Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes

There is increasing interest within the genetics community in estimating the relative contribution of parental genetic effects on offspring phenotypes. Here we describe the user-friendly M-GCTA software package used to estimate the proportion of phenotypic variance explained by maternal (or alternatively paternal) and offspring genotypes on offspring phenotypes. The tool requires large studies where genome-wide genotype data are available on mother- (or alternatively father-) offspring pairs. The software includes several options for data cleaning and quality control, including the ability to detect and automatically remove cryptically related pairs of individuals. It also allows users to construct genetic relationship matrices indexing genetic similarity across the genome between parents and offspring, enabling the estimation of variance explained by maternal (or alternatively paternal) and offspring genetic effects. We evaluated the performance of the software using a range of data simulations and estimated the computing time and memory requirements. We demonstrate the use of M-GCTA on previously analyzed birth weight data from two large population based birth cohorts, the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Norwegian Mother and Child Cohort Study (MoBa). We show how genetic variation in birth weight is predominantly explained by fetal genetic rather than maternal genetic sources of variation

Non-thermal transport of energy driven by photoexcited carriers in switchable solid states of GeTe

Phase change alloys have seen widespread use from rewritable optical discs to the present day interest in their use in emerging neuromorphic computing architectures. In spite of this enormous commercial interest, the physics of carriers in these materials is still not fully understood. Here, we describe the time and space dependence of the coupling between photoexcited carriers and the lattice in both the amorphous and crystalline states of one phase change material, GeTe. We study this using a time-resolved optical technique called picosecond acoustic method to investigate the \textit{in situ} thermally assisted amorphous to crystalline phase transformation in GeTe. Our work reveals a clear evolution of the electron-phonon coupling during the phase transformation as the spectra of photoexcited acoustic phonons in the amorphous ($a$-GeTe) and crystalline ($\alpha$-GeTe) phases are different. In particular and surprisingly, our analysis of the photoinduced acoustic pulse duration in crystalline GeTe suggests that a part of the energy deposited during the photoexcitation process takes place over a distance that clearly exceeds that defined by the pump light skin depth. In the opposite, the lattice photoexcitation process remains localized within that skin depth in the amorphous state. We then demonstrate that this is due to supersonic diffusion of photoexcited electron-hole plasma in the crystalline state. Consequently these findings prove the existence of a non-thermal transport of energy which is much faster than lattice heat diffusion

Smoking during pregnancy and its effect on placental weight: a Mendelian randomization study

This is the final version. Available on open access from BMC via the DOI in this recordAvailability of data and materials: The data in ALSPAC is fully available, via managed systems, to any researchers. The managed system is a requirement of the study funders, but access is not restricted on the basis of overlap with other applications to use the data or on the basis of peer review of the proposed science. The ALSPAC data management plan describes in detail the policy regarding data sharing, which is through a system of managed open access. The following steps highlight how to apply for access to the data included in this paper and all other ALSPAC data. (1) Please read the ALSPAC access policy, which describes the process of accessing the data and samples in detail and outlines the costs associated with doing so. (2) You may also find it useful to browse the fully searchable ALSPAC research proposals database, which lists all research projects that have been approved since April 2011. (3) Please submit your research proposal for consideration by the ALSPAC Executive Committee. You will receive a response within 10 working days to advise you whether your proposal has been approved. If you have any questions about accessing data, please email [email protected]. Data from the Norwegian Mother, Father and Child Cohort Study and the Medical Birth Registry of Norway used in this study are managed by the national health register holders in Norway (Norwegian Institute of public health) and can be made available to researchers, provided approval from the Regional Committees for Medical and Health Research Ethics (REC), compliance with the EU General Data Protection Regulation (GDPR) and approval from the data owners. The consent given by the participants does not open for storage of data on an individual level in repositories or journals. Researchers who want access to data sets for replication should apply through helsedata.no. Access to data sets requires approval from The Regional Committee for Medical and Health Research Ethics in Norway and an agreement with MoBa.Background The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery. Methods We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (N = 690 to 804) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (N = 4267 to 4606). The sample size depends on the smoking definition used for different analyses. The analysis was performed in pre-pregnancy smokers only, due to the specific role of the single-nucleotide polymorphism (SNP) rs1051730 (CHRNA5 – CHRNA3 – CHRNB4) in affecting smoking cessation but not initiation. Results Fixed effect meta-analysis showed a 182 g [95%CI: 29,335] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal effect on placental weight was 11 g [95%CI: 1,21] per cigarette per day. Similarly, smoking at the end of pregnancy was causally associated with higher placental weight. Using the residuals of birth weight regressed on placental weight as the outcome, we showed evidence of lower offspring birth weight relative to the placental weight, both for continuing smoking at the start of pregnancy as well as continuing smoking throughout pregnancy (change in z-score birth weight adjusted for z-score placental weight: -0.8 [95%CI: -1.6,-0.1]). Conclusion Our results suggest that continued smoking during pregnancy causes higher placental weights

Roadmap for a precision-medicine initiative in the Nordic region

The Nordic region, comprising primarily Denmark, Estonia, Finland, Iceland, Norway and Sweden, has many of the necessary characteristics for being at the forefront of genome-based precision medicine. These include egalitarian and universal healthcare, expertly curated patient and population registries, biobanks, large population-based prospective cohorts linked to registries and biobanks, and a widely embraced sense of social responsibility that motivates public engagement in biomedical research. However, genome-based precision medicine can be achieved only through coordinated action involving all actors in the healthcare sector. Now is an opportune time to organize scientists in the Nordic region, together with other stakeholders including patient representatives, governments, pharmaceutical companies, academic institutions and funding agencies, to initiate a Nordic Precision Medicine Initiative. We present a roadmap for how this organization can be created. The Initiative should facilitate research, clinical trials and knowledge transfer to meet regional and global health challenges.Non peer reviewe

Diversity in Protein Glycosylation among Insect Species

status: publishe

A proteomics sample metadata representation for multiomics integration and big data analysis

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.publishedVersio