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, HapMap's 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

Positive parenting in foster care: Testing the effectiveness of a video-feedback intervention program on foster parents’ behavior and attitudes

The current randomized controlled trial examined the effectiveness of Video-feedback Intervention to promote Positive Parenting and Sensitive Discipline in Foster Care (VIPP-FC) on parenting behavior and attitudes in foster parents (N = 60, 31–61 years, 83% female). The intervention group (n = 30) received VIPP-FC, consisting of six sessions. During the first four sessions, a specific theme from Video-feedback Intervention to promote Positive Parenting and Sensitive Discipline (VIPP-SD; e.g., attachment vs. exploration behavior), and an additional foster care theme (e.g., subtle or missing attachment signals) are discussed. Each theme is discussed during the consecutive sessions and the last two sessions are booster sessions during which all themes are discussed. The control group (n = 30) received a dummy intervention consisting of six telephone calls about general child developmental topics. The Ainsworth Scales for sensitivity and non-interference, the Erickson scale for supportive presence, and the Questionnaire Attitudes towards Parenting were used to measure parental sensitivity, sensitive discipline, and attitudes towards parenting, respectively. The intervention and control group did not differ on demographic characteristics or outcome variables at pretest. Multilevel analyses based on the intent-to-treat principle yielded no evidence that VIPP-FC was more effective in improving foster parents’ sensitive parenting behavior or eliciting more positive attitudes compared to the control condition. We suggest that the outcomes in this study may be explained by a possible selection bias, which may have resulted in a ceiling effect. Future research might include foster families that experience more severe challenges (i.e., elevated levels of child behavior problems) or indicate a need for help and support

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

Background: 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 children's 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. Methods: Genetic variants in 12 autosomal dopaminergic genes were available in an ethnically homogenous part of a population-based cohort. Harsh parenting was assessed with maternal (n = 1881) and paternal (n = 1710) reports at age 3. Externalizing behavior was assessed with the Child Behavior Checklist (CBCL) at age 5 (71 ± 3.7 months). We conducted gene-set analyses of the association between variation in dopaminergic genes and externalizing behavior, stratified for harsh parenting. Results: The association was statistically significant or approached significance for children without harsh parenting experiences, but was absent in the group with harsh parenting. Similarly, significant associations between single genes and externalizing behavior were only found in the group without harsh parenting. Effect sizes in the groups with and without harsh parenting did not differ significantly. Gene-environment interaction tests were conducted for individual genetic variants, resulting in two significant interaction effects (rs1497023 and rs4922132) after correction for multiple testing. Conclusion: Our findings are suggestive of G × E interplay, with associations between dopamine genes and externalizing behavior present in children without harsh parenting, but not in children with harsh parenting experiences. Harsh parenting may overrule the role of genetic factors in externalizing behavior. Gene-based and gene-set analyses offer promising new alternatives to analyses focusing on single candidate polymorphisms when examining the interplay between genetic and environmental factors