Cluster-based bagging of constrained mixed-effects models for high spatiotemporal resolution nitrogen oxides prediction over large regions

BACKGROUND

Accurate estimation of nitrogen dioxide (NO₂) and nitrogen oxide (NO_x) concentrations at high spatiotemporal resolutions is crucial for improving evaluation of their health effects, particularly with respect to short-term exposures and acute health outcomes. For estimation over large regions like California, high spatial density field campaign measurements can be combined with more sparse routine monitoring network measurements to capture spatiotemporal variability of NO₂ and NO_x concentrations. However, monitors in spatially dense field sampling are often highly clustered and their uneven distribution creates a challenge for such combined use. Furthermore, heterogeneities due to seasonal patterns of meteorology and source mixtures between sub-regions (e.g. southern vs. northern California) need to be addressed.

OBJECTIVES

In this study, we aim to develop highly accurate and adaptive machine learning models to predict high-resolution NO₂ and NO_x concentrations over large geographic regions using measurements from different sources that contain samples with heterogeneous spatiotemporal distributions and clustering patterns.

METHODS

We used a comprehensive Kruskal-K-means method to cluster the measurement samples from multiple heterogeneous sources. Spatiotemporal cluster-based bootstrap aggregating (bagging) of the base mixed-effects models was then applied, leveraging the clusters to obtain balanced and less correlated training samples for less bias and improvement in generalization. Further, we used the machine learning technique of grid search to find the optimal interaction of temporal basis functions and the scale of spatial effects, which, together with spatiotemporal covariates, adequately captured spatiotemporal variability in NO₂ and NO_x at the state and local levels.

RESULTS

We found an optimal combination of four temporal basis functions and 200 m scale spatial effects for the base mixed-effects models. With the cluster-based bagging of the base models, we obtained robust predictions with an ensemble cross validation R² of 0.88 for both NO₂ and NO_x [RMSE (RMSEIQR): 3.62 ppb (0.28) and 9.63 ppb (0.37) respectively]. In independent tests of random sampling, our models achieved similarly strong performance (R² of 0.87-0.90; RMSE of 3.97-9.69 ppb; RMSEIQR of 0.21-0.27), illustrating minimal over-fitting.

CONCLUSIONS

Our approach has important implications for fusing data from highly clustered and heterogeneous measurement samples from multiple data sources to produce highly accurate concentration estimates of air pollutants such as NO₂ and NO_x at high resolution over a large region.

Exposure measurement error in air pollution studies: A framework for assessing shared, multiplicative measurement error in ensemble learning estimates of nitrogen oxides

BACKGROUND

Increasingly ensemble learning-based spatiotemporal models are being used to estimate residential air pollution exposures in epidemiological studies. While these machine learning models typically have improved performance, they suffer from exposure measurement error that is inherent in all models. Our objective is to develop a framework to formally assess shared, multiplicative measurement error (SMME) in our previously published three-stage, ensemble learning-based nitrogen oxides (NO_x) model to identify its spatial and temporal patterns and predictors.

METHODS

By treating the ensembles as an external dosimetry system, we quantified shared and unshared, multiplicative and additive (SUMA) measurement error components in our exposure model. We used generalized additive models (GAMs) with a smooth term for location to identify geographic locations with significantly elevated SMME and explain their spatial and temporal determinants.

RESULTS

We found evidence of significant shared and unshared multiplicative error (p < 0.0001) in our ensemble-learning based spatiotemporal NO_x model predictions. Unshared multiplicative error was 26 times larger than SMME. We observed significant geographic (p < 0.0001) and temporal variation in SMME with the majority (43%) of predictions with elevated SMME occurring in the earliest time-period (1992-2000). Densely populated urban prediction regions with complex air pollution sources generally exhibited highest odds of elevated SMME.

CONCLUSIONS

We developed a novel statistical framework to formally evaluate the magnitude and drivers of SMME in ensemble learning-based exposure models. Our framework can be used to inform building future improved exposure models.

Short-term effects of airport-associated ultrafine particle exposure on lung function and inflammation in adults with asthma

BACKGROUND

Exposure to ultrafine particles (UFP, particles with aerodynamic diameter < 100 nm) is associated with reduced lung function and airway inflammation in individuals with asthma. Recently, elevated UFP number concentrations (PN) from aircraft landing and takeoff activity were identified downwind of the Los Angeles International Airport (LAX) but little is known about the health impacts of airport-related UFP exposure.

METHODS

We conducted a randomized crossover study of 22 non-smoking adults with mild to moderate asthma in Nov-Dec 2014 and May-Jul 2015 to investigate short-term effects of exposure to LAX airport-related UFPs. Participants conducted scripted, mild walking activity on two occasions in public parks inside (exposure) and outside (control) of the high UFP zone. Spirometry, multiple flow exhaled nitric oxide, and circulating inflammatory cytokines were measured before and after exposure. Personal UFP PN and lung deposited surface area (LDSA) and stationary UFP PN, black carbon (BC), particle-bound PAHs (PB-PAH), ozone (O3), carbon dioxide (CO2) and particulate matter (PM2.5) mass were measured. Source apportionment analysis was conducted to distinguish aircraft from roadway traffic related UFP sources. Health models investigated within-subject changes in outcomes as a function of pollutants and source factors.

RESULTS

A high two-hour walking period average contrast of ~34,000 particles·cm-3 was achieved with mean (std) PN concentrations of 53,342 (25,529) and 19,557 (11,131) particles·cm-3 and mean (std) particle size of 28.7 (9.5) and 33.2 (11.5) at the exposure and control site, respectively. Principal components analysis differentiated airport UFPs (PN), roadway traffic (BC, PB-PAH), PM mass (PM2.5, PM10), and secondary photochemistry (O3) sources. A standard deviation increase in the 'Airport UFPs' factor was significantly associated with IL-6, a circulating marker of inflammation (single-pollutant model: 0.21, 95% CI = 0.08-0.34; multi-pollutant model: 0.18, 0.04-0.32). The 'Traffic' factor was significantly associated with lower Forced Expiratory Volume in 1 s (FEV1) (single-pollutant model: -1.52, -2.28 to -0.77) and elevated sTNFrII (single-pollutant model: 36.47; 6.03-66.91; multi-pollutant model: 64.38; 6.30-122.46). No consistent associations were observed with exhaled nitric oxide.

CONCLUSIONS

To our knowledge, our study is the first to demonstrate increased acute systemic inflammation following exposure to airport-related UFPs. Health effects associated with roadway traffic exposure were distinct. This study emphasizes the importance of multi-pollutant measurements and modeling techniques to disentangle sources of UFPs contributing to the complex urban air pollution mixture and to evaluate population health risks.

Constrained Mixed-Effect Models with Ensemble Learning for Prediction of Nitrogen Oxides Concentrations at High Spatiotemporal Resolution

Spatiotemporal models to estimate ambient exposures at high spatiotemporal resolutions are crucial in large-scale air pollution epidemiological studies that follow participants over extended periods. Previous models typically rely on central-site monitoring data and/or covered short periods, limiting their applications to long-term cohort studies. Here we developed a spatiotemporal model that can reliably predict nitrogen oxide concentrations with a high spatiotemporal resolution over a long time span (>20 years). Leveraging the spatially extensive highly clustered exposure data from short-term measurement campaigns across 1-2 years and long-term central site monitoring in 1992-2013, we developed an integrated mixed-effect model with uncertainty estimates. Our statistical model incorporated nonlinear and spatial effects to reduce bias. Identified important predictors included temporal basis predictors, traffic indicators, population density, and subcounty-level mean pollutant concentrations. Substantial spatial autocorrelation (11-13%) was observed between neighboring communities. Ensemble learning and constrained optimization were used to enhance reliability of estimation over a large metropolitan area and a long period. The ensemble predictions of biweekly concentrations resulted in an R2 of 0.85 (RMSE: 4.7 ppb) for NO2 and 0.86 (RMSE: 13.4 ppb) for NOx. Ensemble learning and constrained optimization generated stable time series, which notably improved the results compared with those from initial mixed-effects models.

