southern California communities with differing levels and types of air pollution. I. Prevalence of respiratory morbidity

To study possible chronic respiratory effects of air pollutants, we initiated a 10-yr prospective cohort study of Southern California children, with a study design focused on four pollutants: ozone, particulate matter, acids, and nitrogen dioxide (NO2). Twelve demographically similar communities were selected on the basis of historic monitoring information to represent extremes of exposure to one or more pollutants. In each community, about 150 public school students in grade 4, 75 in grade 7, and 75 in grade 10 were enrolled through their classrooms. Informed consent and written responses to surveys about students' lifetime residential histories, historic and current health status, residential characteristics, and physical activity were obtained with the help of the parents. In the first testing season, 3,676 students returned questionnaires. We confirmed associations previously reported between respiratory morbidity prevalence and the presence of personal, demographic, and residential risk factors. Rates of respiratory illness were higher for males, those living in houses with pets, pests, mildew, and water damage, those whose parents had asthma, and those living in houses with smokers. Wheeze prevalence was positively associated with levels of both acid (odds ratio [OR] = 1.45; 95% confidence interval [CI], 1.14-1.83) and NO2 (OR = 1.54; 95% CI, 1.08-2.19) in boys. We conclude, based on this cross-sectional assessment of questionnaire responses, that current levels of ambient air pollution in Southern California may be associated with effects on schoolchildren's respiratory morbidity as assessed by questionnaire.

A study of twelve Southern California communities with differing levels and types of air pollution. II. Effects on pulmonary function

To study the possible chronic respiratory effects of air pollutants, we designed and initiated a 10-yr prospective study of Southern California public schoolchildren living in 12 communities with different levels and profiles of air pollution. The design of the study, exposure assessment methods, and survey methods and results related to respiratory symptoms and conditions are described in the accompanying paper. Pulmonary function tests were completed on 3,293 subjects. We evaluated cross-sectionally the effects of air pollution exposures based on data collected in 1986-1990 by existing monitoring stations and data collected by our study team in 1994. Expected relationships were seen between demographic, physical, and other environmental factors and pulmonary function values. When the data were stratified by sex, an association was seen between pollution levels and lower pulmonary function in female subjects, with the associations being stronger for the 1994 exposure data than the 1986-1990 data. After adjustment, PM10, PM2.5, and NO2 were each significantly associated with lower FVC, FEV1, and maximal midexpiratory flow (MMEF); acid vapor with lower FVC, FEV1, peak expiratory flow rate (PEFR), and MMEF; and O3 with lower PEFR and MMEF. Effects were generally larger in those girls spending more time outdoors. Stepwise regression of adjusted pulmonary function values for girls in the 12 communities showed that NO2 was most strongly associated with lower FVC (r = -0.74, p < 0.01), PM2.5 with FEV1 (r = -0.72, p < 0.01), O3 with PEFR (r = -0.75, p < 0.005), and PM2.5 with MMEF (r = -0.80, p < 0.005). There was a statistically significant association between ozone exposure and decreased FVC and FEV1 in girls with asthma. For boys, significant associations were seen between peak O3 exposures and lower FVC and FEV1, but only in those spending more time outdoors. These findings underline the importance of follow-up of this cohort.

A study of twelve Southern California communities with differing levels and types of air pollution. I. Prevalence of respiratory morbidity

To study possible chronic respiratory effects of air pollutants, we initiated a 10-yr prospective cohort study of Southern California children, with a study design focused on four pollutants: ozone, particulate matter, acids, and nitrogen dioxide (NO2). Twelve demographically similar communities were selected on the basis of historic monitoring information to represent extremes of exposure to one or more pollutants. In each community, about 150 public school students in grade 4, 75 in grade 7, and 75 in grade 10 were enrolled through their classrooms. Informed consent and written responses to surveys about students' lifetime residential histories, historic and current health status, residential characteristics, and physical activity were obtained with the help of the parents. In the first testing season, 3,676 students returned questionnaires. We confirmed associations previously reported between respiratory morbidity prevalence and the presence of personal, demographic, and residential risk factors. Rates of respiratory illness were higher for males, those living in houses with pets, pests, mildew, and water damage, those whose parents had asthma, and those living in houses with smokers. Wheeze prevalence was positively associated with levels of both acid (odds ratio [OR] = 1.45; 95% confidence interval [CI], 1.14-1.83) and NO2 (OR = 1.54; 95% CI, 1.08-2.19) in boys. We conclude, based on this cross-sectional assessment of questionnaire responses, that current levels of ambient air pollution in Southern California may be associated with effects on schoolchildren's respiratory morbidity as assessed by questionnaire.

