Surveying the landscape of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data

Even though alternative RNA splicing was discovered in 1977 (nearly 50 years ago), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their functions differ. Human gene annotations suggest remarkable transcriptional complexity, with approximately 252,798 distinct RNA isoform annotations from 62,710 gene bodies (Ensembl v109; 2023), emphasizing the need to understand their biological effects. For example, 256 gene bodies have ≥50 annotated isoforms and 30 have ≥100, where one protein-coding gene (MAPK10) even has 192 distinct RNA isoform annotations. Whether such isoform diversity results from biological noise (i.e., spurious alternative splicing) or whether it represents biological intent and specialized functions (even if subtle) remains a mystery. Recent studies by Aguzzoli-Heberle et al., Leung et al., and Glinos et al. demonstrate long-read RNAseq enables improved RNA isoform quantification for essentially any tissue, cell type, or biological condition (e.g., disease, development, aging, etc.) making it possible to better assess individual isoform expression and function. While each study provided important discoveries related to RNA isoform diversity, deeper exploration is needed. We sought, in part, to quantify real isoform usage across tissues (compared to annotations) and explore whether observed diversity is biological noise or intent. We used long-read RNAseq data from 58 GTEx samples across nine tissues (three brain, two heart, muscle, lung, liver, and cultured fibroblasts) generated by Glinos et al. and found considerable isoform diversity within and across tissues. Cerebellar hemisphere was the most transcriptionally complex tissue (22,522 distinct isoforms; 3,726 unique); liver was least diverse (12,435 isoforms; 1,039 unique). We highlight gene clusters exhibiting high tissue-specific isoform diversity per tissue (e.g., TPM1 expresses 19 in heart's atrial appendage), and specific genes (PAX6 and TPM1) that counterintuitively exhibit evidence that their expressed isoform diversity results from both biological noise and intent. We also validated 447 of the 700 new isoforms discovered by Aguzzoli-Heberle et al. and found that 88 were expressed in all nine tissues, while 58 were specific to a single tissue. This study represents a broad survey of the RNA isoform landscape, demonstrating isoform diversity across nine tissues and emphasizes the need to better understand how individual isoforms from a single gene body contribute to human health and disease.

Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity

Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer's disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinson's disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer's disease genes such as APP (Aβ precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer's cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.

A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology

Models that recapitulate the complexity of human tumors are urgently needed to develop more effective cancer therapies. We report a bank of human patient-derived xenografts (PDXs) and matched organoid cultures from tumors that represent the greatest unmet need: endocrine-resistant, treatment-refractory and metastatic breast cancers. We leverage matched PDXs and PDX-derived organoids (PDxO) for drug screening that is feasible and cost-effective with in vivo validation. Moreover, we demonstrate the feasibility of using these models for precision oncology in real time with clinical care in a case of triple-negative breast cancer (TNBC) with early metastatic recurrence. Our results uncovered a Food and Drug Administration (FDA)-approved drug with high efficacy against the models. Treatment with this therapy resulted in a complete response for the individual and a progression-free survival (PFS) period more than three times longer than their previous therapies. This work provides valuable methods and resources for functional precision medicine and drug development for human breast cancer.

Welm and colleagues present a biobank of human-derived xenografts and organoids and demonstrate its value for high-throughput drug screening and applied precision medicine.

Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping

INTRODUCTION

Mitochondrial genetics are an important but largely neglected area of research in Alzheimer's disease. A major impediment is the lack of data sets.

METHODS

We used an innovative, rigorous approach, combining several existing tools with our own, to accurately assemble and call variants in 809 whole mitochondrial genomes.

RESULTS

To help address this impediment, we prepared a data set that consists of 809 complete and annotated mitochondrial genomes with samples from the Alzheimer's Disease Neuroimaging Initiative. These whole mitochondrial genomes include rich phenotyping, such as clinical, fluid biomarker, and imaging data, all of which is available through the Alzheimer's Disease Neuroimaging Initiative website. Genomes are cleaned, annotated, and prepared for analysis.

DISCUSSION

These data provide an important resource for investigating the impact of mitochondrial genetic variation on risk for Alzheimer's disease and other phenotypes that have been measured in the Alzheimer's Disease Neuroimaging Initiative samples.

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches

Background

Analyzing next-generation sequencing data is difficult because datasets are large, second generation sequencing platforms have high error rates, and because each position in the target genome (exome, transcriptome, etc.) is sequenced multiple times. Given these challenges, numerous bioinformatic algorithms have been developed to analyze these data. These algorithms aim to find an appropriate balance between data loss, errors, analysis time, and memory footprint. Typical analysis pipelines require multiple steps. If one or more of these steps is unnecessary, it would significantly decrease compute time and data manipulation to remove the step. One step in many pipelines is PCR duplicate removal, where PCR duplicates arise from multiple PCR products from the same template molecule binding on the flowcell. These are often removed because there is concern they can lead to false positive variant calls. Picard (MarkDuplicates) and SAMTools (rmdup) are the two main softwares used for PCR duplicate removal.

Results

Approximately 92 % of the 17+ million variants called were called whether we removed duplicates with Picard or SAMTools, or left the PCR duplicates in the dataset. There were no significant differences between the unique variant sets when comparing the transition/transversion ratios (p = 1.0), percentage of novel variants (p = 0.99), average population frequencies (p = 0.99), and the percentage of protein-changing variants (p = 1.0). Results were similar for variants in the American College of Medical Genetics genes. Genotype concordance between NGS and SNP chips was above 99 % for all genotype groups (e.g., homozygous reference).

Conclusions

Our results suggest that PCR duplicate removal has minimal effect on the accuracy of subsequent variant calls.

Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk

INTRODUCTION

Ebbert et al. reported gene-gene interactions between rs11136000-rs670139 (CLU-MS4A4E) and rs3865444-rs670139 (CD33-MS4A4E). We evaluate these interactions in the largest data set for an epistasis study.