Childhood determination of Hodgkin lymphoma among U.S. servicemen

BACKGROUND

Hodgkin lymphoma in young adults is inexplicably linked to economic development.

METHODS

We conducted a nested case-control study of the 656 servicemen with Hodgkin lymphoma diagnosed between ages 17 to 32 while on active duty in the U.S. military during 1950-68. Controls, chosen randomly from the servicemen on duty at the time, were matched on service, birth year, and induction date. Information came from preinduction records and military records for the period ending at onset or the equivalent date.

RESULTS

Risk was independently increased with small sib-ship size [OR, 2.3; confidence interval (CI), 1.6-3.5], low birth order (OR, 1.9; CI, 1.4-2.6), and an interval of at least 5 years between birth and that of a previous or subsequent sibling (OR, 2.1; CI, 1.5-3.1). Other factors independently and significantly associated with elevated risk of Hodgkin lymphoma were: tallness, high body mass index, more education (but not higher income) in the county of birth, BB or AB blood type, and past infectious mononucleosis (but a deficit of other childhood viral infections). Early fatherhood conveyed high risk (OR, 2.6; CI, 1.4-4.8), especially if with a high-risk sibling configuration. Factors unrelated to risk included personal education, preinduction or military occupation, induction test score, and rank. Findings were similar for nodular sclerosis and mixed cell histologic subtypes.

CONCLUSIONS

Protection from the environment in childhood, but not in adulthood, increases the likelihood of young adult Hodgkin lymphoma, which may result from nonspecific isolation from early infections and/or exposure to late infection by a specific but unidentified ubiquitous childhood virus.

IMPACT

Events in childhood protect against later Hodgkin lymphoma.

Association of improved air quality with lung development in children

BACKGROUND

Air-pollution levels have been trending downward progressively over the past several decades in southern California, as a result of the implementation of air quality-control policies. We assessed whether long-term reductions in pollution were associated with improvements in respiratory health among children.

METHODS

As part of the Children's Health Study, we measured lung function annually in 2120 children from three separate cohorts corresponding to three separate calendar periods: 1994-1998, 1997-2001, and 2007-2011. Mean ages of the children within each cohort were 11 years at the beginning of the period and 15 years at the end. Linear-regression models were used to examine the relationship between declining pollution levels over time and lung-function development from 11 to 15 years of age, measured as the increases in forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) during that period (referred to as 4-year growth in FEV1 and FVC).

RESULTS

Over the 13 years spanned by the three cohorts, improvements in 4-year growth of both FEV1 and FVC were associated with declining levels of nitrogen dioxide (P<0.001 for FEV1 and FVC) and of particulate matter with an aerodynamic diameter of less than 2.5 μm (P= 0.008 for FEV1 and P<0.001 for FVC) and less than 10 μm (P<0.001 for FEV1 and FVC). These associations persisted after adjustment for several potential confounders. Significant improvements in lung-function development were observed in both boys and girls and in children with asthma and children without asthma. The proportions of children with clinically low FEV1 (defined as <80% of the predicted value) at 15 years of age declined significantly, from 7.9% to 6.3% to 3.6% across the three periods, as the air quality improved (P = 0.001).

CONCLUSIONS

We found that long-term improvements in air quality were associated with statistically and clinically significant positive effects on lung-function growth in children. (Funded by the Health Effects Institute and others.).

Dog ownership enhances symptomatic responses to air pollution in children with asthma

BACKGROUND

Experimental data suggest that asthma exacerbation by ambient air pollutants is enhanced by exposure to endotoxin and allergens; however, there is little supporting epidemiologic evidence.

METHODS

We evaluated whether the association of exposure to air pollution with annual prevalence of chronic cough, phlegm production, or bronchitis was modified by dog and cat ownership (indicators of allergen and endotoxin exposure). The study population consisted of 475 Southern California children with asthma from a longitudinal cohort of participants in the Children's Health Study. We estimated average annual ambient exposure to nitrogen dioxide, ozone, particulate matter < 10, 2.5, and 10-2.5 microm in aerodynamic diameter (PM10, PM2.5, and PM10-2.5, respectively), elemental and organic carbon, and acid vapor from monitoring stations in each of the 12 study communities. Multivariate models were used to examine the effect of yearly variation of each pollutant. Effects were scaled to the variability that is common for each pollutant in representative communities in Southern California.

RESULTS

Among children owning a dog, there were strong associations between bronchitic symptoms and all pollutants examined. Odds ratios ranged from 1.30 per 4.2 microg/m3 for PM10-2.5 [95% confidence interval (CI), 0.91-1.87) to 1.91 per 1.2 microg/m3 for organic carbon (95% CI, 1.34-2.71). Effects were somewhat larger among children who owned both a cat and dog. There were no effects or small effects with wide CIs among children without a dog and among children who owned only a cat.

CONCLUSION

Our results suggest that dog ownership, a source of residential exposure to endotoxin, may worsen the relationship between air pollution and respiratory symptoms in asthmatic children.

Hypereosinophilic syndrome: two case reports of contrasting variants

Two cases of hypereosinophilic syndrome that illustrate different variants are reported. Recognition of the specific variant is important because the treatments differ. Patients with hypereosinophilic syndrome should be monitored for evidence of a myeloproliferative process because treatment with tyrosine kinase inhibitors in these patients is effective and may prevent significant morbidity.

The effect of air pollution on lung development from 10 to 18 years of age

BACKGROUND

Whether exposure to air pollution adversely affects the growth of lung function during the period of rapid lung development that occurs between the ages of 10 and 18 years is unknown.

METHODS

In this prospective study, we recruited 1759 children (average age, 10 years) from schools in 12 southern California communities and measured lung function annually for eight years. The rate of attrition was approximately 10 percent per year. The communities represented a wide range of ambient exposures to ozone, acid vapor, nitrogen dioxide, and particulate matter. Linear regression was used to examine the relationship of air pollution to the forced expiratory volume in one second (FEV(1)) and other spirometric measures.

RESULTS

Over the eight-year period, deficits in the growth of FEV(1) were associated with exposure to nitrogen dioxide (P=0.005), acid vapor (P=0.004), particulate matter with an aerodynamic diameter of less than 2.5 microm (PM(2.5)) (P=0.04), and elemental carbon (P=0.007), even after adjustment for several potential confounders and effect modifiers. Associations were also observed for other spirometric measures. Exposure to pollutants was associated with clinically and statistically significant deficits in the FEV(1) attained at the age of 18 years. For example, the estimated proportion of 18-year-old subjects with a low FEV(1) (defined as a ratio of observed to expected FEV(1) of less than 80 percent) was 4.9 times as great at the highest level of exposure to PM(2.5) as at the lowest level of exposure (7.9 percent vs. 1.6 percent, P=0.002).