Bidirectional case-crossover designs for exposures with time trends

In the case-crossover design (Maclure, 1991, American Journal of Epidemiology 133, 144-153), only cases are sampled, and risk estimates are based on within-subject comparisons of exposures at failure times with exposures at times prior to failure, using matched case-control methods. While the design provides considerable advantages, unidirectional retrospective control sampling (selecting control times only prior to failure) can cause risk estimates to be confounded by time trends in exposure. However, when subsequent exposures are not influenced by failures, as in studies of environmental exposures such as air pollutants, it is possible to determine at times postfailure what a subject's level of exposure would have been had the subject not failed. We describe a bidirectional case-crossover design in which exposures at failure are compared with exposures both before and after failure. Simulation analyses show that relative risk estimates are resistant to confounding by time trend. We also extend the method to studies involving multiple failure times.

Individual variation in recombination among human males

Studies of recombination between the markers D6S291 and D6S109 in individuals by sperm typing provide direct evidence for significant variation in recombination among humans. A statistically significant difference in the recombination fraction (range 5.1%-11.2%) was detected among five donors. This variation could reflect polymorphisms in genes affecting recombination or in chromosome structure. Ignoring this variability in studies designed to examine the relationship between physical and genetic distances could lead to incorrect inferences. Individual variation in recombination makes it difficult to predict the recombination fraction for an interval in any particular individual. This could be important in certain genetic counseling situations.

The mutation rate of the human mtDNA deletion mtDNA4977

The human mitochondrial mutation mtDNA4977 is a 4,977-bp deletion that originates between two 13-bp direct repeats. We grew 220 colonies of cells, each from a single human cell. For each colony, we counted the number of cells and amplified the DNA by PCR to test for the presence of a deletion. To estimate the mutation fate, we used a model that describes the relationship between the mutation rate and the probability that a colony of a given size will contain no mutants, taking into account such factors as possible mitochondrial turnover and mistyping due to PCR error. We estimate that the mutation rate for mtDNA4977 in cultured human cells is 5.95 x 10(-8) per mitochondrial genome replication. This method can be applied to specific chromosomal, as well as mitochondrial, mutations.

Somatic microsatellite mutations as molecular tumor clocks

Microsatellite (MS) mutations can potentially unravel the past of mutator phenotype tumors, with greater genetic diversity expected in older regions. Rapid clonal expansions of xenografts were characterized by relatively homogenous MS alleles, whereas greater diversity was observed in a colorectal cancer with the greatest variation in its adjacent adenoma. A subcutaneous lung cancer metastasis demonstrated diversity consistent with its one-month clinical duration and evidence of active mitosis during dormancy. The genetic legacy inherent to multistep tumorigenesis provides direct estimates of tumor ages, with up to thousands of cell divisions and high death rates necessary to yield the observed diversities. MS molecular tumor clocks have the unique potential to systematically reconstruct the early and occult evolution of individual human mutator phenotype tumors.

Los Angeles study of residential magnetic fields and childhood brain tumors

A measurement study of residential magnetic fields and brain tumors in children that was added onto an ongoing case-control interview study in Los Angeles County, California, include 298 children under age 20 years with a primary brain tumor diagnosed from 1984 to 1991 and 298 control children identified by random digit dialing. Magnetic fields were determined for all Los Angeles homes where these 596 children lived from conception to diagnosis (1,131 homes) by mapping and coding the wiring configurations outside the home and by taking a series of exterior spot and profile measurements. In addition, for a subset of subjects (35%; 211 homes) 24-hour measurements were taken in the child's room and one other room. Although measured fields are consistently highest in the highest of the five wire code categories, fields in homes in this category are much lower in Los Angeles than in Denver, where the code originated. Brain tumor risk appears not to relate to measured fields inside (p for trend for child's room = 0.98) or outside (p for trend for front wall = 0.82) the home. An apparent increase in risk among children living at diagnosis in homes with underground wiring appears to be an artifact introduced by using current controls for historical cases because this apparent excess risk disappeared in an analysis restricted to the later years of the study when cases and controls were accrued concurrently. Our study does not show an overall association of pediatric brain tumors with measured fields, with "very high" wiring configurations, or with any of several other potential sources of exposure, such as use of various electrical appliances, but the prevalence of high fields (> 2 mG) and very high fields (> 3 mG) in Los Angeles homes was too low to detect a moderate effect of the magnitude reported in other studies.

