Biomedical subjects

Nicholas H de Klerk

Publications and source records attributed to Nicholas H de Klerk.

At least 19 recordsLinked to original sources

PubMed2006

Translating microarray data for diagnostic testing in childhood leukaemia.

BACKGROUND: Recent findings from microarray studies have raised the prospect of a standardized diagnostic gene expression platform to enhance accurate diagnosis and risk stratification in paediatric acute lymphoblastic leukaemia (ALL). However, the robustness as well as the format for such a diagnostic test remains to be determined. As a step towards clinical application of these findings, we have systematically analyzed a published ALL microarray data set using Robust Multi-array Analysis (RMA) and Random Forest (RF). METHODS: We examined published microarray data from 104 ALL patients specimens, that represent six different subgroups defined by cytogenetic features and immunophenotypes. Using the decision-tree based supervised learning algorithm Random Forest (RF), we determined a small set of genes for optimal subgroup distinction and subsequently validated their predictive power in an independent patient cohort. RESULTS: We achieved very high overall ALL subgroup prediction accuracies of about 98%, and were able to verify the robustness of these genes in an independent panel of 68 specimens obtained from a different institution and processed in a different laboratory. Our study established that the selection of discriminating genes is strongly dependent on the analysis method. This may have profound implications for clinical use, particularly when the classifier is reduced to a small set of genes. We have demonstrated that as few as 26 genes yield accurate class prediction and importantly, almost 70% of these genes have not been previously identified as essential for class distinction of the six ALL subgroups. CONCLUSION: Our finding supports the feasibility of qRT-PCR technology for standardized diagnostic testing in paediatric ALL and should, in conjunction with conventional cytogenetics lead to a more accurate classification of the disease. In addition, we have demonstrated that microarray findings from one study can be confirmed in an independent study, using an entirely independent patient cohort and with microarray experiments being performed by a different research team.

Cell Line, Tumor↗

PubMed2006

Is there a folate-related gene-environment interaction in the etiology of childhood acute lymphoblastic leukemia?

Acute lymphoblastic leukaemia (ALL) is the commonest childhood cancer in developed countries. Little is known about its causes, although its early age at diagnosis has focused interest on maternal and perinatal factors. We have previously observed a protective effect of maternal folate supplementation during pregnancy against ALL, and a number of studies have reported protective effects of some common polymorphisms of the methylenetetrahydrofolate reductase (MTHFR) gene. One study has suggested that the effect of MTHFR polymorphisms on risk of ALL may depend on folate status. This study aimed to look for evidence of an interaction between maternal folate supplementation and child's genotype among the cases from our previous study. Bone marrow specimens from 82 of 83 case children were available. DNA was extracted and genotyped for MTHFR C677T and A1298C using standard techniques. We used a case-only analysis to estimate the case-only odds ratio (COR) for MTHFR genotype and folate supplementation in association with ALL. None of the CORs indicated a significant departure from a multiplicative model. Adjustment for sex, age or genotype at the other locus had little effect on the results. Other studies of this gene and environment interaction in ALL and other cancers have produced contradictory results, perhaps because of varying definitions of folate exposure. Further research into the interaction of folate intake and genotype in causing ALL and other cancers is needed. We are specifically studying it in an Australian national case-control study of genetic and environmental causes of ALL.

Alanine↗

PubMed2006

Patterns, trends, and increasing disparities in mortality for Aboriginal and non-Aboriginal infants born in Western Australia, 1980-2001: population database study.