CONCLUSIONS

The results of this study indicate that current levels of air pollution have chronic, adverse effects on lung development in children from the age of 10 to 18 years, leading to clinically significant deficits in attained FEV(1) as children reach adulthood.

Environmental tobacco smoke and absenteeism related to respiratory illness in schoolchildren

Household environmental tobacco smoke (ETS) exposure accounts for substantial morbidity among young children, but the ETS-associated morbidity burden among school-age children is less well defined. Illness-related school absenteeism is a measure of a broad spectrum of adverse effects of ETS exposure in school-age children. The authors investigated the relations between ETS exposure, asthma status, and illness-related school absenteeism in a cohort of 1,932 fourth-grade schoolchildren from 12 southern California communities during January-June 1996. Incidence rates and adjusted relative risks of illness-related absences were determined by using an active surveillance system. The effects of ETS exposure on absenteeism were assessed by using stratified incidence rates and Poisson regression to adjust for sociodemographic factors. ETS exposure was associated with an increased risk of respiratory-illness-related school absences (relative risk (RR) = 1.27, 95% confidence interval (CI): 1.04, 1.56). Children living in a household with two or more smokers were at increased risk of such absences (RR = 1.75, 95% CI: 1.33, 2.30). Children's asthma status affected their response to ETS. Compared with unexposed children without asthma, children with asthma were at increased risk of respiratory-illness-related school absences when exposed to one (RR = 2.35, 95% CI: 1.49, 3.71) or two or more (RR = 4.45, 95% CI: 2.80, 7.07) household smokers. Children without asthma also had an increased risk if exposed to two or more smokers (RR = 1.44, 95% CI: 1.04, 2.00). Therefore, ETS exposure is associated with increased respiratory-related school absenteeism among children, especially those with asthma.

Effects of glutathione-S-transferase M1, T1, and P1 on childhood lung function growth

The effects of glutathione-S-transferase (GST) M1, GSTT1, and GSTP1 genotypes on lung function growth were investigated in 1,940 children enrolled in the Children's Health Study as fourth graders (aged 8-11 years) in two cohorts during 1993 and 1996 and were followed annually over a 4-year period. Genotypes for GSTM1 and GSTT1 and GSTP1 codon 105 variants (ile105 and val105) were determined using DNA from buccal cell specimens. We used two-level regression models to estimate the effects of GSTM1, GSTT1, and GSTP1 genotypes on the adjusted annual average lung function growth. GSTM1 null was associated with deficits in annual growth rates for FVC (-0.21%; 95% confidence interval [CI], -0.40, -0.03) and FEV(1) (-0.27%; 95% CI, -0.50, -0.04). Children who were homozygous for the GSTP1 val105 allele had slower lung function growth (FVC -0.35%; 95% CI, -0.62, -0.07; and FEV(1) -0.34%; 95% CI, -0.68, 0.00) than children with one or more ile105 alleles. Children with asthma who were homozygous for the GSTP1 val105 allele had substantially larger deficits in FVC, FEV(1), and maximal mid-expiratory flow than children without asthma. The deficits in FVC and FEV(1) growth associated with both GSTM1 null and the GSTP1 val105 allele were largest and were statistically significant in non-Hispanic white children. We conclude that GSTM1 and GSTP1 genotypes are associated with lung function growth in school children.

Homozygosity for the V37I Connexin 26 mutation in three unrelated children with sensorineural hearing loss

Mutations in the Connexin 26 (Cx26) gene have been found to account for approximately 20% of all childhood deafness. This number approaches 50% in documented recessive cases of hearing loss. Two mutations, 35delG and 167delT, account for the majority of reported mutations in this gene, but to date, more than 60 mutations have been described. No other single gene has yet been identified that contributes this significantly to the aetiology of hearing loss. Several mutations in this gene have been found to predominate in specific ethnic populations (167delT in Ashkenazi Jews and 235delC in Japanese individuals). While the majority of mutations found in Cx26 result in frame shifts and premature terminations, a number of missense mutations have also been identified. The V37I missense mutation has been reported as both a polymorphism and as a potentially disease-causing missense mutation. The present authors have identified three unrelated individuals with sensorineural hearing loss who are homozygous for this mutation. One individual is of Philippine ancestry, another is from a Chinese and Cambodian background, while the third is of Chinese ancestry, raising the possibility that this mutation may be more frequent among populations in eastern Asia.

Sex-specific effects of asthma on pulmonary function in children

To evaluate the effects on lung function of asthma, time since diagnosis of asthma, and age at diagnosis of asthma, we examined school children in a cohort of 2,277 fourth- and seventh-graders at least twice during a 4-yr follow-up period. Sex-specific models for each lung function were fitted through mixed-effects models that used regression splines and captured age-dependent trends in the effect of asthma on lung function. In males, a history of asthma was associated with large and statistically significant deficits in maximum midexpiratory flow (MMEF) (-4.89%) and forced expiratory flow at 75% of expired FVC (FEF(75)) (-6.62%), whereas in females these deficits were smaller (-1.93% and -2.45%, respectively) and were not statistically significant. However, larger deficits were seen in both males and females with longer time since diagnosis. In males with more than 6 yr since diagnosis, there were significant deficits in FEV(1) (-3.91%), MMEF (-7.39%), FEF(75) (-8.12%), and peak expiratory flow rate (PEFR) (-4.65%) as compared with children with less than 3 yr since diagnosis. There were fewer females with more than 6 yr since diagnosis, but deficits were similar to those of males for FEV(1) (-2.52%), MMEF (-9.26%), and FEF(75) (-14.28%). Large deficits in flow rates in both large and small airways were observed in males and females for whom asthma was reported to have been diagnosed before age 3 yr. There was little evidence that lung growth in children with asthma "catches up" at older ages. Therefore, because a constant percent deficit in lung function implies an increasingly large absolute deficit in older children with larger lungs, these results are consistent with prior evidence that lung function deficits in children with asthma persist into adulthood. We also suggest that in children, commonly observed differences between sexes in the impact of asthma on lung function may reflect differences in the duration and age of onset of asthma in males and females.

Skin characteristics and risk of superficial spreading and nodular melanoma (United States)

OBJECTIVE

To assess the risk for melanoma associated with moles and pigmentary characteristics.

METHODS

Representative melanoma cases (773) among non-Hispanic white residents under age 65 occurring between 1 June 1978 and I December 1983 in Los Angeles County were compared to controls (752) matched to cases by age, sex, race and neighborhood of residence. Factors considered include hair, eye, and skin color; numbers of freckles and moles; and propensity to burn and tan obtained during an in-person interview.

RESULTS

Five hundred and fifty-one cases were classified as superficial spreading melanoma (SSM) and 110 as nodular melanoma (NM). For SSM, the important risk determinants were hair and skin color, freckling, and mole prevalence. Light skin and more freckles were found to be more highly associated with SSM for younger compared to older subjects, whereas the associations between SSM and both hair color and moles remained independent of age. NM showed patterns of risk similar to SSM with the exception of skin color. NM showed no evidence of increasing risk with lighter skin, as compared to the strong association seen for SSM.

CONCLUSION

Hair and skin color, freckling and, especially, numbers and size of moles are important determinants of melanoma risk.

Effect of spirometer temperature on FEV1 in a longitudinal epidemiological study

OBJECTIVES

To assess the magnitude of error in pulmonary function measurements introduced by variation in spirometer temperature under field conditions. In a large scale epidemiological study of school children, the influence was investigated of spirometer temperature on forced expiratory volume in 1 second (FEV1) measured with dry rolling seal volumetric spirometers and conventional body temperature, pressure, and saturation (BTPS) corrections.

METHODS

Linear regression analyses were performed on data from 995 test-retest pairs on 851 different children, with 1-110 days between test and retest, and spirometer temperature differences between -13 degrees C and +9 degrees C.

RESULTS

After adjusting for effects of growth (test-retest intervals) and circadian variation (changes in times of testing), differences in standard BTPS corrected FEV1 showed significant (p < 0.05) dependence on differences in spirometer temperature between tests (-0.24%/degree C).

CONCLUSIONS

When spirometer temperatures vary widely, standard BTPS correction does not fully adjust for gas contraction. To improve accuracy of volume measurements in epidemiological studies, additional correction for variation in spirometer temperature should be considered.

Analysis of 31 CFTR mutations by polymerase chain reaction/oligonucleotide ligation assay in a pilot screening of 4476 newborns for cystic fibrosis

OBJECTIVES

Molecular biological testing for genetic diseases has grown rapidly, but speed, accuracy, specificity, sensitivity, throughput, and cost become more important as large scale screening is considered. This is a pilot study of an assay for the simultaneous detection of up to 31 cystic fibrosis mutations in a multicentre population based screening of 4476 Italian newborns.

METHODS

The assay is a polymerase chain reaction, followed by an oligonucleotide ligation assay (PCR/OLA) and finally a sequence coded separation. It allows the detection of up to 31 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Guthrie spots were used as a source of template DNA.

RESULTS

144 carriers were detected during the analysis of 4476 samples, which translates into a carrier frequency of 1/31.1. Forty two carriers were detected from 1341 samples in Pavia (1/31.9), 53 from 1574 in Turin (1/29.7), and 49 from 1561 in San Giovanni Rotondo (1/31.8). Fifteen different mutations were detected, the most common being delta F508 (0.625). Other common mutations included G542X (16 of 144), which was particularly common in southern Italy (14 of 49), N1303K (8 of 144), and R117H (8 of 144), detected only in the northern centres.

CONCLUSIONS

PCR/OLA is a robust, accurate, user friendly method for cystic fibrosis screening of newborns using blood spots in a semiautomated way at a low cost per mutation (0.8 Euro).

Genetic analysis in Italian families with inflammatory bowel disease supports linkage to the IBD1 locus--a GISC study

Epidemiological studies suggest that inherited factors influence susceptibility to inflammatory bowel disease (IBD), and some candidate loci have been described. In order to verify whether the same loci are responsible for predisposition to IBD in our population, we carried out a linkage study in a series of 58 Italian families with Crohn's disease (CD) and ulcerative colitis (UC). HLA-DQ alleles, motilin gene, and 34 microsatellites flanking the previously described loci on chromosomes 3, 6, 7, 12 and 16 were analysed by non-parametric linkage analysis in 16 and 23 families with CD and UC, respectively, and in 19 families where CD and UC coexisted. Non parametric analysis using GENEHUNTER yielded maximum NPL scores for marker D16S408 in all IBD families combined (2.71, P = 0.003), for marker D16S419 in CD (1.97, P = 0.026) and for marker D16S514 in UC families (2.44, P = 0.007). These markers map in the previously described IBD1 region. No significant linkage was found for markers of chromosomes 3, 6, 7 and 12. The present study performed in a Southern European population provides additional support for the conclusion with the IBD1 locus has a clear role in the genetic susceptibility to IBD.

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.

Identification of a delta isoform of preprotachykinin mRNA in human mononuclear phagocytes and lymphocytes

We have characterized preprotachykinin (PPT-A) gene transcript splicing products and identified a fourth isoform of PPT-A mRNA transcript in human peripheral blood-isolated monocytes and PBL. Using RT-PCR, Southern blot analysis and nucleotide sequencing analysis, we have identified the four isoforms of PPT-A transcripts (alpha, beta, gamma and delta) in human peripheral blood-isolated monocytes and PBL. The delta-PPT transcript present in the immune cells lacks exons 4 and 6. The sequences of exons 3, 5 and 7 of delta-PPT transcript completely match those of beta-PPT transcript. The alpha-PPT and beta-PPT sequences in these cells are identical to those obtained by Tan and Too (GenBank accession number U37539) and Harmar et al. (Genbank accession number X54469), but differ by a single nucleotide from another entry by Chiwakata et al. (Genbank accession number M68906). In comparison to this latter sequence, there was a C-->T change at amino acid position 87 (CCT-->CTT) which may result in a Pro to Leu change. Identification of the new SP mRNA transcript in both human CNS and immune cells supports the concept of an important biological link between CNS and immune system.

Parallel molecular genetic analysis

We describe recent progress in parallel molecular genetic analyses using DNA microarrays, gel-based systems, and capillary electrophoresis and utilization of these approaches in a variety of molecular biology assays. These applications include use of polymorphic markers for mapping of genes and disease-associated loci and carrier detection for genetic diseases. Application of these technologies in molecular diagnostics as well as fluorescent technologies in DNA analysis using immobilized oligonucleotide arrays on silicon or glass microchips are discussed. The array-based assays include sequencing by hybridization, cDNA expression profiling, comparative genome hybridization and genetic linkage analysis. Developments in non microarray-based, parallel analyses of mutations and gene expression profiles are reviewed. The promise of and recent progress in capillary array electrophoresis for parallel DNA sequence analysis and genotyping is summarized. Finally, a framework for decision making in selecting available technology options for specific molecular genetic analyses is presented.

Connexin-26 mutations in sporadic and inherited sensorineural deafness

BACKGROUND

Hearing impairment affects one infant in 1000 and 4% of people aged younger than 45 years. Congenital deafness is inherited or apparently sporadic. We have shown previously that DFNB1 on chromosome 13 is a major locus for recessive deafness in about 80% of Mediterranean families and that the connexin-26 gene gap junction protein beta2 (GJB2) is mutated in DFNB1 families. We investigated mutations in the GJB2 gene in familial and sporadic cases of deafness.

METHODS

We obtained DNA samples from 82 families from Italy and Spain with recessive non-syndromic deafness and from 54 unrelated participants with apparently sporadic congenital deafness. We analysed the coding region of the GJB2 gene for mutations. We also tested 280 unrelated people from the general populations of Italy and Spain for the frameshift mutation 35delG.

FINDINGS

49% of participants with recessive deafness and 37% of sporadic cases had mutations in the GJB2 gene. The 35delG mutation accounted for 85% of GJB2 mutations, six other mutations accounted for 6% of alleles, and no changes in the coding region of GJB2 were detected in 9% of DFNB1 alleles. The carrier frequency of mutation 35delG among people from the general population was one in 31 (95% CI one in 19 to one in 87).

INTERPRETATION

Mutations in the GJB2 gene are a major cause of inherited and apparently sporadic congenital deafness. Mutation 35delG is the most common mutation for sensorineural deafness. Identification of 35delG and other mutations in the GJB2 gene should facilitate diagnosis and counselling for the most common genetic form of deafness.

