Ralph C.A. Rippe

Splitting hair for cortisol? Associations of socio-economic status, ethnicity, hair color, gender and other child characteristics with hair cortisol and cortisone

The aim of this study was to examine associations of SES and ethnicity with hair cortisol and cortisone and to identify potential child and family characteristics that can assist in choosing covariates and potential confounders for analyses involving hair cortisol and cortisone concentrations. Hair samples were collected in 2484 6-year-old children from the Generation R Study, a prospective cohort in Rotterdam, the Netherlands. Measurements for cortisol and cortisone were used as the outcome in regression analyses. Predictors were SES, ethnicity, hair color and child characteristics such as birthweight, gestational age at birth, BMI, disease, allergy, and medication use. Lower family income, more children to be supported by this income, higher BMI and darker hair color were associated with higher hair cortisol and cortisone levels. Boys also showed higher levels. Ethnicity (Dutch and North European descent) was related to lower levels. High amounts of sun in the month of hair collection was related to higher levels of cortisone only. More recent hair washing was related to lower levels of cortisol and cortisone. Gestational age at birth, birth weight, age, medication use, hair washing frequency, educational level of the mother, marital status of the mother, disease and allergy were not associated with cortisol or cortisone levels. Our results serve as a starting point for choosing covariates and confounders in studies of substantive predictors or outcomes. Gender, BMI, income, the number of persons in a household, ethnicity, hair color and recency of hair washing are strongly suggested to take into account.

An epigenome-wide association meta-analysis of prenatal maternal stress in neonates: A model approach for replication

ABSTRACT Prenatal maternal stress exposure has been associated with neonatal differential DNA methylation. However, the available evidence in humans is largely based on candidate gene methylation studies, where only a few CpG sites were evaluated. The aim of this study was to examine the association between prenatal exposure to maternal stress and offspring genome-wide cord blood methylation using different methods. First, we conducted a meta-analysis and follow-up pathway analyses. Second, we used novel region discovery methods [i.e., differentially methylated regions (DMRs) analyses]. To this end, we used data from two independent population-based studies, the Generation R Study (n = 912) and the Avon Longitudinal Study of Parents and Children (ALSPAC, n = 828), to (i) measure genome-wide DNA methylation in cord blood and (ii) extract a prenatal maternal stress composite. The meta-analysis (ntotal = 1,740) revealed no epigenome-wide (meta P <1.00e-07) associations of prenatal maternal stress exposure with neonatal differential DNA methylation. Follow-up analyses of the top hits derived from our epigenome-wide meta-analysis (meta P <1.00e-04) indicated an over-representation of the methyltransferase activity pathway. We identified no Bonferroni-corrected (P <1.00e-06) DMRs associated with prenatal maternal stress exposure. Combining data from two independent population-based samples in an epigenome-wide meta-analysis, the current study indicates that there are no large effects of prenatal maternal stress exposure on neonatal DNA methylation. Such replication efforts are essential in the search for robust associations, whether derived from candidate gene methylation or epigenome-wide studies.

Visualization of genomic changes by segmented smoothing using an L0 penalty.

Copy number variations (CNV) and allelic imbalance in tumor tissue can show strong segmentation. Their graphical presentation can be enhanced by appropriate smoothing. Existing signal and scatterplot smoothers do not respect segmentation well. We present novel algorithms that use a penalty on the norm of differences of neighboring values. Visualization is our main goal, but we compare classification performance to that of VEGA.

Expectations about the effectiveness of pain- and itch-relieving medication administered via different routes

Placebo effects on pain have been found to vary in size for different routes of medication administration (e.g. oral vs. injection). This has important implications for both clinical research and practice. To enhance our understanding of these differential placebo effects, research on the underlying expectations about multiple routes and symptoms other than pain is vital.

Mild perinatal adversities moderate the association between maternal harsh parenting and hair cortisol: Evidence for differential susceptibility

It has been shown that following exposure to mild perinatal adversity, children have greater susceptibility to both the negative and positive aspects of their subsequent environment. In a large population-based cohort study (N = 1,776), we investigated whether mild perinatal adversity moderated the association between maternal harsh parenting and childrens hair cortisol levels, a biomarker of chronic stress. Mild perinatal adversity was defined as late preterm birth (gestational age at birth of 34-37 weeks, 6 days) or small for gestational age (birth weight between the 2.5th and 10th percentile for full term gestational age). Harsh parenting was assessed by maternal self-report at 3 years. Childrens hair cortisol concentrations were measured from hair samples collected at age 6. There were no significant bivariate associations between mild perinatal adversities and harsh parenting and hair cortisol. However, mild perinatal adversities moderated the association between maternal harsh parenting and hair cortisol levels. Children with mild perinatal adversity had lower cortisol levels if parented more harshly and higher cortisol levels in the absence of harsh parenting than children who did not experience mild perinatal adversity. These results provide further evidence that mild perinatal adversity is a potential marker of differential susceptibility to environmental influences.

Beyond main effects of gene‐sets: harsh parenting moderates the association between a dopamine gene‐set and child externalizing behavior

In a longitudinal cohort study, we investigated the interplay of harsh parenting and genetic variation across a set of functionally related dopamine genes, in association with childrens externalizing behavior. This is one of the first studies to employ gene‐based and gene‐set approaches in tests of Gene by Environment (G × E) effects on complex behavior. This approach can offer an important alternative or complement to candidate gene and genome‐wide environmental interaction (GWEI) studies in the search for genetic variation underlying individual differences in behavior.

Changes in face-specific neural processing explain reduced cuteness and approachability of infants with cleft lip

ABSTRACT The current study investigated whether changes in the neural processing of faces of infants with a facial abnormality – a cleft lip – mediate effects of the cleft lip on judgments of infant cuteness and approachability. Event-related potentials (ERPs) in response to pictures of faces of healthy infants and infants with a cleft lip, and ratings of cuteness and approachability of these infant faces, were obtained from 30 females. Infants with a cleft lip were rated as less attractive (less cute and approachable) than healthy infants, and both the N170 and P2 components of the ERP were of reduced amplitude in response to pictures of infants with a cleft lip. Importantly, decreased configural processing of infant faces with a cleft lip, as evidenced by reduced N170 amplitudes, mediated the reduced attractiveness ratings for infants with a cleft lip compared to healthy infants. Our findings help elucidate the mechanisms behind the less favorable responses to infants with a cleft lip, highlighting the role of face-specific rather than domain-general neural processes.

Reliable Single Chip Genotyping with Semi-Parametric Log-Concave Mixtures

The common approach to SNP genotyping is to use (model-based) clustering per individual SNP, on a set of arrays. Genotyping all SNPs on a single array is much more attractive, in terms of flexibility, stability and applicability, when developing new chips. A new semi-parametric method, named SCALA, is proposed. It is based on a mixture model using semi-parametric log-concave densities. Instead of using the raw data, the mixture is fitted on a two-dimensional histogram, thereby making computation time almost independent of the number of SNPs. Furthermore, the algorithm is effective in low-MAF situations. Comparisons between SCALA and CRLMM on HapMap genotypes show very reliable calling of single arrays. Some heterozygous genotypes from HapMap are called homozygous by SCALA and to lesser extent by CRLMM too. Furthermore, HapMaps NoCalls (NN) could be genotyped by SCALA, mostly with high probability. The software is available as R scripts from the website www.math.leidenuniv.nl/~rrippe.

Correction of fluorescence bias on Affymetrix genotyping microarrays

Fluorescence signals obtained from microarrays for single nucleotide polymorphism genotyping show systematic strong variations in the levels for single nucleotide polymorphisms and arrays as well as genotypes. Linear models that take all three effects into account fit very well. Once the model parameters have been estimated for a set of reference arrays, they can be used to calibrate new arrays in a simple way, thereby improving genotyping and analysis of copy number variations and allelic imbalance. Copyright