METHODS

We tested interactions using 3837 cases and 4145 controls from Alzheimer's Disease Genetics Consortium using meta-analyses and permutation analyses. We repeated meta-analyses stratified by apolipoprotein E (APOE) ε4 status, estimated combined odds ratio (OR) and population attributable fraction (cPAF), and explored causal variants.

RESULTS

Results support the CLU-MS4A4E interaction and a dominant effect. An association between CLU-MS4A4E and APOE ε4 negative status exists. The estimated synergy factor, OR, and cPAF for rs11136000-rs670139 are 2.23, 2.45, and 8.0, respectively. We identified potential causal variants.

DISCUSSION

We replicated the CLU-MS4A4E interaction in a large case-control series and observed APOE ε4 and possible dominant effect. The CLU-MS4A4E OR is higher than any Alzheimer's disease locus except APOE ε4, APP, and TREM2. We estimated an 8% decrease in Alzheimer's disease incidence without CLU-MS4A4E risk alleles and identified potential causal variants.

Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation

Cerebrospinal fluid (CSF) 42 amino acid species of amyloid beta (Aβ42) and tau levels are strongly correlated with the presence of Alzheimer's disease (AD) neuropathology including amyloid plaques and neurodegeneration and have been successfully used as endophenotypes for genetic studies of AD. Additional CSF analytes may also serve as useful endophenotypes that capture other aspects of AD pathophysiology. Here we have conducted a genome-wide association study of CSF levels of 59 AD-related analytes. All analytes were measured using the Rules Based Medicine Human DiscoveryMAP Panel, which includes analytes relevant to several disease-related processes. Data from two independently collected and measured datasets, the Knight Alzheimer's Disease Research Center (ADRC) and Alzheimer's Disease Neuroimaging Initiative (ADNI), were analyzed separately, and combined results were obtained using meta-analysis. We identified genetic associations with CSF levels of 5 proteins (Angiotensin-converting enzyme (ACE), Chemokine (C-C motif) ligand 2 (CCL2), Chemokine (C-C motif) ligand 4 (CCL4), Interleukin 6 receptor (IL6R) and Matrix metalloproteinase-3 (MMP3)) with study-wide significant p-values (p<1.46×10⁻¹⁰) and significant, consistent evidence for association in both the Knight ADRC and the ADNI samples. These proteins are involved in amyloid processing and pro-inflammatory signaling. SNPs associated with ACE, IL6R and MMP3 protein levels are located within the coding regions of the corresponding structural gene. The SNPs associated with CSF levels of CCL4 and CCL2 are located in known chemokine binding proteins. The genetic associations reported here are novel and suggest mechanisms for genetic control of CSF and plasma levels of these disease-related proteins. Significant SNPs in ACE and MMP3 also showed association with AD risk. Our findings suggest that these proteins/pathways may be valuable therapeutic targets for AD. Robust associations in cognitively normal individuals suggest that these SNPs also influence regulation of these proteins more generally and may therefore be relevant to other diseases.

The use of quantitative endophenotypes from cerebrospinal fluid has led to the identification of several genetic variants that alter risk or rate of progression of Alzheimer's disease. Here we have analyzed the levels of 58 disease-related proteins in the cerebrospinal fluid for association with millions of variants across the human genome. We have identified significant, replicable associations with 5 analytes, Angiotensin-converting enzyme, Chemokine (C-C motif) ligand 2, Chemokine (C-C motif) ligand 4, Interleukin 6 receptor and Matrix metalloproteinase-3. Our results suggest that these variants play a regulatory role in the respective protein levels and are relevant to the inflammatory and amyloid processing pathways. Variants in associated with ACE and those associated with MMP3 levels also show association with risk for Alzheimer's disease in the expected directions. These associations are consistent in cerebrospinal fluid and plasma and in samples with only cognitively normal individuals suggesting that they are relevant in the regulation of these protein levels beyond the context of Alzheimer's disease.

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files

Background

Since the advent of next-generation sequencing many previously untestable hypotheses have been realized. Next-generation sequencing has been used for a wide range of studies in diverse fields such as population and medical genetics, phylogenetics, microbiology, and others. However, this novel technology has created unanticipated challenges such as the large numbers of genetic variants. Each caucasian genome has more than four million single nucleotide variants, insertions and deletions, copy number variants, and structural variants. Several formats have been suggested for storing these variants; however, the variant call format (VCF) has become the community standard.

Results

We developed new software called the Variant Tool Chest (VTC) to provide much needed tools to work with VCF files. VTC provides a variety of tools for manipulating, comparing, and analyzing VCF files beyond the functionality of existing tools. In addition, VTC was written to be easily extended with new tools.

Conclusions

Variant Tool Chest brings new and important functionality that complements and integrates well with existing software. VTC is available at https://github.com/mebbert/VariantToolChest

Coping with stress during childhood and adolescence: problems, progress, and potential in theory and research

Progress and issues in the study of coping with stress during childhood and adolescence are reviewed. Definitions of coping are considered, and the relationship between coping and other aspects of responses to stress (e.g., temperament and stress reactivity) is described. Questionnaire, interview, and observation measures of child and adolescent coping are evaluated with regard to reliability and validity. Studies of the association of coping with symptoms of psychopathology and social and academic competence are reviewed. Initial progress has been made in the conceptualization and measurement of coping, and substantial evidence has accumulated on the association between coping and adjustment. Problems still remain in the conceptualization and measurement of coping in young people, however, and aspects of the development and correlates of coping remain to be identified. An agenda for future research on child-adolescent coping is outlined.

Birth weight and cognitive function in the British 1946 birth cohort: longitudinal population based study

OBJECTIVE

To examine the association between birth weight and cognitive function in the normal population.

DESIGN

A longitudinal, population based, birth cohort study.

PARTICIPANTS

3900 males and females born in 1946.

MAIN OUTCOME MEASURES

Cognitive function from childhood to middle life (measured at ages 8, 11, 15, 26, and 43 years).