Connexin26 mutations associated with the most common form of non-syndromic neurosensory autosomal recessive deafness (DFNB1) in Mediterraneans

Non-syndromic neurosensory autosomal recessive deafness (NSRD) is the most common form of genetic hearing loss. Previous studies defined at least 15 human NSRD loci. Recently we demonstrated that DFNB1, located on the long arm of chromosome 13, accounts for approximately 80% of cases in the Mediterranean area. Further analysis with additional markers now identifies several recombinants which narrow the candidate region to approximately 5 cM, encompassed by markers D13S141 and D13S232 and including several ESTs and candidate genes, including the connexin26 (GJB2) gene. Analysis of PCR products from our affected patients' DNA shows two frameshift mutations in the connexin26 gene. Deletion of a G within a stretch of six Gs at position 35 of the GJB2 cDNA (mutation 35delG) leads to premature chain termination and is present in 63% of NSRD chromosomes, demonstrating linkage to chromosome 13. Deletion of a T at position 167 of GJB2 (mutation 167delT), also resulting in premature chain termination, was detected in another patient. Four neutral sequence polymorphisms were also identified. These findings are in agreement with a recent study showing that mutations in the connexin26 gene are associated with genetic forms of deafness in three Pakistani families and that GJB2 is DFNB1. Connexin26 is a member of a large family of proteins involved in formation of gap junctions, which are involved in electrical synapses and the direct transfer of small molecules and ionic currents between neighboring cells. The identification of GJB2 as the DFNB1 gene should provide a better understanding of the biology of normal and abnormal hearing, help form the basis for diagnosis and may facilitate development of strategies for treatment of this common genetic disorder.

Sensitivity, reproducibility, and accuracy in short tandem repeat genotyping using capillary array electrophoresis

The Human Genome Initiative has increased significantly the rate at which disease-causing genes are being mapped and sequenced. New cost-effective methods to locate the genes and to characterize disease-causing mutations require robust, reproducible, and accurate protocols for measuring DNA fragment lengths. Capillary array electrophoresis (CAE) offers rapid, high-resolution separations, high throughput, and sensitive detection. To assess the utility of CAE for the accumulation of genetic information, we tested both sizing accuracy and reproducibility using 48-capillary prototype systems. Two multiplex PCR allelic ladder standards and several CA-repeat markers were analyzed in > 100 runs. Reproducibility in typing > 8000 genotypes reveals a standard deviation of less than 0.2 bp on these systems under optimized conditions. However, sequence-dependent migration anomalies were observed at most simple sequence loci even when analyzed under denaturing conditions, resulting in a systematic bias in estimated fragment sizes. We show here that, by normalizing results to known typing controls, one can obtain locus-averaged accuracies of < 0.06 bp and normalized results within 1 bp of actual. We detect as little as a 1:30,000 dilution of a DNA quantitation standard stained with highly sensitive intercalating dyes, indicating an 80-zeptomole sensitivity limit. However, to obtain reproducible electrokinetic injection, approximately 200 attomoles of fluorescein-labeled DNA is required. These sensitivity limits, sizing precision, and accuracy, together with the 1-hr run times for 48-96 samples, indicate that CAE is a viable method for high-throughput genetic analysis of simple sequence repeat polymorphisms.

Allelic association of microsatellites of 6p in Italian hemochromatosis patients

Hemochromatosis (HC) is an inherited disorder of iron metabolism and is frequently seen in Caucasians. The biochemical defect and the responsible gene are unknown, but the HC locus is closely linked to HLA-A on human chromosome 6 in the region 6p21.3. Although extensive studies have been performed in several populations, the precise location of the gene is still undefined. Linkage disequilibrium with HC has been detected for loci that are 3 cM apart: HLA class I and D6S105, which is located on the telomeric side of HLA-A. We have analyzed the inheritance of several multi-allele polymorphisms that map to 6p (D6S265, Y52, HLA-F, D6S306, D6S105, D6S464, D6S299) in 34 Italian HC families and in 17 unrelated patients. Significant association with HC was shown for alleles of multiple markers in the HLA-A region, for the distant marker D6S105, but not for the D6S299 marker at 4 cM from HLA-A on the telomeric side. HC status was unambiguously assigned to 70 affected and 63 unaffected chromosomes from family studies. Thirty five different haplotypes were found in 70 HC chromosomes when considering four markers most tightly associated with the disease. A predominant haplotype comprising alleles 1-3-1-8 (marker order D6S265, HLA-A, Y52, D6S105) accounted for 30% of the HC chromosomes and was absent in normals. A minority of other HC haplotypes could be related to the major haplotype by assuming single crossover events. Results of haplotype studies suggest a founder effect in the Italian population, as previously shown in Australian patients, and a possible common mutation shared with affected individuals of Celtic origin.

Infundibulopelvic stenosis, multicystic kidney, and calyectasis in a kindred: clinical observations and genetic analysis

Congenital obstructive anomalies of the urinary tract usually occur sporadically. We describe inheritance in a three-generation kindred of a spectrum of kidney anomalies consistent with an autosomal-dominant mode of transmission, with incomplete penetrance, calyectasis (maternal grandmother), infundibulopelvic stenosis (uncle), and multicystic kidney (male proband, age 4 years). The proband's mother, father and half sister had normal renal imaging studies. Inheritance of informative polymorphic markers (3'-HVR, GGG1, GGG9, SM-7, KG8, and CW3) mapping close to the adult polycystic kidney disease type 1 (PKD-1) and tuberous sclerosis (TSC-2) loci on chromosome 16p was evaluated by Southern blot studies and by PCR-based, fluorescent genotyping for linkage to phenotype. The 3 affected individuals, as well as the unaffected mother (obligate carrier) and unaffected half-sister, inherit a common chromosome haplotype linked to the PKD1 locus. Our findings support the hypothesis that these anomalies may be part of a spectrum of obstructive renal dysplasia which are inherited as a simple Mendelian trait exhibiting an autosomal-dominant mode of transmission with variable expression and incomplete penetrance.

Nucleic acid detection using non-radioactive labelling methods

Nucleic acid probe-based assays are now widely used in genetic research, human identification, forensics and in a broad spectrum of clinical assays in the fields of microbiology, haematology/oncology and virology. Labelled probes are used in a variety of assay formats including dot-blots, Southern blots (DNA target), Northern blots (RNA target), Western blots (protein target), in situ hybridization, plaque or colony screening and immobilized arrays on silicon or glass surfaces. Traditionally, the probes used in these assays have a radioactive 32phosphorous label that has a short shelf-life, is dangerous, has high disposal costs and, when labelled to high specific-activity, may be unstable. Extensive efforts to develop alternative labelling techniques have resulted in colorimetric, chemiluminescent and fluorescent assay formats. This review summarizes the properties desired in a probe, describes the advantages and disadvantages of the different non-radioactive labelling strategies, and illustrates examples of probe-based assays in which detection is facilitated by imaging samples using a general purpose fluorescence scanner.

Fluorescence-based DNA minisequence analysis for detection of known single-base changes in genomic DNA

We describe a rapid, automated method for direct detection of known single-base changes in genomic DNA. Fluorescence-based DNA minisequence analysis is employed in a template-dependent reaction which involves a single nucleotide extension of an oligonucleotide primer by the correct fluorescently-tagged dideoxynucleotide chain terminator. Detection following electrophoresis on denaturing acrylamide gels is facilitated by alkaline phosphatase treatment of reaction products after extension followed by isopropanol precipitation of the dye-tagged, single-base-extended primer to remove unincorporated deoxynucleotides. Fluorescence analysis of the incorporated dye tag reveals the identity of the template nucleotide immediately 3' to the primer site. This technique does not require radioactivity or biotinylated PCR product, relies on the incorporation of a single dideoxynucleotide terminator to extend the primer by one nucleotide and takes advantage of the sensitivity of fluorescent terminators developed for automated DNA sequence analysis. As a demonstration, we have applied the assay to human genomic DNA for detection of the sickle mutation in the beta-globin gene, and have also examined feasibility for simultaneous delineation using a multiplex-like strategy in a single gel-lane of some of the most common beta-thalassemia mutations in the Mediterranean basin.