BACKGROUND: Since there are known disparities between Aboriginal and non-Aboriginal populations in Australia, trends in infant mortality rates can be used to assess the effectiveness of programmes designed to improve the health of Aboriginal populations. We have examined mortality rates in these populations in Western Australia. METHODS: We used the most comprehensive and valid total population data available for an Australian state to determine all-cause and cause-specific mortality for Aboriginal and non-Aboriginal infants born in Western Australia from 1980 to 2001. FINDINGS: Overall, infant mortality rates fell in both populations, but less so in Aboriginal (from 25.0 in 1980-84 to 16.1 in 1998-2001) than in non-Aboriginal infants (from 8.4 in 1980-84 to 3.7 in 1998-2001) such that disparities between the two groups increased for all major causes of infant death. The relative risk for Aboriginal compared with non-Aboriginal infants rose from 3.0 (95% CI 2.5-3.6) to 4.4 (3.5-5.5), and there were significantly more potentially preventable deaths, such as those caused by infections (5.9 per 1000 livebirths vs 0.7 per 1000 livebirths, RR 8.5, 95% CI 7.1-10.2). Additionally, for Aboriginal infants, postneonatal mortality rates were higher than neonatal mortality rates (11.2 per 1000 livebirths vs 9.7 per 1000 livebirths), trend analyses showed that previous reductions in deaths due to preterm birth (4.3 per 1000 livebirths--1.4 per 1000 livebirths from 1980-97) were not sustained in the most recent years studied (3.5 per 1000 livebirths), and rates of sudden infant death syndrome did not fall significantly (4.9 per 1000 livebirths vs 4.7 per 1000 livebirths). INTERPRETATION: These increasing disparities between Aboriginal and non-Aboriginal infants, especially in remote areas, demand immediate action in partnership with Aboriginal communities, focusing on both access to primary health care and better living conditions. Implementation and assessment of policies to reduce the continuing social and economic disadvantage faced by Aboriginal families are vital.

Adolescent↗

PubMed2006

Plasma vitamin concentrations and incidence of mesothelioma and lung cancer in individuals exposed to crocidolite at Wittenoom, Western Australia.

Increased rates of death from asbestos-related diseases have been reported in former workers and residents exposed to crocidolite (blue asbestos) at Wittenoom (Western Australia). The relationships between plasma concentrations of retinol, carotene and vitamin E and incidence of mesothelioma and lung cancer in a cohort of people from this town were examined. The relationships were evaluated by survival analyses using data obtained at the first visit, at each visit and with the rate of change of each vitamin during the period of follow-up. Of 1953 study participants, 65 developed mesothelioma during the follow-up, and 47 developed lung cancer. A lower incidence of mesothelioma was related to plasma concentrations of retinol at the first visit [hazard ratio (HR)=0.63, 95% confidence interval=0.41-0.99], and to measurements at each visit (HR=0.71, 95% confidence interval=0.50-1.00). Plasma carotene concentrations at the first measurement, but not during the follow-up period, were associated with lower incidence of lung cancer in men and in workers. No significant associations were found between carotene concentrations and incidence of mesothelioma. Vitamin E concentrations were not significantly associated with mesothelioma or lung cancer incidence. These findings suggest that people with chronically low plasma levels of retinol have increased risk of developing mesothelioma and lung cancer.

Adult↗

PubMed2006

Role of respiratory viruses in acute upper and lower respiratory tract illness in the first year of life: a birth cohort study.

INTRODUCTION: Although acute respiratory illnesses (ARI) are major causes of morbidity and mortality in early childhood worldwide, little progress has been made in their control and prophylaxis. Most studies have focused on hospitalized children or children from closed populations. It is essential that the viral etiology of these clinical diseases be accurately defined in the development of antiviral drugs. OBJECTIVE: To investigate the role of all common respiratory viruses as upper and lower respiratory tract pathogens in the first year of life. STUDY DESIGN: This community-based birth cohort study prospectively collected detailed information on all ARI contracted by 263 infants from birth until 1 year of age. Nasopharyngeal aspirates were collected for each ARI episode, and all common respiratory viruses were detected by polymerase chain reaction. Episodes were classified as upper respiratory illnesses or lower respiratory illnesses (LRI), with or without wheeze. RESULTS: The majority reported 2-5 episodes of ARI in the first year (range, 0-11 episodes; mean, 4.1). One-third were LRI, and 29% of these were associated with wheeze. Viruses were detected in 69% of ARI; most common were rhinoviruses (48.5%) and respiratory syncytial virus (RSV) (10.9%). Compared with RSV, >10 times the number of upper respiratory illnesses and >3 times the number of both LRI and wheezing LRI were attributed to rhinoviruses. CONCLUSION: Rhinoviruses are the major upper and lower respiratory pathogens in the first year of life. Although RSV is strongly associated with severe LRI requiring hospitalization, the role of rhinoviruses as the major lower respiratory pathogens in infants has not previously been recognized.

