Les vestiges humains gravettiens dans le Sud-Ouest de la France : bilan du projet Gravett’os

Cette communication présente les principaux résultats du projet Gravett’Os, qui porte sur du matériel anthropologique du Sud-Ouest de la France (découvertes récentes et reprises des collections anciennes) associé au Gravettien (34-24 000 cal BP). Ce projet a permis l’identification de 32 individus provenant de 5 sites (Cussac, Fournol, Gargas, Abri Pataud, Cro-Magnon). Nos études confortent les analyses précédentes sur les comportements au Gravettien : extrême mobilité et division sexuelle du..

The Genome of the Netherlands:design, and project goals

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean = 53 years; SD = 16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.</p

LEARN 2 MOVE 7-12 years: a randomized controlled trial on the effects of a physical activity stimulation program in children with cerebral palsy

<p>Abstract</p> <p>Background</p> <p>Regular participation in physical activities is important for all children to stay fit and healthy. Children with cerebral palsy have reduced levels of physical activity, compared to typically developing children. The aim of the LEARN 2 MOVE 7-12 study is to improve physical activity by means of a physical activity stimulation program, consisting of a lifestyle intervention and a fitness training program.</p> <p>Methods/Design</p> <p>This study will be a 6-month single-blinded randomized controlled trial with a 6-month follow up. Fifty children with spastic cerebral palsy, aged 7 to 12 years, with Gross Motor Function Classification System levels I-III, will be recruited in pediatric physiotherapy practices and special schools for children with disabilities. The children will be randomly assigned to either the intervention group or control group. The children in the control group will continue with their regular pediatric physiotherapy, and the children in the intervention group will participate in a 6-month physical activity stimulation program. The physical activity stimulation program consists of a 6-month lifestyle intervention, in combination with a 4-month fitness training program. The lifestyle intervention includes counseling the child and the parents to adopt an active lifestyle through Motivational Interviewing, and home-based physiotherapy to practise mobility-related activities in the daily situation. Data will be collected just before the start of the intervention (T0), after the 4-month fitness training program (T4), after the 6-month lifestyle intervention (T6), and after six months of follow-up (T12). Primary outcomes are physical activity, measured with the StepWatch Activity Monitor and with self-reports. Secondary outcomes are fitness, capacity of mobility, social participation and health-related quality of life. A random coefficient analysis will be performed to determine differences in treatment effect between the control group and the intervention group, with primary outcomes and secondary outcomes as the dependent variables.</p> <p>Discussion</p> <p>This is the first study that investigates the effect of a combined lifestyle intervention and fitness training on physical activity. Temporary effects of the fitness training are expected to be maintained by changes to an active lifestyle in daily life and in the home situation.</p> <p>Trial registration</p> <p>This study is registered in the Dutch Trial Register as NTR2099.</p

The Genome of the Netherlands: Design, and project goals

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project

Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations

Osteoarthritis affects over 300 million people worldwide. Here, we conduct a genome-wide association study meta-analysis across 826,690 individuals (177,517 with osteoarthritis) and identify 100 independently associated risk variants across 11 osteoarthritis phenotypes, 52 of which have not been associated with the disease before. We report thumb and spine osteoarthritis risk variants and identify differences in genetic effects between weight-bearing and non-weight-bearing joints. We identify sex-specific and early age-at-onset osteoarthritis risk loci. We integrate functional genomics data from primary patient tissues (including articular cartilage, subchondral bone, and osteophytic cartilage) and identify high-confidence effector genes. We provide evidence for genetic correlation with phenotypes related to pain, the main disease symptom, and identify likely causal genes linked to neuronal processes. Our results provide insights into key molecular players in disease processes and highlight attractive drug targets to accelerate translation

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with ‘true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05–0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r2, increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals