Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. Results: We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. Availability: The R package absfilter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

ICT-based system to predict and prevent falls (iStoppFalls): study protocol for an international multicenter randomized controlled trial

[EN] Background: Falls are very common, especially in adults aged 65 years and older. Within the current international European Commission's Seventh Framework Program (FP7) project 'iStoppFalls' an Information and Communication Technology (ICT) based system has been developed to regularly assess a person's risk of falling in their own home and to deliver an individual and tailored home-based exercise and education program for fall prevention. The primary aims of iStoppFalls are to assess the feasibility and acceptability of the intervention program, and its effectiveness to improve balance, muscle strength and quality of life in older people. Methods/Design: This international, multicenter study is designed as a single-blinded, two-group randomized controlled trial. A total of 160 community-dwelling older people aged 65 years and older will be recruited in Germany (n = 60), Spain (n = 40), and Australia (n = 60) between November 2013 and May 2014. Participants in the intervention group will conduct a 16-week exercise program using the iStoppFalls system through their television set at home. Participants are encouraged to exercise for a total duration of 180 minutes per week. The training program consists of a variety of balance and strength exercises in the form of video games using exergame technology. Educational material about a healthy lifestyle will be provided to each participant. Final reassessments will be conducted after 16 weeks. The assessments include physical and cognitive tests as well as questionnaires assessing health, fear of falling, quality of life and psychosocial determinants. Falls will be followed up for six months by monthly falls calendars. Discussion: We hypothesize that the regular use of this newly developed ICT-based system for fall prevention at home is feasible for older people. By using the iStoppFalls sensor-based exercise program, older people are expected to improve in balance and strength outcomes. In addition, the exercise training may have a positive impact on quality of life by reducing the risk of falls. Taken together with expected cognitive improvements, the individual approach of the iStoppFalls program may provide an effective model for fall prevention in older people who prefer to exercise at home.The authors are members of the iStoppFalls project. This project has received funding from the European Union’s Seventh Framework Programme for research, technological development, and demonstration under grant agreement no [287361]. The Australian arm is funded by an Australian National Health and Medical Research Council (NHMRC) EU collaboration grant (#1038210). The content of the manuscript does not represent the opinion of the European Community or NHMRC. The funding sources have no role in any aspects of this study. Yves J. Gschwind has been financially supported by a research grant from the Margarete and Walter Lichtenstein Foundation, Basel, Switzerland. Stephen R. Lord is supported by NHMRC as a Senior Principal Research Fellow and Kim Delbaere as a NHMRC Career Development Fellow. All other authors are supported by the iStoppFalls project, European Community Grant Agreement 287361. On behalf the iStoppFalls consortium, we would like to thank all the participants who take part in the study.Gschwind, YJ.; Eichberg, S.; Marston, HR.; Ejupi, A.; De Rosario Martínez, H.; Kroll, M.; Drobics, M.... (2014). ICT-based system to predict and prevent falls (iStoppFalls): study protocol for an international multicenter randomized controlled trial. BMC Geriatrics. 14(91):1-13. https://doi.org/10.1186/1471-2318-14-91S1131491Berchicci M, Lucci G, Di Russo F: Benefits of physical exercise on the aging brain: the role of the prefrontal cortex. 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The design of a purpose-built exergame for fall prediction and prevention for older people

Background Falls in older people represent a major age-related health challenge facing our society. Novel methods for delivery of falls prevention programs are required to increase effectiveness and adherence to these programs while containing costs. The primary aim of the Information and Communications Technology-based System to Predict and Prevent Falls (iStoppFalls) project was to develop innovative home-based technologies for continuous monitoring and exercise-based prevention of falls in community-dwelling older people. The aim of this paper is to describe the components of the iStoppFalls system. Methods The system comprised of 1) a TV, 2) a PC, 3) the Microsoft Kinect, 4) a wearable sensor and 5) an assessment and training software as the main components. Results The iStoppFalls system implements existing technologies to deliver a tailored home-based exercise and education program aimed at reducing fall risk in older people. A risk assessment tool was designed to identify fall risk factors. The content and progression rules of the iStoppFalls exergames were developed from evidence-based fall prevention interventions targeting muscle strength and balance in older people. Conclusions The iStoppFalls fall prevention program, used in conjunction with the multifactorial fall risk assessment tool, aims to provide a comprehensive and individualised, yet novel fall risk assessment and prevention program that is feasible for widespread use to prevent falls and fall-related injuries. This work provides a new approach to engage older people in home-based exercise programs to complement or provide a potentially motivational alternative to traditional exercise to reduce the risk of falling

Microarray-Based Maps of Copy-Number Variant Regions in European and Sub-Saharan Populations