Acute Disease↗

PubMed2006

Atopy, eczema and breast milk fatty acids in a high-risk cohort of children followed from birth to 5 yr.

BACKGROUND: The incidence of atopic diseases such as eczema is increasing in westernized societies. The suggestion that there is a "protective" association between the unique fatty acid composition of breast milk, particularly the omega-3 (n-3) and omega-6 (n-6) essential polyunsaturated fatty acid content, and the development of atopic disease in children was investigated in a cohort study of 263 infants born into families with a history of allergy (one or both parents had asthma, hayfever, eczema). The objectives of this study were to determine the lipid profile [specifically in relation to long-chain polyunsaturated fatty acid (LC-PUFA) composition] in maternal breast milk samples collected at 6 wk and at 6 months following birth, and to investigate the potential role of these fatty acids in modulating the phenotype of children at high genetic risk of developing atopic disease. METHOD: Breast milk samples were available from 91 atopic mothers at their child's ages of 6 wk and 6 months. These samples were analysed for the fatty acid spectrum. Analysis of variance was used to detect differences between groups of outcomes (no atopy or eczema, non-atopic eczema, atopy, atopic eczema) at ages 6 months and 5 yr, and a multiple comparisons procedure was conducted to isolate the parameters producing the different results (F-test, LSD test). For the exposure variables, n-3 and n-6 fatty acids are expressed as weight percentage and as a ratio (at both time-points). RESULTS: The fatty acid profiles of maternal breast milk at 6 wk and 6 months were similar. An increased ratio of n-6: n-3 fatty acids in both 6 wk and 6 month milk samples was associated with non-atopic eczema (p < 0.005) but not atopy alone or atopic eczema. CONCLUSION: We found milk fatty acids were a significant modulator of non-atopic eczema but not atopy or atopic eczema in infants at 6 months. In mothers with a history of asthma, hayfever or eczema, their 6-month-old infants were more likely to develop non-atopic eczema if their milk had a higher ratio of n-6: n-3 LC-PUFA.

Child, Preschool↗

PubMed2006

Asbestos-related disease from recycled hessian superphosphate bags in rural Western Australia.

OBJECTIVES: To describe the dissemination of asbestos fibres within the Western Australian community. METHODS: A case report. RESULTS: A 60-year-old female was referred for investigation of calcified pleural plaques. On questioning, she recalled exposure to asbestos as a child on the family farm. She had shaken hessian bags prior to recycling to the fertiliser supplier. Her father survived to 90 years. Her mother died from malignant pleural mesothelioma. Four of five siblings had shaken the bags, two had radiographic evidence of pleural plaques while two others had not had recent chest x-rays. CONCLUSIONS: It appears that the use of recycled hessian bags for the fertiliser industry was endemic in the State during the period 1943-66. It is possible that many farmers and their families have had similar exposure to asbestos. IMPLICATIONS: The risk of developing an asbestos-related disease is not restricted to any specific social or employment groups within the Australian community.

Asbestos↗

PubMed2005

Effects of asbestos and smoking on gas diffusion in people exposed to crocidolite.

OBJECTIVE: To examine the effects of asbestos exposure and tobacco smoking on the level and rate of change of the diffusing capacity of the lung for carbon monoxide (DLCO). DESIGN AND PARTICIPANTS: A cohort study of 934 people (including both mine workers and town residents) exposed to crocidolite (blue asbestos) at the asbestos mines and in the town of Wittenoom, Western Australia, between 1943 and 1966. DLCO measurements were taken during a follow-up period from 1992 to 2002. MAIN OUTCOME MEASURES: Baseline levels of DLCO and change in levels over time. RESULTS: 2980 DLCO measurements were done on 934 people (of whom 818 were men and 724 were workers) who underwent a median of 2 (range, 1-17) measurements during the follow-up period. Radiographic asbestosis at baseline and asbestos exposure at a younger age were associated with lower DLCO values. The average rate of decline in DLCO was 0.33 (95% CI, 0.31-0.35) units per year, plus an additional decrement of 0.22 (95% CI, 0.12-0.32) units per year if the participant had radiographic asbestosis at the beginning of the follow-up period. Compared with never-smokers, current smokers and ex-smokers had lower DLCO at baseline, but smoking status did not affect the change in DLCO during the follow-up period. CONCLUSIONS: Our results confirm a continuous deleterious effect of crocidolite on DLCO, especially on people with asbestosis. Smoking was associated with lower DLCO levels, but was not a significant predictor of rate of change in DLCO. Smoking status did not affect the relationships between crocidolite exposure and the level or rate of change of DLCO in this population.

Age Distribution↗

PubMed2005

Optimal fetal growth for the Caucasian singleton and assessment of appropriateness of fetal growth: an analysis of a total population perinatal database.

BACKGROUND: The appropriateness of an individual's intra uterine growth is now considered an important determinant of both short and long term outcomes, yet currently used measures have several shortcomings. This study demonstrates a method of assessing appropriateness of intrauterine growth based on the estimation of each individual's optimal newborn dimensions from routinely available perinatal data. Appropriateness of growth can then be inferred from the ratio of the value of the observed dimension to that of the optimal dimension. METHODS: Fractional polynomial regression models including terms for non-pathological determinants of fetal size (gestational duration, fetal gender and maternal height, age and parity) were used to predict birth weight, birth length and head circumference from a population without any major risk factors for sub-optimal intra-uterine growth. This population was selected from a total population of all singleton, Caucasian births in Western Australia 1998-2002. Births were excluded if the pregnancy was exposed to factors known to influence fetal growth pathologically. The values predicted by these models were treated as the optimal values, given infant gender, gestational age, maternal height, parity, and age. RESULTS: The selected sample (N = 62,746) comprised 60.5% of the total Caucasian singleton birth cohort. Equations are presented that predict optimal birth weight, birth length and head circumference given gestational duration, fetal gender, maternal height, age and parity. The best fitting models explained 40.5% of variance for birth weight, 32.2% for birth length, and 25.2% for head circumference at birth. CONCLUSION: Proportion of optimal birth weight (length or head circumference) provides a method of assessing appropriateness of intrauterine growth that is less dependent on the health of the reference population or the quality of their morphometric data than is percentile position on a birth weight distribution.

Anthropometry↗

PubMed2005

Plasma retinol, carotene and vitamin E concentrations and lung function in a crocidolite-exposed cohort from Wittenoom, Western Australia: a cohort study.

BACKGROUND: Increased rates of death from asbestos related diseases have been reported for people previously employed in the mining and milling operations at Wittenoom (Western Australia), and people who lived in the nearby town, where they were environmentally exposed to crocidolite. METHODS: Annual measurements of forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) and plasma concentrations of retinol, carotene and vitamin E have been made since 1992. Mixed effects models were used to examine the associations between lung function and the plasma vitamin levels of retinol, carotene and vitamin E. RESULTS: After adjusting for potential confounders, higher plasma retinol and carotene concentrations were significantly associated with higher levels of lung function at entry into the study, while vitamin E concentrations were associated with lower entry lung function. Retinol was associated with a less steep decline of lung function over time, while carotene concentrations were associated with an increased decline of lung function over time and vitamin E levels were not associated with changes of lung function over time. CONCLUSION: These results support a beneficial relationship between plasma concentrations of retinol on the levels and rates of change of lung function, while showing no such consistent beneficial effect for plasma levels of beta-carotene or vitamin E.

Asbestos, Crocidolite↗

PubMed2005

Plasma concentrations of retinol, carotene, and vitamin E and mortality in subjects with asbestosis in a cohort exposed to crocidolite in Wittenoom, Western Australia.

OBJECTIVE: We sought to examine the relationships between plasma concentrations of retinol, carotene, and vitamin E and mortality associated with asbestosis in people previously exposed to crocidolite. METHODS: Cox regression modeling was applied to examine these relationships at the first measurement of each vitamin, at the measurement at each visit, and with the rate of change of each vitamin during the follow-up. RESULTS: There were 76 deaths of people with asbestosis during the follow-up period and 1885 subjects censored. Mortality in subjects with asbestosis was inversely related to plasma levels of retinol and Vitamin E concentrations and to their rate of increase during the follow-up. Carotene concentrations at first visit were associated with lower mortality but not during the follow up period. CONCLUSIONS: Chronically low levels of these vitamins are associated with an increased risk of dying with asbestosis.

Aged↗

PubMed2005

Gene expression levels in small specimens from patients detected using oligonucleotide arrays.

Large-scale gene expression profiling using microarray technology is often limited by the amount of tissue or cells available. A number of RNA amplification protocols have been published to overcome this problem. However, additional amplification steps can result in both a 3' bias and poor reproducibility for low abundance transcripts. We performed microarray experiments using HG-U133A GeneChip arrays to ascertain whether less than the recommended amount of RNA can be used, thus avoiding additional amplification steps. In a titration experiment, 2-10 microg of total RNA from a single cryopreserved patient specimen was used to prepare biotinylated cRNA, and the recommended standard amount of 15 microg of each preparation was used for hybridization. Statistical analysis using box plots, correlation coefficients, MvA plots, and concordance percentages revealed almost identical levels of gene expression, independent of the amount of RNA used for target preparation. Most importantly, there was no statistically significant difference when the concordance percentages for low abundance genes were compared, demonstrating that as little as 2 microg of total RNA is sufficient to perform GeneChip analysis.

Child↗

PubMed2004

Benefits of routine immunizations on childhood survival in Tari, Southern Highlands Province, Papua New Guinea.

BACKGROUND: Non-specific beneficial as well as deleterious effects of childhood immunizations have been reported in areas of high mortality. This study aimed to determine the effects of diphtheria-tetanus-whole-cell-pertussis (DTP), BCG, hepatitis B, and measles vaccines on mortality in the highlands of Papua New Guinea (PNG). METHODS: Demographic events for children born in 1989-1994 who were under monthly demographic surveillance in Tari were recorded from birth until age 2 years, out-migration, death, or the end of the study period. Data on BCG, hepatitis B, DTP, measles and pneumococcal polysaccharide vaccination were collected monthly from clinic records. To allow for different characteristics of immunized and non-immunized children, analysis included conditioning on a propensity score for vaccination, adjusting for differences in children's background characteristics. RESULTS: In all, 101/3502 children (3%) who had at least one vaccine died between ages 29 days and 24 months were compared to 112/546 (21%) who had none. BCG was associated with lower mortality in the 1-5 month age group (hazard ratio [HR] = 0.17, 95% CI: 0.09, 0.34), measles vaccine with lower mortality at age 6-11 months (HR = 0.42, 95% CI: 0.17, 1.01), and pneumococcal polysaccharide vaccine with lower mortality at age 12-23 months (HR = 0.42, 95% CI: 0.19, 0.93). One or more doses of DTP was associated with lower overall mortality (HR = 0.27, 95% CI: 0.16, 0.44), particularly in the 1-5 month age group (HR = 0.19, 95% CI: 0.10, 0.34), and also in those who had had prior BCG (HR = 0.45, 95% CI: 0.22, 0.91). CONCLUSION: Routine immunizations are effective in reducing overall mortality in young children in an area of high mortality. In particular, DTP, whether considered separately or in addition to BCG, was associated with a lowering of overall mortality, in contrast to findings reported from Guinea-Bissau.

BCG Vaccine↗

PubMed2004

Lung function, bronchial responsiveness, and asthma in a community cohort of 6-year-old children.

KEYWORDS: Children as young as 6 years old can perform spirometry, yet the relationship between current asthma, lung function, and bronchial responsiveness has not been described at this age; 2,537 children from a community-based birth cohort were assessed at 6 years of age, with history (n = 2,141), physical examination (n = 1,995), standard spirometry (n = 1,735), and a random sample (n = 711) offered methacholine challenge. Males had greater values of FVC and FEV(1) but not of mean forced expiratory flow during the middle half of the FVC or FEV(1)/FVC than females. The greatest influences on lung function at 6 years were height, sex, birth weight, and wheezing in the first year of life. Children with current asthma had small but significant deficits in lung function and were more sensitive to methacholine. The optimal cutpoint for determining heightened bronchial responsiveness was found to be a 15% fall in FEV(1) at a dose of 1.8 mg/ml. A negative test could be useful in excluding a diagnosis of asthma (negative predictive value of 92%). Lung function testing, including methacholine challenge, is feasible in 5- to 7-year-old children and has the potential to contribute to the clinical management of children with asthma.

Age Factors↗

PubMed2004

Epidemiology of malignant mesothelioma in Australia.

In Australia, consumption of asbestos peaked in about 1975 at around 70,000t per year--the majority being used for asbestos cement manufacture. Chrysotile, amphibole and crocidolite have all been mined in Australia and employment records from the single company which mined most of the crocidolite deposits at Wittenoom have formed the basis of an ongoing cohort mortality study of the workforce.

Asbestos, Crocidolite↗

PubMed2004

The Western Australian Register of Childhood Multiples: effects of questionnaire design and follow-up protocol on response rates and representativeness.

Twin registers have been established worldwide to study the roles of genes and the environment in health and behaviour. While questionnaire surveys are thought to be the most cost-effective way of collecting large amounts of data, low response rates can result in response bias. Many different strategies have been proposed to maximise response rates. A register of all multiple births occurring in Western Australia (WA) from 1980 onwards has been established using probabilistic record linkage techniques. Families who had not experienced the death of one or more of their multiples were invited to participate in the Western Australian Twin Child Health (WATCH) study, which studied the genetic and environmental determinants of childhood asthma and atopy. Several questionnaire designs and follow-up methods were assessed. We have shown that it was feasible to use a population-based register of multiple births to contact families for a questionnaire study. Questionnaire length, mode of follow-up, the number of responses required and the of participants all seemed to affect response.

Follow-Up Studies↗

PubMed2004

The relation of breastfeeding and body mass index to asthma and atopy in children: a prospective cohort study to age 6 years.

OBJECTIVES: We investigated the relationship between breastfeeding, asthma and atopy, and child body mass index (BMI). METHODS: From a prospective birth cohort (n = 2860) in Perth, Western Australia, 2195 children were followed up to age 6 years. Asthma was defined as doctor-diagnosed asthma and wheeze in the last year, and atopy was determined by skin prick test of 1596 children. Breastfeeding, BMI, asthma, and atopy were regressed allowing for confounders and the propensity score for overweight. RESULTS: Using fractional polynomials, we found no association between breastfeeding and overweight. Less exclusive breastfeeding was associated with increased asthma and atopy, and BMI increased with asthma. CONCLUSIONS: Less exclusive breastfeeding leads to increases in child asthma and atopy and a higher BMI is a risk factor for asthma.

Asthma↗

PubMed2003

Respiratory symptoms and lung-function changes with exposure to five substances in aluminium smelters.

OBJECTIVES: To determine whether exposure to five different occupational substances contributes to respiratory symptoms in aluminium smelter workers. METHODS: A cross-sectional survey of 1,615 male employees of two Australian aluminium smelters was conducted in 1995. Subjects underwent spirometry and were asked about respiratory symptoms and the relationship of those symptoms to work. Their job histories were combined with a task exposure matrix to produce individual quantitative measures of cumulative exposure to fluoride, sulphur dioxide, inspirable dust, the benzene-soluble fraction of coal tar pitch volatiles (BSF), and oil mist. RESULTS: After adjusting for smoking and age, we found that subjects with the highest cumulative exposure to fluoride (>0.16 mg/m(3) years) and inspirable dust (>2.9 mg/m(3) years) were two to four times more likely to report work-related wheeze and chest tightness than were unexposed subjects. Lower prevalence ratios for the same symptoms were seen with sulphur dioxide and BSF. Levels of lung function decreased slightly with exposure to oil mist, but not with cumulative exposure to other substances. CONCLUSIONS: This study suggests that the relevant causative agents for respiratory symptoms in aluminium smelters are fluoride and inspirable dust.

Adult↗