Interaction of rare illegitimate recombination event and a poly A addition site mutation resulting in a severe form of alpha thalassemia

The clinical diversity of thalassemia depends on interaction of diverse genetic defects. We have characterized a severe form of alpha thalassemia caused by coinheritance of a rare alpha-globin gene deletion and a nondeletional defect in a southern Italian family. The proband, a 7-year-old girl, exhibited an abnormal hemoglobin electrophoresis pattern with hemoglobin H and hemoglobin Barts, indicating inheritance of H and hemoglobin Barts, indicating inheritance of a severe form of alpha thalassemia. Southern blot analysis of DNA showed normal as well as aberrant alpha-globin gene fragments indicating heterozygosity for a deletional form of alpha thalassemia in the proband and her mother. The coinheritance of a nondeletional form of alpha thalassemia (alpha alpha T) was suspected because of the severity of the proband's phenotype and the presence of normal alpha-globin gene fragments in the father. Selective polymerase chain reaction of the paternal alpha 1- and alpha 2-globin genes in the proband followed by DNA sequence analysis showed an AATAAA to AATGAA mutation in the polyadenylation signal sequence of the alpha 2-globin gene. Genomic DNA mapping and sequence analysis of a unique polymerase chain reaction product generated across the deletion breakpoint of the maternal allele showed a 5,201-bp deletion extending from 870 nucleotides 5' of the alpha 2-globin gene to nucleotide +519 in the alpha 1-globin gene. This deletion is similar to that previously suggested by blotting studies in a Greek family (Pressley et al, Nucleic Acids Res 8:4889, 1980) and removes the entire alpha 2-globin gene and a portion of the 5' end of the alpha 1-globin gene. Sequence characterization of the resultant aberrant truncated alpha 1-globin gene from the proband showed a 27 nucleotide duplication corresponding to the 3' end of the alpha-globin gene IVS-2 region separated by the insertion of a tetranucleotide (GGTT), suggesting that this deletion is caused by an illegitimate recombination event.

Duchenne/Becker muscular dystrophy carrier detection using quantitative PCR and fluorescence-based strategies

Dystrophin gene deletions account for up to 68% of all Duchenne (DMD) and Becker (BMD) muscular dystrophy mutations. In affected males, these deletions can be detected easily using multiplex PCR tests which monitor for exon presence. In addition, quantitative dosage screening can discriminate female carriers. We previously analyzed multiplex PCR products by gel electrophoresis and quantitation of fluorescently labeled primers with the Gene Scanner in order to test carrier status. These multiplex PCR protocols detect DMD gene deletions adequately, but require up to 18 pairs of fluorochrome-labeled primers. We previously described two alternative fluorescent labeling strategies, each with approximately 1,000-fold greater sensitivity than ethidium bromide staining, which can be used to quantify the products of multiplex PCR. The first method uses the DNA intercalating thiazole orange dye TOTO-1 to stain PCR products after 20 cycles. In the second method, fluorescein-12,2'-dUTP is incorporated into products during PCR as a fluorescent tag for subsequent quantitative dosage studies. Both methods label all multiplexed exons including the 506 bp exon 48 fragment that is difficult to detect and quantify by standard ethidium bromide staining. Using this approach, we determined DMD/BMD carrier status in 24 unrelated families using a fluorescent fragment analyzer. Analysis of fluorochrome-labeled PCR products facilitates quantitative multiplex PCR for gene-dosage analysis.

Fluorescent approaches to diagnosis of Lesch-Nyhan syndrome and quantitative analysis of carrier status

Lesch-Nyhan syndrome is an X-linked recessive disorder caused by molecular defects within the HPRT gene. Deletional forms of this syndrome, most of which are inherited, account for 15% of the cases. In addition, a large percentage of cases are due to de novo point mutations. We have used complementary fluorescence-based PCR assays to analyse disease-causing mutations in three unrelated families: (1) inheritance of dye-labelled PCR products of linked polymorphic loci mapping within and flanking the HPRT gene; (2) dye-labelled exon dosage analysis and (3) automated fluorescence-based DNA sequence analysis. Our results using fluorescent, dye-tagged PCR products show that inheritance of two polymorphic small tandem repeats, HPRTB [AGAT]n, mapping within intron 3 of the HPRT gene, and the CA-repeat at DXS294 can be used to establish linkage to the disease. In addition, we modified a previously described PCR protocol to use fluorescent dye-labelled oligoprimers and an ABI Gene Scanner in order to rapidly quantitate deletional forms of Lesch-Nyhan syndrome. Quantitative PCR analysis of individual exons followed by dosage analysis confirmed a deletion encompassing exon 9. A similar approach was used to confirm a previously described HPRT gene duplication involving exons 2 and 3. In this analysis, we co-amplified the HPRTB [AGAT]n and HUMARA [AGC]n repeats and confirmed increased exon dosage in carriers for the duplication. DNA sequence analysis remains the method of choice for delineating new disease-causing mutations, most of which are non-deletional forms of Lesch-Nyhan syndrome. We have also used a cycle-sequencing strategy employing dye-labelled dideoxy terminators and a laser-activated, fluorescence-emission DNA sequencer in order to define carrier status in 10 family members at risk for Lesch-Nyhan syndrome due to a splice donor mutation in intron 7. Our DNA sequence analyses corroborate small tandem repeat (STR) inheritance patterns in this family. Multiple fluorescence-based strategies should facilitate rapid diagnosis of the various Lesch-Nyhan disease-causing mutations.

Hb Shelby [beta 131(H9)Gln-->Lys] in association with Hb S [beta 6(A3)Glu-->Val]: characterization, stability, and effects on Hb S polymerization

When first tested for abnormal hemoglobins, a 2-year-old boy, appeared to have Hb F, Hb S and Hb A2. Confirmatory testing revealed a beta chain variant inherited from his father and beta S from his mother. Analysis of tryptic peptides in conjunction with automated DNA sequence analysis showed that the variant hemoglobin was Hb Shelby [beta 131(H9)Gln-->Lys (CAG-->AAG)]. Heat and mechanical stabilities of various liganded Hb Shelby tetramers were compared to those of Hb A and Hb S. Oxy-Hb Shelby precipitated more readily than oxy-Hb A, but was much more stable than oxy-Hb S during mechanical agitation. In contrast, oxy-Hb Shelby was much less stable than oxy-Hb A and oxy-Hb S following heat treatment. Met-Hb Shelby was most unstable compared to other liganded forms of Hb Shelby, while deoxy- and carbonmonoxy-forms of Hb Shelby showed similar heat-induced precipitation rates. These data indicate that heat instability of Hb Shelby is accompanied by heme oxidation, and that denaturation by mechanical agitation occurs in the absence of heme oxidation. Hb Shelby, like Hb A, can form hybrids with Hb S which participate in polymer formation in vitro. However, Hb S/Hb Shelby hybrids copolymerized with Hb S less than A/S hybrids. Since the patient's MCHC value is normal, this finding coupled with the elevated Hb A2 and Hb F levels, both of which are known to inhibit polymerization of Hb S, may contribute to the patient's mild clinical presentation.

Transrectal hyperthermia as palliative treatment for advanced adenocarcinoma of prostate and studies of cell-mediated immunity

During a fifteen-month period, 15 patients with progressive adenocarcinoma of the prostate (CaP) were treated with transrectal microwave hyperthermia (TRHT). There were 5 Stage T4 and 11 Stage T3 patients including 6 patients with skeletal metastases. Nine of the patients had severe and 6 had moderately severe signs and symptoms of CaP. TRHT was given six times at 2,450 MHz with temperature controlled at 43.5 degrees for thirty minutes. Cell-mediated immunity tests were performed before TRHT and at two, four, and six months post-therapy. The results of these tests were compared with those of 15 patients with benign prostatic hyperplasia (BPH) treated with the same TRHT and with 30 untreated normal volunteers. TRHT was well tolerated with mild acute toxicity noted in 3 patients (20%). Of the 15 patients treated, 2 (13%) showed scintigraphic evidence of regression of bone metastases. Five patients survived more than five years since treatment, and in 3 patients there was no evidence of CaP. A decrease of marked or moderate degree in signs and symptoms of CaP was noted in 8 patients (53%). The results of cell-mediated immunity tests were of interest. The 15 CaP patients prior to TRHT had lower OKT4/OKT8 ratio, lower PHA transformation index, and lower Con-A induced T-cell suppressor activity as compared with the 15 BPH patients and 30 healthy volunteers, who had normal immune parameters (p < 0.01). Following TRHT there was a significant increase in the monitored immune parameters noted in the 15 CaP patients (p < 0.01). This immune stimulation peaked at two months and gradually decreased to near pretreatment levels at six months. In the 15 BPH patients post-TRHT changes in immune tests were less apparent. The results of this small study, if confirmed, could be of clinical importance in patients with advanced prostate cancer.

Non-radioactive detection of the most common mutations in the cystic fibrosis transmembrane conductance regulator gene by multiplex allele-specific polymerase chain reaction

A rapid, simple, nonradioactive method for detection of four common mutations causing cystic fibrosis (CF) has been developed combining multiplexing with allele-specific polymerase chain reaction amplification. This approach (MASPCR) provides an easy assay for direct genotyping of normal and mutant CF alleles in homozygotes and heterozygotes. The strategy involves multiplex PCR of exons 10, 11, and 21 within the cystic fibrosis transmembrane conductance regulator (CFTR) gene in a single reaction containing three common oligoprimers and either the four normal or four mutant oligos corresponding to the delta F508, G551D, G542X, and N1303K mutations. Primers are chosen so that the size of the four PCR products differ, thereby facilitating detection on agarose gels following amplification in the same reaction. Patient samples are primed with either four normal or four mutant oligo mixtures, and PCR products run in parallel on gels to detect band presence or absence. This approach provides a simple and potentially automated method for cost-effective population screening.

Detection of the most common mutations causing beta-thalassemia in Mediterraneans using a multiplex amplification refractory mutation system (MARMS)

A rapid, simple, cost-effective, non-radioactive method for detection of the most common mutations causing beta-thalassemia in Mediterranean people has been developed by combining multiplexing with the amplification refractory system. This approach, the multiplex amplification refractory mutation system (MARMS), provides an easy assay for direct detection of normal and mutant beta-globin genes in homozygotes and heterozygotes. The strategy involves multiplex PCR of four of the five regions of interest within the beta-globin gene in a single reaction containing a common oligoprimer and either the normal or mutant oligonucleotides corresponding to IVS-1 nucleotide 1 or IVS-1 nucleotide 6, IVS-1 nucleotide 110, codon 39, and IVS-2 nucleotide 1 regions. Primers are chosen so that the sizes of the four PCR products differ, thereby facilitating detection on agarose gels following amplification. Patient samples are primed with either four normal or four mutant oligonucleotide mixtures and the common oligoprimer, and PCR products run in parallel on gels to detect band presence or absence. This approach simplifies mutation detection and shows promise for automation employing fluorescent-tagged primers.

Fluorescence-based, multiplex allele-specific PCR (MASPCR) detection of the delta F508 deletion in the cystic fibrosis transmembrane conductance regulator (CFTR) gene

Cystic fibrosis (CF) is a common genetic disorder in Caucasians, and in some populations 70% of cases are associated with a 3 base pair (bp) deletion (delta F508) in the CFTR gene. We have implemented a fluorescence-based, multiplex allele-specific polymerase chain reaction (MASPCR) assay for deletion of the delta F508 mutation. Different allele-specific fluorescently-tagged primers are used in the PCR reaction to distinguish between normal and delta F508 alleles. Fluorescent PCR products are then visualized in a single lane on an agarose gel following electrophoresis combined with real-time multicolour fluorescence detection. The approach simplifies diagnosis of the most common mutation in the CFTR gene, and holds promise for a multiplex allele-specific, fluorescence-tagged gene amplification strategy for detection of additional CF mutations which may result in more cost-effective testing without increasing the risk of missed or erroneous diagnoses.

The Xmn I site (-158, C----T) 5' to the G gamma gene: correlation with the Senegalese haplotype and G gamma globin expression

There are three major African haplotypes associated with the sickle mutation: Benin (#19), Senegalese (#3), and Central African Republic (#20). Previous studies have suggested that the Xmn I site (-158 bp 5' to the G gamma gene) is associated with elevated levels of G gamma and with the Senegalese haplotype, while other investigators questioned this association. In order to clarify the issue, we have determined beta haplotypes, tested for the presence of the Xmn I site, and measured Hb F and G gamma expression levels in 143 American Black patients with sickle cell anemia. Haplotypes were determined using eight polymorphic sites in the beta-like globin gene cluster: Hinc II 5' to epsilon, Hind III in IVS-II G gamma and A gamma, Hinc II within and 3' to psi beta, Ava II in IVS-II of beta, and Hpa I and Bam HI 3' to beta. The G gamma /A gamma ratio was analyzed by high performance liquid chromatography using a C18 column. The Xmn I site was present in all 31 chromosomes with the Sengalese haplotype. Of the remaining 255 chromosomes with other haplotypes, only 2 (0.8%) had the Xmn I site present. There was significant correlation between the presence of the Xmn I site and increased G gamma /A gamma ratio in a dose-dependent manner. The Hb F level was not significantly increased in the presence of the Xmn I site. The data indicate that the Xmn I site maintains a G gamma /A gamma ratio typical of fetal life but does not necessarily cause elevation of Hb F. The latter seems to depend on factors other than the Xmn I site.

A greater than 200 kb deletion removing the entire beta-like globin gene cluster in a family of Irish descent

We describe a new deletional form of gamma delta beta-thalassemia segregating in two generations of a family of Irish descent. Affected family members present with a beta-thalassemia minor phenotype, normal Hb A2 and Hb F levels. Genomic blotting analyses on DNA from affected family members show heterozygosity for a large deletion beginning at least 15 kb upstream of the 5' endpoint of the gamma delta beta-thalassemia-1 deletion, extending through the entire beta-like globin gene cluster, and continuing for at least 10 kb beyond the 3' endpoint of the deletion associated with the Spanish form of delta beta 0-thalassemia. This deletion is among the largest described so far, and removes at least 205 kb encompassing the entire beta-like globin gene cluster on chromosome 11.

Polymerization and solubility of recombinant hemoglobins alpha 2 beta 2 (6Val) (Hb S) and alpha 2 beta 2(6Leu) (Hb Leu)

In an effort to clarify the role of amino acid hydrophobicity at the beta 6 position in sickling we have made recombinant hemoglobin tetramers containing beta 6 Val (Hb S) and beta 6 Leu (Hb Leu). Recombinant Hb S and Hb Leu had the same electrophoretic mobility, chromatographic behavior, and absorption spectrum. The deoxy form of both tetramers polymerized in high phosphate buffer (1.8 M) and exhibited distinct delay times prior to polymerization. The kinetics of polymerization for recombinant and native Hb S were similar, while recombinant Hb Leu polymerized more readily. The solubility of deoxy Hb Leu was less than deoxy Hb S, indicating that rapid polymerization and decreased solubility of deoxyhemoglobin is accelerated with increasing hydrophobicity at the beta 6 position.

Assessment of serum gamma glutamyl transpeptidase levels in low stage renal cell carcinoma

In the past, serum levels of various enzymes have been studied to aid in the evaluation of neoplastic diseases. Gamma glutamyl transpeptidase (GGTP) is present in highest amounts in the proximal convoluted tubules of the kidney, which are considered to be the site of origin for renal cell carcinomas. A retrospective study of 63 patients who had serum GGTP levels tested within 10 days before the resection of a renal cell carcinoma was performed to determine whether serum GGTP was elevated in low stage (stages I and II) renal cell carcinomas. Only 5 of the 63 patients had elevated GGTP levels (two of which were only slightly elevated). The authors conclude that serum GGTP levels as routinely measured in clinical laboratories are not reliably elevated in low stage renal cell carcinomas.

Beta-globin gene cluster haplotypes in Hb C heterozygotes

Previous work has suggested that the beta C mutation arose on a relatively rare beta A chromosome with a unique haplotype, and these data have been used to postulate a single origin of the beta C allele. Most characteristic of this haplotype has been the absence of a Hpa I recognition site 3' to the beta-globin gene. We studied 40 patients with Hb SC, 11 with Hb AC, and one with Hb CC. Complete haplotyping was possible on 44 beta C alleles and 3' haplotyping was possible on an additional four beta C alleles. Our results support the predominence of a unique beta C haplotype which is characterized by the absence of the Hpa I site. However, one patient who was homozygous for Hb C had one beta C allele with an atypical haplotype which contained the Hpa I site. It is unclear at this time whether or not this represents a second origin of the beta C mutation.

A large deletion encompassing the entire alpha-like globin gene cluster in a family of northern European extraction

We describe a new deletional form of alpha thalassemia segregating in three generations of a family of northern European origin. A full-term female girl had hypochromic, microcytic anemia since early infancy associated with delayed language development, slow growth and weight gain. Hematologic studies suggested the presence of alpha thalassemia. Gene-blotting studies showed no abnormal alpha-like globin gene fragments; however, studies of inheritance of informative polymorphic restriction fragments using zeta, alpha and 3'-alpha-hypervariable region (3'-HVR) probes showed evidence for an extensive deletion encompassing the entire alpha-like globin gene cluster. The 3' breakpoint of this deletion maps beyond the 3'-HVR, a region implicated as a hot spot for the generation of other large deletional events within the alpha-like cluster. The 5' breakpoint maps at least 10 kilobases (kb) 5' to the zeta-globin gene. The minimum size estimate for this deletion is greater than 47 kilobases.

Protection of uninfected human bone marrow cells in long-term culture from G418 toxicity after retroviral-mediated transfer of the NEOr gene

The long-term effect of retroviral-mediated gene transfer into human hematopoietic cells in vitro was studied in bone marrow culture. Two retroviral vectors (pN2 or pZIP NEO) were used to transfer the gene coding for neomycin phosphotransferase, which confers neomycin resistance, as a dominant selectable marker. Following infection, bone marrow cells of multiple hematopoietic lineages displayed resistance for the duration of the cultures (greater than 80 days) to normally cytotoxic doses of the neomycin analog G418. However, upon DNA analysis of cells surviving in G418, the NEOr (neomycin resistance) gene was not detected under conditions where single copy genes could readily be seen, despite the presence of NEOr RNA sequences. In order to investigate this observation further, infected and uninfected cells were separated by a filter, and cultured in the same medium containing G418. The uninfected cells continued to survive in the presence of normally toxic concentrations of G418. Medium alone from infected cells was able to protect uninfected cells the same way. Efficiency of transfer of this and perhaps other selectable marker genes to cells in the long-term culture system may consequently be overestimated if survival of cells alone is quantitated. These results indicate that long-term cultures are a useful in vitro model for the study of retroviral-mediated gene transfer to human hematopoietic cells.

Thalassemia syndromes. Recent advances

Laboratory and clinical investigators in the past several years have provided many advancements in the understanding of the thalassemia syndromes and in the care of affected patients. The diversity of genetic defects causing thalassemia has been extensively explored, with major benefits to our knowledge of normal globin gene function and of the consequences of specific mutations. In addition, the use of molecular biology methods in these studies has provided major advances in population genetics, gene transfer, and prenatal diagnosis of thalassemia. In the clinical area, guidelines for transfusion, splenectomy, prevention of postsplenectomy infection, and effective iron chelation have been considerably improved, and bone marrow transplantation is now available as an alternative means of treatment. Despite these advances, a great deal remains to be done in the areas of understanding the developmental regulation of globin gene expression, effective gene transfer, oral chelation therapy, safer blood products, and other important areas that will benefit patients afflicted with thalassemia.

Childhood leukemia and parents' occupational and home exposures

A case-control study of children of ages 10 years and under in Los Angeles County was conducted to investigate the causes of leukemia. The mothers and fathers of acute leukemia cases and their individually matched controls were interviewed regarding specific occupational and home exposures as well as other potential risk factors associated with leukemia. Analysis of the information from the 123 matched pairs showed an increased risk of leukemia for children whose fathers had occupational exposure after the birth of the child to chlorinated solvents [odds ratio (OR) = 3.5, P = .01], spray paint (OR = 2.0, P = .02), dyes or pigments (OR = 4.5, P = .03), methyl ethyl ketone (CAS: 78-93-3; OR = 3.0, P = .05), and cutting oil (OR = 1.7, P = .05) or whose fathers were exposed during the mother's pregnancy with the child to spray paint (OR = 2.2, P = .03). For all of these, the risk associated with frequent use was greater than for infrequent use. There was an increased risk of leukemia for the child if the father worked in industries manufacturing transportation equipment (mostly aircraft) (OR = 2.5, P = .03) or machinery (OR = 3.0, P = .02). An increased risk was found for children whose parents used pesticides in the home (OR = 3.8, P = .004) or garden (OR = 6.5, P = .007) or who burned incense in the home (OR = 2.7, P = .007). The risk was greater for frequent use. Risk of leukemia was related to mothers' employment in personal service industries (OR = 2.7, P = .04) but not to specified occupational exposures. Risk related to fathers' exposure to chlorinated solvents, employment in the transportation equipment-manufacturing industry, and parents' exposure to household or garden pesticides and incense remains statistically significant after adjusting for the other significant findings.