The genetic basis of phenotypic variation can be partially explained by the presence of copy-number variations (CNVs). Currently available methods for CNV assessment include high-density single-nucleotide polymorphism (SNP) microarrays that have become an indispensable tool in genome-wide association studies (GWAS). However, insufficient concordance rates between different CNV assessment methods call for cautious interpretation of results from CNV-based genetic association studies. Here we provide a cross-population, microarray-based map of copy-number variant regions (CNVRs) to enable reliable interpretation of CNV association findings. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to scan the genomes of 1167 individuals from two ethnically distinct populations (Europe, N = 717; Rwanda, N = 450). Three different CNV-finding algorithms were tested and compared for sensitivity, specificity, and feasibility. Two algorithms were subsequently used to construct CNVR maps, which were also validated by processing subsamples with additional microarray platforms (Illumina 1M-Duo BeadChip, Nimblegen 385K aCGH array) and by comparing our data with publicly available information. Both algorithms detected a total of 42669 CNVs, 74% of which clustered in 385 CNVRs of a cross-population map. These CNVRs overlap with 862 annotated genes and account for approximately 3.3% of the haploid human genome

ICT-based system to predict and prevent falls (iStoppFalls): results from an international multicenter randomized controlled trial

Background: Falls and fall-related injuries are a serious public health issue. Exercise programs can effectively reduce fall risk in older people. The iStoppFalls project developed an Information and Communication Technology-based system to deliver an unsupervised exercise program in older people’s homes. The primary aims of the iStoppFalls randomized controlled trial were to assess the feasibility (exercise adherence, acceptability and safety) of the intervention program and its effectiveness on common fall risk factors. Methods: A total of 153 community-dwelling people aged 65+ years took part in this international, multicentre, randomized controlled trial. Intervention group participants conducted the exercise program for 16 weeks, with a recommended duration of 120 min/week for balance exergames and 60 min/week for strength exercises. All intervention and control participants received educational material including advice on a healthy lifestyle and fall prevention. Assessments included physical and cognitive tests, and questionnaires for health, fear of falling, number of falls, quality of life and psychosocial outcomes. Results: The median total exercise duration was 11.7 h (IQR = 22.0) over the 16-week intervention period. There were no adverse events. Physiological fall risk (Physiological Profile Assessment, PPA) reduced significantly more in the intervention group compared to the control group (F1,127 = 4.54, p = 0.035). There was a significant three-way interaction for fall risk assessed by the PPA between the high-adherence (>90 min/week; n = 18, 25.4 %), low-adherence (n = 53, 74.6 %) and control group (F2,125 = 3.12, n = 75, p = 0.044). Post hoc analysis revealed a significantly larger effect in favour of the high-adherence group compared to the control group for fall risk (p = 0.031), postural sway (p = 0.046), stepping reaction time (p = 0.041), executive functioning (p = 0.044), and quality of life (p for trend = 0.052). Conclusions: The iStoppFalls exercise program reduced physiological fall risk in the study sample. Additional subgroup analyses revealed that intervention participants with better adherence also improved in postural sway, stepping reaction, and executive function

Statistical Epistasis and Functional Brain Imaging Support a Role of Voltage-Gated Potassium Channels in Human Memory

Despite the current progress in high-throughput, dense genome scans, a major portion of complex traits' heritability still remains unexplained, a phenomenon commonly termed “missing heritability.” The negligence of analytical approaches accounting for gene-gene interaction effects, such as statistical epistasis, is probably central to this phenomenon. Here we performed a comprehensive two-way SNP interaction analysis of human episodic memory, which is a heritable complex trait, and focused on 120 genes known to show differential, memory-related expression patterns in rat hippocampus. Functional magnetic resonance imaging was also used to capture genotype-dependent differences in memory-related brain activity. A significant, episodic memory-related interaction between two markers located in potassium channel genes (KCNB2 and KCNH5) was observed (Pnominal combined = 0.000001). The epistatic interaction was robust, as it was significant in a screening (Pnominal = 0.0000012) and in a replication sample (Pnominal = 0.01). Finally, we found genotype-dependent activity differences in the parahippocampal gyrus (Pnominal = 0.001) supporting the behavioral genetics finding. Our results demonstrate the importance of analytical approaches that go beyond single marker statistics of complex traits

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells.

Medullary thymic epithelial cells (mTECs) play a critical role in central immune tolerance by mediating negative selection of autoreactive T cells through the collective expression of the peripheral self-antigen compartment, including tissue-specific antigens (TSAs). Recent work has shown that gene-expression patterns within the mTEC compartment are heterogenous and include multiple differentiated cell states. To further define mTEC development and medullary epithelial lineage relationships, we combined lineage tracing and recovery from transient in vivo mTEC ablation with single-cell RNA-sequencing in Mus musculus. The combination of bioinformatic and experimental approaches revealed a non-stem transit-amplifying population of cycling mTECs that preceded Aire expression. We propose a branching model of mTEC development wherein a heterogeneous pool of transit-amplifying cells gives rise to Aire- and Ccl21a-expressing mTEC subsets. We further use experimental techniques to show that within the Aire-expressing developmental branch, TSA expression peaked as Aire expression decreased, implying Aire expression must be established before TSA expression can occur. Collectively, these data provide a roadmap of mTEC development and demonstrate the power of combinatorial approaches leveraging both in vivo models and high-dimensional datasets

Targeted Perturb-seq enables genome-scale genetic screens in single cells

The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer–target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer–target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans Article Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Graphical Abstract Highlights SUMMARY Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain