The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three diverse human populations. We show that rates of indel mutagenesis are highly heterogeneous, with 43%-48% of indels occurring in 4.03% of the genome, whereas in the remaining 96% their prevalence is 16 times lower than SNPs. Polymerase slippage can explain upwards of three-fourths of all indels, with the remainder being mostly simple deletions in complex sequence. However, insertions do occur and are significantly associated with pseudo-palindromic sequence features compatible with the fork stalling and template switching (FoSTeS) mechanism more commonly associated with large structural variations. We introduce a quantitative model of polymerase slippage, which enables us to identify indel-hypermutagenic protein-coding genes, some of which are associated with recurrent mutations leading to disease. Accounting for mutational rate heterogeneity due to sequence context, we find that indels across functional sequence are generally subject to stronger purifying selection than SNPs. We find that indel length modulates selection strength, and that indels affecting multiple functionally constrained nucleotides undergo stronger purifying selection. We further find that indels are enriched in associations with gene expression and find evidence for a contribution of nonsense-mediated decay. Finally, we show that indels can be integrated in existing genome-wide association studies (GWAS); although we do not find direct evidence that potentially causal protein-coding indels are enriched with associations to known disease-associated SNPs, our findings suggest that the causal variant underlying some of these associations may be indels.

Changes in Motor Competence after a Brief Physical Education Intervention Program in 4 and 5-Year-Old Preschool Children.

Low motor competence (MC) can cause low participation in physical activities in preschool children, and together with a high caloric intake, it can lead to obesity. Interventions on motor skills are effective in the short term to improve MC, therefore the objectives of this study were (1) to investigate the effect of a short six-week program on levels of motor competence in preschool children, and (2) to examine the effects of gender-based intervention. A total of 156 preschool children (5.20 ± 0.54 years old) from Lugo (Spain) participated. A quasi-experimental pre-post-test design was used with a control group of 76 students. The Movement Assessment Battery for Children-2nd Edition (MABC-2) was used to collect the data. Significant differences between the control and experimental groups were found after the intervention program in aiming and catching (p < 0.001), balance (p < 0.001), the total score of eight tests (p < 0.001), and total percentile score (p < 0.001). The results regarding gender in the experimental group showed a reduction in differences with respect to the initial results except in aiming and catching, where scores were higher in boys. The data suggest that the application of specific intervention programs in MC could positively influence the improvement of MC in preschool children, thus reducing differences between genders.

Perceptions of the Body and Body Dissatisfaction in Primary Education Children According to Gender and Age. A Cross-Sectional Study.

Body image (BI) is a trending topic of study since health problems derived from a negative perception of the body are increasing and affecting people of all ages, with an increasing incidence among children from the age of eight. The objective of this study was to evaluate the current perception of the body against the desired body and the degree of body satisfaction of Galician primary education students. A total of 355 students (167 boys (47%)) between 9 and 12 years old participated (mean = 10.53; SD = 0.84). Sociodemographic data (sex, age, height, and weight) were collected, and the Figure Rating Scale was used. There are statistically significant differences between boys and girls in the current perceived figure (p = 0.003) and in the desired figure (p < 0.001). Depending on age, the differences were in current (p = 0.010) and desired (p = 0.021) body perception. In conclusion, boys perceive themselves as having a larger figure than girls do, but this perception is far from reality according to the body mass index. For the desired figure, both boys and girls want to be slimmer, but girls want a slimmer figure. Regarding age, the current perceived figure size increases with age as it increases in those students dissatisfied with their body.

Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export.

Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells. We also observe more interindividual variability between exosomal samples than between cellular ones and identify four miRNA expression quantitative trait loci shared between cells and exosomes. Our findings indicate that genomically colocated miRNAs can be exported together and highlight the variability in exosomal miRNA levels between individuals as relevant for exosome use as diagnostics.

Transcriptome analysis reveals differential splicing events in IPF lung tissue.

Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%), and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%). We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10) and POSTN (RNA-Seq adjusted pval = 2.06e-09), which encode the extracellular matrix proteins collagen alpha-3(VI) and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.

Transcriptome analysis reveals differential splicing events in IPF lung tissue.

Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of proteins and networks are disrupted. Interrogation of the transcriptome through RNA sequencing (RNA-Seq) enables the determination of genes whose differential expression is most significant in IPF, as well as the detection of alternative splicing events which are not easily observed with traditional microarray experiments. We sequenced messenger RNA from 8 IPF lung samples and 7 healthy controls on an Illumina HiSeq 2000, and found evidence for substantial differential gene expression and differential splicing. 873 genes were differentially expressed in IPF (FDR<5%), and 440 unique genes had significant differential splicing events in at least one exonic region (FDR<5%). We used qPCR to validate the differential exon usage in the second and third most significant exonic regions, in the genes COL6A3 (RNA-Seq adjusted pval = 7.18e-10) and POSTN (RNA-Seq adjusted pval = 2.06e-09), which encode the extracellular matrix proteins collagen alpha-3(VI) and periostin. The increased gene-level expression of periostin has been associated with IPF and its clinical progression, but its differential splicing has not been studied in the context of this disease. Our results suggest that alternative splicing of these and other genes may be involved in the pathogenesis of IPF. We have developed an interactive web application which allows users to explore the results of our RNA-Seq experiment, as well as those of two previously published microarray experiments, and we hope that this will serve as a resource for future investigations of gene regulation in IPF.