RESULTS

Birth weight was significantly and positively associated with cognitive ability at age 8 (with an estimated standard deviation score of 0.44 (95% confidence interval 0.28 to 0.59)) between the lowest and highest birthweight categories after sex, father's social class, mother's education, and birth order were controlled for. This association was evident across the normal birthweight range (>2.5 kg) and so was not accounted for exclusively by low birth weight. The association was also observed at ages 11, 15, and 26, and weakly at age 43, although these associations were dependent on the association at age 8. Birth weight was also associated with education, with those of higher birth weight more likely to have achieved higher qualifications, and this effect was accounted for partly by cognitive function at age 8.

CONCLUSIONS

Birth weight was associated with cognitive ability at age 8 in the general population, and in the normal birthweight range. The effect at this age largely explains associations between birth weight and cognitive function at subsequent ages. Similarly, the association between birth weight and education was accounted for partly by earlier cognitive scores.

Latent class analysis of child behavior checklist anxiety/depression in children and adolescents

OBJECTIVE

Comorbidity of psychiatric problems such as anxiety and depression poses challenges to treatment and research. This study tested whether problem items from the Anxious/Depressed scale of the Child Behavior Checklist (CBCL) can be separated into distinct anxiety and depression classes or are continuously distributed throughout a population.

METHOD

A CBCL was completed by a parent or guardian of each of 1,987 children and adolescents selected to represent nonreferred children in the United States, as well as by a parent or guardian of each of a demographically matched sample of 1,987 clinically referred children and adolescents. Problem items from the Anxious/Depressed scale of the CBCL were subjected to latent class analysis.

RESULTS

Analyses revealed three levels of problem presentation in both samples. Children in the nonreferred sample were classified as having no problems, mild problems, or moderate anxiety/depression problems. Children and adolescents in the referred group were classified as having mild, moderate, or severe levels of problems. No pure anxiety or depression classes were found, only classes containing a mixture of both anxiety and depressive problems. Age, gender, and sample differences were found in class groupings, with nonreferred adolescent girls showing elevated levels of problems.

CONCLUSIONS

Results suggest that the comorbid conditions of anxiety and depression, as assessed by the CBCL anxiety/depression problem items, can be thought of as part of the same continuum of problems. Implications for assessment and treatment utilization are discussed.

Responses to stress in adolescence: measurement of coping and involuntary stress responses

The development of a measure of coping and involuntary stress responses in adolescence is described. The Responses to Stress Questionnaire (RSQ) reflects a conceptual model that includes volitional coping efforts and involuntary responses to specific stressful events or specified domains of stress. The psychometric characteristics of the RSQ were examined across 4 domains of stress in 3 samples of adolescents and parent reports obtained in 2 samples. The factor structure of the RSQ was tested and replicated with an adequate degree of fit using confirmatory factor analysis across 3 stressors in 2 samples. Internal consistency and retest reliability for the 5 factors were adequate to excellent. Concurrent validity was established through correlations with another measure of coping, heart rate reactivity, and correlations of self- and parent-reports. Significant correlations with both adolescents' and parents' reports of internalizing and externalizing symptoms were consistent with hypotheses.

Menstrual patterns during the inception of perimenopause: what are the predictors and what do they predict?

Using data from a British national cohort of women born in 1946, this study aims to identify menstrual patterns during the first year of perimenopause (based on the frequency of periods, the numbers of days bled each month, and menstrual flow) to see if they are related to health and behaviors earlier in adult life and if they predict entry into menopause and hormone replacement therapy (HRT) use. Three groups of women were identified using cluster analysis: those who experienced more of these characteristics, those who experienced less, and those who experienced few changes. In polychotomous logistic regression models, the likelihood ratio tests indicated that parity and body mass index (BMI) were significant at the 5% level. The odds ratios from the parity models showed a gradient, with women from the Less cluster being most likely to have no children and those from the More cluster most likely to have at least one child. A similar gradient was detected for BMI, with the Less cluster tending to be underweight. The Less cluster came into menopause significantly faster than the Same and the More groups, where the estimated hazard ratios (HR) (95% confidence interval [CI]) were, respectively, 0.61 (0.37-0.99) and 0.24 (0.11-0.52). There was no association between the clusters and later HRT use. The findings suggest that menstrual characteristics should be more carefully studied in population studies of the climacteric.

Early determinants of inflammatory bowel disease: use of two national longitudinal birth cohorts

OBJECTIVE

To examine previously cited early risk factors for inflammatory bowel disease.

DESIGN

The 1946 National Survey of Health & Development (NSHD) and the 1958 National Child Development Study (NCDS) are on-going, longitudinal birth cohort studies. A nested case-control design was used combining data from both cohorts; eight controls per case, matched for gender and social class, were selected randomly.

METHODS

Data concerning maternal infection in pregnancy (NCDS only), childhood infection (measles, mumps and whooping cough), birth order, appendicectomy, breast-feeding and measures of poor housing conditions in childhood were analysed. In both cohorts, the member's hospital physician or medical records were used to confirm the diagnosis.

RESULTS

Twenty-six cases of Crohn's disease and 29 cases of ulcerative colitis were identified. No significant association was found between the development of Crohn's disease or ulcerative colitis and any of the studied factors. There was a trend that those with Crohn's disease were more likely not to have been breast-fed (OR 0.4, 95% CI 0.15-1.03) and not to have had an appendicectomy (OR < 1.00). The opposite was true of those with ulcerative colitis (OR 2.76, 95% CI 0.86-9.81 and OR 2.34, 95% CI 0.69-7.46, respectively). The prevalence of inflammatory bowel disease was 5.12/1000 by the age of 43 years in NSHD and 2.02-2.54/1000 by the age of 33 years in NCDS.

CONCLUSIONS

The prevalence of inflammatory bowel disease in these cohorts is among the highest recorded in Europe. Childhood factors may be different for those with Crohn's disease and ulcerative colitis. These cohorts will be increasingly valuable data sources.

Food and nutrient intake of a national sample of 4-year-old children in 1950: comparison with the 1990s

OBJECTIVE

To evaluate the food and nutrient intake of members of a birth cohort study when young children in 1950 and investigate differences from present-day children's diets.

DESIGN

One-day recall diet records from the MRC National Survey of Health and Development (NSHD) (1946 Birth Cohort) at age 4 years were analysed for energy and selected nutrients and compared to the published results for 4-year-olds in the 1992/93 National Diet and Nutrition Survey (NDNS).

SETTING

England, Scotland and Wales in 1950 and 1992/93.

SUBJECTS

4,599 children in 1950 and 493 children in 1992/93.

RESULTS

Mean (SD) daily intakes in 1950 were energy 1,445 (343) kcal, or 6.1 (1.4) MJ, protein 46 (11)g, fat 64 (20)g, starch 117 (33)g, sugar 62 (24)g, unavailable carbohydrate 13 (4)g, calcium 736 (230) mg, iron 7.7 (2.1) mg, retinol 738 (1,273) microg, carotene 1,049 (1,130) microg and vitamin C 40 (26) mg. Compared to 1992/93, the 1950 diet contained substantially more bread and vegetables and less sugar and soft drinks, giving it a higher starch and fibre content and making it more in line with current recommendations on healthy eating. However, fat provided 40% of energy in 1950, compared to 35% in 1992/93. In 1950, red meat was an important source of iron, but by 1992 most iron came from fortified breakfast cereals. Vitamin C came mainly from vegetables in 1950, but from soft drinks in 1992.

CONCLUSIONS

The relative austerity of post-war food supplies resulted in food and nutrient intakes in 1950 which in many respects may well have been beneficial to the health of young children, despite fat intake being higher than present-day recommendations.

Gender differences in the relationship between alcohol consumption and drink problems are largely accounted for by body water

It is widely reported that women drink less and have a lower prevalence of drink problems than men, but the gender differences in the relationship between level of drinking and drink problems have rarely been investigated quantitatively. This paper reports results from the Medical Research Council National Survey of Health and Development (the 1946 British Cohort) when the subjects were 43 years old. Using 7-day recall for alcohol consumption and CAGE scores of 2, 3 or 4 for drink problems, it was found that the prevalence of drink problems increased with level of alcohol consumption. Women were more likely than men to report drink problems at the same level of alcohol consumption. However, this gender difference was largely accounted for by individual differences in weight of body water. Beer accounted for the excess of men's drinking over women's and the proportion of alcohol consumed as beer was inversely related to drink problems. Eighty per cent of women and 52% of men who had drink problems in the past year reported drinking less than an average of 3 U (women) or 4 U (men) a day in the past week. As drinking levels in women begin to approach those in men, rates of drink problems in women are likely to overtake those in men because of women's greater physiological sensitivity to the effects of alcohol.

Latent class analysis of Child Behavior Checklist attention problems

OBJECTIVE

To test whether attention problems in children are continuously distributed or categorically discrete, the authors performed latent class analyses (LCA) of items from the Attention Problems scale of the Child Behavior Checklist (CBCL) using data from the clinical and nonclinical samples used in the derivation of the CBCL syndromes.

METHOD

A CBCL was completed by a parent or guardian of each of 2,100 nonreferred children selected to be representative of U.S. nonreferred children and a demographically matched sample of 2,100 clinically referred children. Attention problems symptoms were subjected to LCA.

RESULTS

LCAs were consistent with the presence of 3 levels of symptom presentation in both samples. Children in the nonclinical sample were classified as having no symptoms, mild symptoms, or moderate symptoms. Children in the clinical group had mild, moderate, or severe symptoms.

CONCLUSIONS

These results suggest that child and adolescent psychiatric symptoms such as attention problems can be thought of as continuously distributed phenomena rather than discrete disease entities, lending support for an empirical approach to both clinical work and research. In addition, high prevalence rates of attention problems in both clinical and nonclinical samples suggest the need for careful screening of attention problems in clinic and academic settings.

The persisting effect of unemployment on health and social well-being in men early in working life

In our studies of the effects of unemployment in the early working life of men in a British national birth cohort we have shown elsewhere that this experience was part of a longer term accumulation of social and health disadvantage. This present study asks whether men's unemployment also inflicted potential longterm damage to future socio-economic chances and health. We therefore constructed indicators of socio-economic circumstances and health at 33 years from factors already shown to be associated with health in later life. For the socio-economic indicator we used a combination of income, occupational status and home ownership and described this as socio-economic capital. For the health indicator we combined scores of body mass index, leisure time exercise, frequency of eating fresh fruit and of smoking, and described this as health capital. After controlling for pre-labour market socio-economic and health factors, prolonged unemployment is shown here to reduce significantly both socio-economic and health capital by age 33 years. We conclude that the experience of prolonged unemployment early in the working life of this population of young men looks likely to have a persisting effect on their future health and socio-economic circumstances.

Unemployment pre-dates symptoms of depression and anxiety resulting in medical consultation in young men

BACKGROUND

There is evidence to support a link between unemployment and lower levels of psychological well-being, but debate continues as to whether unemployment results in psychological morbidity, or whether the association is due to those who are more vulnerable to mental illness becoming unemployed. Here we assess the effect of recent and accumulated unemployment in young men on the risk of developing depression and anxiety leading to medical consultation. Adjustment was made for a measure of pre-existing tendency to depression, behavioural maladjustment, social class, qualifications and region of residence.

METHODS

Some 3241 men from the National Child Development Study (the 1958 British birth cohort) with data from birth to age 33 years, collected at birth and ages 7, 11, 16, 23 and 33 years were used in these analyses. The outcome measure was onset age of anxiety or depression between ages 24 and 33 years, that resulted in consultation with a GP or a specialist. This was used in Cox proportional hazards models where two measures of unemployment were modelled as time varying covariates. Pre-existing tendency to depression was measured by the Malaise Inventory prior to the experience of unemployment at age 23 years. Two measures of unemployment were investigated: any unemployment in the year prior to onset (recent unemployment) and all accumulated unemployment prior to onset (divided into four categories: 0, 1-12, 13-36 and 37+ months of unemployment).

RESULTS

After adjustment for potential confounding factors including pre-existing tendency to depression, the relative risk (RR) for developing symptoms resulting in consultation was 2.10 (95% CI: 1.21-3.63), when those who were unemployed in the year prior to onset were compared with those who were not. Accumulated unemployment was not statistically significantly related to onset of symptoms in all men after adjustment for the potential confounding factors: an RR of 1.63 (95% CI: 0.95-2.79) for men with 37+ months of accumulated unemployment when compared with none. However, exclusion of men with a pre-existing tendency to depression indicated by the Malaise Inventory score, increased the RR to 2.30 (95% CI: 1.44-3.65) for recent unemployment and 2.04 (95% CI: 1.17-3.54) for 37+ months of accumulated unemployment when compared with none.

CONCLUSIONS

Unemployment is a risk factor for psychological symptoms of depression requiring medical attention, even in those men without previous psychological vulnerability.

Childhood laterality and later risk of schizophrenia in the 1946 British birth cohort

An increased rate on non-righthandedness and other abnormalities of lateralization have been reported in schizophrenia. We investigated childhood hand preference and eye dominance as risk factors for adult schizophrenia among a general population birth cohort. Pre-schizophrenic children showed a significant excess of left-eye dominance at age 11 when compared with controls (OR 2.5, 1.0-5.8, p = 0.03), but there was no significant difference in hand preference between pre-schizophrenic children and controls.

Characteristics of the low-energy reporters in a longitudinal national dietary survey

The aim of the present study was to establish whether the characteristics of members of a large national birth cohort study who submitted diet diaries with implausibly low-energy intake differed from those whose recorded energy intake was more plausible. Survey members (n 1898) recorded their diets in a 7 d diary in household measures. Those whose reported energy intake (EI) as a fraction of their estimated BMR was less than 1.10, here termed low-energy reporters (LER) but often called under-reporters, constituted 20.6% of the study population. None of the variables describing dietary, smoking or exercise behaviour bore a significant relationship with low EI/BMR (< 1.10), neither did those describing region of residence, subjective adequacy of income, current social class, social relations or the social environment of the subjects. Results of logistic regression analysis showed that the only independently significant characteristic for men was higher BMI. In women, in addition to higher BMI, having been overweight or obese as an adult independently, but less significantly, predicted low EI/BMR, while membership as a child of social class III (non-manual), having more children in the household and having a paid job marginally but independently decreased the probability of reporting low EI/BMR. Submission of a diary with EI/BMR < 1.10 7 years earlier in the same survey was an even more powerful predictor of current low EI/BMR than higher BMI in both sexes. The average reported diet-composition of LER was more micronutrient- and protein-rich than that of the others, indicating different dietary, or diet-recording, behaviour in this group of subjects. LER are not a random sample of the survey population, and their characteristics, definable to some extent, put them at risk for lower health status. Although EI/BMR cut-off points can be used to identify LER, the problem of how to use their data is still unresolved.

Health inequalities in the life course perspective

Life history approaches to the study of inequalities in health provide evidence that the biological and the social beginnings of life carry important aspects of the child's potential for adult health. Biological programming may set the operational parameters for certain organs and processes. Social factors in childhood influence the processes of biological development, and are the beginnings of socially determined pathways to health in adult life. Life history studies of health are beginning to show the important factors associated with the development of these pathways, and the life stages at which intervention to reduce adult health inequalities may be most effective.

Childhood influences on adult health: a review of recent work from the British 1946 national birth cohort study, the MRC National Survey of Health and Development

Research in this study has shown that growth in utero and early-life development were associated with a range of adult outcomes, including blood pressure, respiratory function and schizophrenia. It has also been shown that childhood social and educational factors are strongly associated with adult mental and physical health, and with adult health-related behaviour. It is suggested that the observed long-term effects of early-life physical development do not represent an inevitable outcome of childhood development, but one which is mediated by the chain of social factors that also begins in early life. The conclusions emphasise that since the social and economic circumstances that affect child health have changed greatly in recent years in some ways which are particularly adverse, we need now to be aware of the implications of such change not only for the health of children today, but also for their health in adulthood.

Health and social precursors of unemployment in young men in Great Britain

OBJECTIVE

To identify health and socioeconomic factors in childhood that are precursors of unemployment in early adult life and to examine the hypothesis that young men who become unemployed are more likely to have accumulated risks to health during childhood.

DESIGN

Longitudinal birth cohort study. The amount of unemployment experienced in early adult life up to age 32 years was the outcome measure used. Exposure measures to indicate vulnerability to future ill health were: height at age 7 years and the Bristol social adjustment guide (BSAG) at age 11 years, a measure of behavioural maladjustment. Socioeconomic measures were: social class at birth, crowding at age 7, qualifications attained before labour market entry, and region of residence.

SETTING

Great Britain.

SUBJECTS

Altogether 2256 men with complete data from the national child development study (NCDS). The NCDS has collected data on all men and women born in one week in 1958 and has followed them up using interviews, self completion questionnaires, and medical examinations at birth and at ages 7, 11, 16, 23 and 33 years.

RESULTS

A total of 269 men (11.9%) experienced more than one year of unemployment between ages 22 and 32 years. Poor socioeconomic conditions in childhood and a lack of qualifications were associated with an increased risk of unemployment. Geographical region was also significant in determining the risk of unemployment. Men with short stature and poor social adjustment in childhood were more likely to experience unemployment in adult life, even after controlling for socioeconomic background, education, and parental height. These differences remained when those with chronic childhood illnesses were excluded from the analysis. The adjusted relative odds for experiencing more than one year of unemployment between ages 22 and 32 years for men who were in the top fifth of the BSAG distribution (most maladjusted) compared with those in the bottom fifth were 2.36 (95% CI 1.49, 3.73). The adjusted relative odds for experiencing more than one year of unemployment between ages 22 and 32 years for men who were in the bottom fifth of the distribution of height at age 7 years (indicating slowest growth) compared with those in the top fifth, were 2.41 (95% CI 1.43, 4.04). Adult height was not significantly associated with unemployment.

CONCLUSION

The relationship between unemployment and poor health arises, in part, because men who become unemployed are more likely to have accumulated risks to health during childhood, reflected by slower growth and a greater tendency to behavioural maladjustment. Short stature in childhood is a significant indicator of poor socioeconomic circumstances in childhood and reflects earlier poor development.

Adjustment of children and adolescents to parental cancer. Parents' and children's perspectives

BACKGROUND

Little empirical evidence exists to address the impact of a diagnosis of cancer of a father or mother on his or her children. Previous studies have found inconsistencies in the levels of distress reported for children of a parent with cancer, which may be a function of who (parent or child) was reporting on the child's symptoms and when the reports were taken (near diagnosis or months or years later).

METHODS

This study examined parents' and children's reports of emotional and behavioral problems in children and adolescents from 76 patient families in which a mother or father was recently diagnosed with cancer.

RESULTS

Parents' reports indicated little or no evidence of emotional distress or disruptive behavior in their children regardless of the child's age or sex, or whether the mother or father was ill. Children's reports differed significantly from those of their parents, with adolescent girls reporting the highest levels of symptoms of anxiety/depression and aggressive behavior. Children's reports of their emotional distress declined from an initial assessment 10 weeks after their parents' diagnosis to a follow-up 4 months later, whereas parents' reports of their children's distress did not change with time.

CONCLUSIONS

Children's symptoms of psychologic distress varied considerably according to their age, sex, whether their mother or father had cancer, and whether they themselves or their parents were reporting the symptoms. Adolescent girls whose mothers had cancer reported the highest levels of distress. When children did report elevated levels of psychologic symptoms, their parents did not appear to be aware of their distress and rated their children as asymptomatic. These findings suggest that health professionals may need to assist parents in recognizing and coping with their children's distress when it is present.

The changing pattern of in-patient care

BACKGROUND

A nationally representative longitudinal study presented the opportunity to describe National Health Service (NHS) and private in-patient care used over seven years by a population of young adults in relation to known risk factors for admission and for future health.

METHODS

Information on each hospital admission between ages 36 and 43 years, comprising length of admission and whether under NHS or private care, was collected from 1625 men and 1623 women, the population of the 1946 birth cohort study. Obstetric care was excluded from most analyses.

RESULTS

From this population, 22 per cent of men and 39 per cent of women were admitted to hospital at least once during the seven-year period, for a total of 11,276 days, a mean of 3.5 days (SD 13.1) for each person in the study, and 11.6 (SD 21.9) days for those admitted. The proportion of admissions not under NHS care rose from 14 per cent of all admissions in 1982 to 23 per cent in 1989. Employers contributed to health insurance for 25 per cent of employed men and 7 per cent of employed women. Risk of admission was greater, and admissions were longer, in those least educated and from poorest circumstances; men with largest waist-hip ratios were admitted for longer than others. Private admissions were proportionately greater in nonmanual classes and among those from favourable social and educational backgrounds, that is, those known to be at least risk of serious and chronic illness.

CONCLUSION

Heaviest users of in-patient care were those most likely to be at greatest health risk, who were least likely to have private health insurance. The rising mid-life uptake of private health insurance through employers (25 per cent of employed men by age 43 years) may foreshadow a future problem in a return to NHS care on retirement in this population, which represents the beginning of the future population bulge in the elderly.

Burden of disability in a post war birth cohort in the UK

STUDY OBJECTIVE

To report the prevalence of physical disability in a national sample of 43 year old men and women, and examine the relationship between disability and the consumption of hospital care. To assess the contribution of childhood health and social circumstances to the risk of adult disability, and the socioeconomic consequences of disability.

DESIGN

The assessment of disabilities of physical movement was based on criteria developed by OPCS for their national survey of disability. The analysis used data on socioeconomic circumstances from childhood to 43 years and on serious illness in the first 25 years of life collected prospectively on members of the MRC National Survey of Health and Development, the 1946 birth cohort study.

SETTING

England, Wales, and Scotland.

PARTICIPANTS

A general population sample of 3235 men and women aged 43 years.

MAIN RESULTS

Seven per cent of cohort survivors at 43 years were physically disabled and a further 3% reported difficulties although they were not assessed as disabled according to OPCS criteria. The prevalence of severe disability at this age was similar to that derived from the OPCS survey but the prevalence of mild disability was substantially greater. Disability was associated with a greater use of hospital care in recent years and throughout life. Those who had experienced a serious illness in earlier life were over twice as likely to be disabled; certain conditions, such as polio, were associated with a particularly high relative risk. Those who had had a socially disadvantaged start to life were more likely to be physically disabled at 43 years but the strength of this relationship was considerably weakened by adjustment for later social factors, suggesting that social disadvantage throughout life, or during adult life, increased the risk of disability. Taking these results into account the relative impact of disability on income and employment was found to be greatest for those from the unskilled and semi-skilled classes.

CONCLUSIONS

The prevalence of physical disability among those in early middle age may be greater than previously estimated. The strong links between childhood ill health and adult disability and its association with high levels of hospital care support longstanding recommendations for better coordination between child and adult health services. Social disadvantages affects the risk of disability and its financial and employment consequences.

Physical health status at 36 years in a British national birth cohort

In a nationally representative British sample of over 3000 men and women aged 36 years, those in the best or worst of health were identified on the basis of measured blood pressure, lung function and body weight, self reported health problems and disability, and recent hospital admission. Serious illness in earlier life was strongly predictive of current adult health status. Even after adjusting for this and for current social circumstances and health related behaviour, those who came from poorer family backgrounds or were least well educated did not have an equal chance of being in the best of health at 36 years. Living in adverse social circumstances in adult life increased the risk of having the worst health. The analysis suggests that a number of pathways link childhood experiences to adult health and shows the need for a lifetime research perspective on health.