Measurement error in air pollution exposure assessment

The exposure of an individual to an air pollutant can be assessed indirectly, with a "microenvironmental" approach, or directly with a personal sampler. Both methods of assessment are subject to measurement error, which can cause considerable bias in estimates of health effects. If the exposure estimates are unbiased and the measurement error is nondifferential, the bias in a linear model can be corrected when the variance of the measurement error is known. Unless the measurement error is quite large, estimates of health effects based on individual exposures appear to be more accurate than those based on ambient levels.

Design and analysis of multilevel analytic studies with applications to a study of air pollution

We discuss a hybrid epidemiologic design that aims to combine two approaches to studying exposure-disease associations. The analytic approach is based on comparisons between individuals, e.g., case-control and cohort studies, and the ecologic approach is based on comparisons between groups. The analytic approach generally provides a stronger basis for inference, in part because of freedom from between-group confounding and better quality data, but the ecologic approach is less susceptible to attenuation bias from measurement error and may provide greater variability in exposure. The design we propose entails selection of a number of groups and enrollment of individuals within each group. Exposures, outcomes, confounders, and modifiers would be assessed on each individual; but additional exposure data might be available on the groups. The analysis would then combine the individual-level and the group-level comparisons, with appropriate adjustments for exposure measurement errors, and would test for compatibility between the two levels of analysis, e.g., to determine whether the associations at the individual level can account for the differences in disease rates between groups. Trade-offs between numbers of groups, numbers of individuals, and the extent of the individual and group measurement protocols are discussed in terms of design efficiency. These issues are illustrated in the context of an on-going study of the health effects of air pollution in southern California, in which 12 communities with different levels and types of pollution have been selected and 3500 school children are being enrolled in a ten-year cohort study.(ABSTRACT TRUNCATED AT 250 WORDS)

Whole genome amplification from a single cell: implications for genetic analysis

We have developed an in vitro method for amplifying a large fraction of the DNA sequences present in a single haploid cell by repeated primer extensions using a mixture of 15-base random oligonucleotides. We studied 12 genetic loci and estimate that the probability of amplifying any sequence in the genome to a minimum of 30 copies is not less than 0.78 (95% confidence). Whole genome amplification beginning with a single cell, or other samples with very small amounts of DNA, has significant implications for multipoint mapping by sperm or oocyte typing and possibly for genetic disease diagnosis, forensics, and the analysis of ancient DNA samples.

Gene-centromere linkage mapping by PCR analysis of individual oocytes

We describe a general method of determining the recombination fraction between a polymorphic locus and the centromere in any species where single oocytes can be obtained. After removal of the first polar body, each oocyte is analyzed by PCR. The frequency of oocytes heterozygous at the polymorphic locus is used to estimate the recombination fraction. We estimate a recombination fraction of 0.15 between the mouse major histocompatibility complex (H-2) and the centromere of chromosome 17.

A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations

A multiple-tubes procedure is described for using PCR to determine the genotype of a very small DNA sample. The procedure involves dividing the sample among several tubes, then amplifying and typing the contents of each tube separately. The results are analyzed by a statistical procedure which determines whether a genotype can be conclusively assigned to the DNA sample. Simulation studies show that this procedure usually gives correct results even when the number of double-stranded fragments in the sample is as small as 30. The procedure remains effective even in the presence of small amounts of laboratory contamination. We find that the multiple-tubes procedure is superior to the standard one-tube procedure, either when the sample is small or when laboratory contamination is a potential problem; and we recommend its use in these situations. Because the procedure is statistical, it allows the degree of certainty in the result to be quantified and may be useful in other PCR applications as well.

Using PCR in preimplantation genetic disease diagnosis

Preimplantation diagnosis of genetic disease can be accomplished by embryo biopsy or polar body analysis using in-vitro gene amplification (PCR). PCR analysis of single cells is subject to a number of errors which decrease the reliability of the diagnosis. Using realistic assumptions about error rates based on experimental data, we analyse some of the practical consequences to be faced by whose wishing to use this diagnostic procedure. We considered both autosomal dominant and recessive diseases. We calculate the probability of making mistakes in the diagnosis, assuming a realistic range in the magnitude of PCR efficiency, cell transfer, and contamination errors. We conclude that, in general, analysing blastomeres is subject to less mis-diagnosis than polar body analysis, except in the case of dominant diseases which are caused by genes which lie extremely close to the centromere. We also show that typing multiple blastomeres from a single embryo or combining polar body typing with blastomere analysis results in significantly lower levels of mis-diagnosis with unacceptable consequences. The preimplantation diagnosis of X-linked diseases based upon Y chromosome sequence analysis is also discussed.