Generation differences in hospital inpatient care of children aged 1 to 5 years

STUDY OBJECTIVE

To describe differences in childhood hospital admissions at ages 1 to 5 years in two generations, and to compare the intergenerational differences in risks of admission.

DESIGN

Information was taken from a longitudinal birth cohort study of a national sample and their firstborn offspring.

SETTING

England, Wales, and Scotland.

SUBJECTS

the 5022 birth cohort members for whom information is available from ages 1 to 5 years and their 2205 firstborn offspring.

MEASUREMENTS AND MAIN RESULTS

Data comprised reports of hospital admissions, which were checked with hospitals. Mean numbers of days spent in hospital were fewer in the offspring generation than in their parents, but the proportion ever admitted fell by only 1%. Low birth weight babies (< 2500 g), who comprised 6% of cohort births and 7% of the following generation, used a high proportion of all inpatient time in the offspring population, rising from 3% to 14% of all days of admission.

CONCLUSIONS

Compared with the early years of the NHS, published statistics show that the effectiveness of paediatric care has improved greatly, and that childhood mortality and the risk of serious illness have decreased significantly. This study reports intergenerational changes in the reasons for hospital admission and shows, with the benefit of good denominator data, that although there was only a small intergenerational decrease in the proportion of children treated in hospital, there was a large reduction in the time spent in hospital and an increase in admissions of children of low birth weight.

Application of Raman spectroscopy to metal-sulfide surface analysis

The surface products of electrochemically oxidized pyrite (FeS(2)) are investigated as a function of applied potential by using Raman spectroscopy. The parameters necessary for sulfur formation on the pyrite surface were determined. An optical multichannel apparatus, consisting of an argon laser, a triple spectrograph, and a charge-coupled-device detector, was utilized for the Raman measurements. The advantages of this system for surface characterization include high resolution and high sensitivity as well as the capability of identifying compounds and making in-situ measurements.

Loss and representativeness in a 43 year follow up of a national birth cohort

STUDY OBJECTIVE

The aim was to describe rates of loss and assessment of representativeness during 43 years of a national birth cohort study.

DESIGN

The study population is a class stratified random sample of all single, legitimate births that occurred during one single week in 1946; it has been studied at regular intervals, so far to 1989.

MAIN RESULTS

Losses through death and emigration were comparable to those in the national population of the same age. Response rates from the population resident in Britain have remained high, and the responding population is in most respects representative of the native population born in the early postwar years. Response rates within some serious physical illnesses did not differ from those of the healthy population.

CONCLUSIONS

The continuing high response rate and representativeness of this national birth cohort is likely to be the result of home based data collections and of the regular contact to provide feedback of information and to check addresses of the study population.

Accumulation of factors influencing respiratory illness in members of a national birth cohort and their offspring

STUDY OBJECTIVE

The aim was to investigate predictors of childhood lower respiratory tract illness in two generations, and predictors of adult lower respiratory disorders in the first generation.

DESIGN

Data on respiratory health and environmental factors from a national birth cohort study were examined from birth to 36 years. Data were also collected on the parents of the subjects and on the subjects' first born offspring from birth to eight years. Main outcome measures were: reports of lower respiratory tract illness before 2 years; lower respiratory tract illness of a week or more between age 20 and 36 years; regular phlegm production at 25 and 36 years; reports of wheeze or asthma at age 36 years; peak expiratory flow rate (PEFR) at age 36 years measured by nurses during home visits; and mothers' reports of lower respiratory illness in first born offspring before 2 years.

SUBJECTS

Subjects were a sample of 5362 single, legitimate births taken from all those occurring in England, Wales, and Scotland in one week in 1946, and studied regularly from birth to age 43 years. Data on the subjects' parents and on their 1676 first offspring born while they were aged 19-25 years were also collected.

MAIN RESULTS

Lower respiratory tract illness before 2 years fell from 25% in the population born in 1946 to 13% in their first born offspring. In those born in 1946, poor home environment, parental bronchitis, and atmospheric pollution were the best predictors of lower respiratory illness before 2 years, and these three factors and childhood lower respiratory illness and later smoking were the best predictors of adult lower respiratory tract problems. Risk factors for lower respiratory illness in the offspring were manual social class, parental and grandparental lower respiratory disease, and parental smoking.

CONCLUSIONS

Risks for adult lower respiratory problems accumulated in childhood through illness, poor social circumstances, and atmospheric pollution. Smoking exacerbated early life risks and was an independent risk factor. In the offspring generation, parental smoking was a risk factor for early life chest illness, together with parental illness and low social class. Reduction of prevalence in the offspring generation was probably accounted for by improvement in home circumstances, reduced atmospheric pollution, and lower rates of parental lower respiratory illness, but current rates of smoking seem likely to prevent much further reduction in early life lower respiratory illness, and thus in this aspect of risk for subsequent adult lower respiratory problems. The accumulation of risk in childhood and adolescence for later adult problems implies a long time scale for the reduction of adult lower respiratory disorders.

Chronic physical illness in childhood: psychological and social effects in adolescence and adult life

A national birth cohort followed for 36 years was used to compare the life chances of individuals with chronic physical illness in childhood with those of controls. The majority of those who had been chronically physically ill in childhood were found to differ very little in social and psychological circumstances by 36 years of age, but earlier in adult life there had been signs of difficulties. However, there was a disturbing tendency for those from lower social-group families to be in significantly worse social and psychological circumstances, and by 36 years they showed signs of relatively poor life chances and of basic social support, including the death of both parents.

Growth in utero, blood pressure in childhood and adult life, and mortality from cardiovascular disease

In national samples of 9921 10 year olds and 3259 adults in Britain systolic blood pressure was inversely related to birth weight. The association was independent of gestational age and may therefore be attributed to reduced fetal growth. This suggests that the intrauterine environment influences blood pressure during adult life. It is further evidence that the geographical differences in average blood pressure and mortality from cardiovascular disease in Britain partly reflect past differences in the intrauterine environment. Within England and Wales 10 year olds living in areas with high cardiovascular mortality were shorter and had higher resting pulse rates than those living in other areas. Their mothers were also shorter and had higher diastolic blood pressures. This suggests that there are persisting geographical differences in the childhood environment that predispose to differences in cardiovascular mortality.

Social and regional differences in food and alcohol consumption and their measurement in a national birth cohort

The problem of collecting detailed dietary information on a large population scattered throughout England, Wales and Scotland was resolved by use of a 7 day dietary diary, introduced at home interviews. Information on food types and quantities was coded to provide data on a wide range of nutrients. Reported levels of iron and fibre intake were found to be particularly low in relation to current recommended daily intakes, which were more often achieved by men than by women. Best dietary habits were associated with good educational attainment, whatever the social class of origin, but in women this was in some circumstances associated also with relatively high intakes of alcohol, protein and fats. Worst dietary habits were associated with low social class of family of origin and low educational attainment. Mean intakes of some nutrients varied significantly by region, in most cases independently of class and education. The implications of these findings are discussed.

Acute appendicitis and bathrooms in three samples of British children

The occurrence of appendicectomy in three national samples of British children was analysed in relation to household amenities, crowding in the home, and social class. The risk of having the operation depended on the amenities present in the home, in particular whether or not there was a bathroom. This risk was independent of social class. The findings support a relation between acute appendicitis and Western hygiene, which would explain the geographical distribution of the disease and its changing incidence over time. In the developing world, where children grow up in conditions of poor hygiene, there may be outbreaks of appendicitis when housing improves.

Follow-up of the first national birth cohort: findings from the Medical Research Council National Survey of Health and Development

The medical work of a 40 year birth cohort study is described in order to show the continuing associations of childhood factors with later life health, behaviour, illness and survival. Comparisons with the health of children born at later times show the importance of a sensitive monitoring of changes in child health. A summary of work on social and psychological topics is also given, together with a complete list of publications from the study.

Onset of obesity in a 36 year birth cohort study

A large national cohort of children studied from birth to 36 years was used to test the predictive value of childhood obesity for obesity in adult life. Only 21% (39) of obese 36 year olds had been obese at age 11 years, and even when associated social factors were taken into account the correctly predicted percentage was much lower than the prediction rate achieved using body mass data from age 26 years. The comparatively poor predictive value of childhood obesity and the association of adult obesity with educational achievements and socioeconomic circumstances of family of origin emphasise the need for encouraging good nutritional and exercise habits rather than placing undue emphasis on the control of childhood obesity.

Blood pressure in a national birth cohort at the age of 36 related to social and familial factors, smoking, and body mass

Blood pressure was measured in a birth cohort of 5362 subjects at the age of 36. The prevalence of hypertension in men (blood pressure greater than 140/90 mm Hg) was almost twice that in women, although women received treatment more often. Deaths of fathers of subjects from hypertensive and ischaemic heart disease were associated with significantly higher mean systolic and diastolic pressures in both sexes. Cigarette smoking was not strongly associated with blood pressure in men and not associated at all in women. Of the social factors, low social class of family of origin was associated with high blood pressure in both sexes; but the strongest association was with current body mass, and birth weight also contributed. Differences in blood pressures between the sexes may have been related to protective biological factors, such as endogenous sex hormones, in women and also to differences in types of employment, smoking habits, and body mass. Differences in blood pressures related to the social class of family of origin may reflect long term influences of class differences on diet, exercise, and educational achievement. The importance of measuring secular trends in obesity and blood pressures is emphasised.

Stigma in patients with early epilepsy: a national longitudinal study

Forty six cases of epilepsy were identified from the National Survey of Health and Development. An index of social visibility at school was constructed from teachers' reports of survey members' behaviour at 15 years of age. For the sample as a whole this index was significantly associated with poorer educational outcomes, after adjusting for social background and measured attainment, but was not associated with poor occupational achievement. However the index did not differentiate between epileptic and non-epileptic children. Although cases with epilepsy were shown to be more at risk of psychiatric disturbance, it is concluded that their lives were less disrupted than might have been expected, and that there is no evidence from this study that stigma affects the lives of those whose epilepsy was not complicated by other pathologies.

Apparent doubling of frequency of undescended testis in England and Wales in 1962-81

Examination of Hospital Inpatient Enquiry data for England and Wales for the years 1962-81 shows that the annual number of discharges with a diagnosis of undescended testicle has risen by a factor of 2.3. Cohort analysis suggests that the cumulative rate to age 15 of discharge for undescended testis has risen from 1.4% for the 1952 birth-cohort to 2.9% for the 1977 birth-cohort. Whether this is a reflection of an increase in true cryptorchidism is not known. Changes in known risk factors for cryptorchidism--exogenous oestrogen exposure, being first-born, and low birth-weight--cannot fully account for the apparent increase. With the tendency to carry out orchidopexies on apparently undescended testes at younger ages in order to preserve fertility, it is possible that a considerable number of boys with retractile testes that would have descended naturally at puberty are now being operated upon.

Assessing changes of hospital admission in preschool children. Critical evaluation

In discussing social class differentials in childhood mortality and morbidity a recent report on the British child health services suggests that it is possible to identify children at risk, and a government publication has indicated that health visitors (community nurses) could do this. The National Survey of Health and Development, a longitudinal study of over 5000 children regularly investigated from birth so far to age 31 years, gives an opportunity to test the usefulness of these propositions, since it has complete illness records of the study population and health visitors' assessments of their home circumstances, maternal care, and use of child welfare services. This study shows that these assessments were not particularly successful in identifying children at risk of hospital admissions for certain illnesses, even when more than one hospital admission or a serious illness later occurred. The maximum reduction of hospital costs by such identification would be little better than one-third and there would be an unquantifiable, but very real, stress imposed on families in which children were wrongly identified as at risk. It is suggested that further development of health visitors' work as family nurses would give a more effective form of child health care by providing greater sensitivity of surveillance, by involving parents in preventive care, and by making appropriate use of health visitors' skills.