Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline—NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications

The health and housing in transition study: A longitudinal study of the health of homeless and vulnerably housed adults in three Canadian cities

Objectives: While substantial research has demonstrated the poor health status of homeless populations, the health status of vulnerably housed individuals is largely unknown. Furthermore, few longitudinal studies have assessed the impact of housing transitions on health. The health and housing in transition (HHiT) study is a prospective cohort study that aims to track the health and housing status of a representative sample of homeless and vulnerably housed single adults in three Canadian cities (Toronto, Ottawa, and Vancouver). This paper discusses the HHiT study methodological recruitment strategies and follow-up procedures, including a discussion of the limitations and challenges experienced to date. Methods: Participants (n = 1,192) were randomly selected at shelters, meal programmes, community health centres, drop-in centres, rooming houses, and single-room occupancy hotels from January to December 2009 and are being re-interviewed every 12 months for a 2-year period. Results: At baseline, over 85% of participants reported having at least one chronic health condition, and over 50% reported being diagnosed with a mental health problem. Conclusions: Our findings suggest that, regardless of housing status, participants had extremely poor overall health

Domain Altering SNPs in the Human Proteome and Their Impact on Signaling Pathways

Single nucleotide polymorphisms (SNPs) constitute an important mode of genetic variations observed in the human genome. A small fraction of SNPs, about four thousand out of the ten million, has been associated with genetic disorders and complex diseases. The present study focuses on SNPs that fall on protein domains, 3D structures that facilitate connectivity of proteins in cell signaling and metabolic pathways. We scanned the human proteome using the PROSITE web tool and identified proteins with SNP containing domains. We showed that SNPs that fall on protein domains are highly statistically enriched among SNPs linked to hereditary disorders and complex diseases. Proteins whose domains are dramatically altered by the presence of an SNP are even more likely to be present among proteins linked to hereditary disorders. Proteins with domain-altering SNPs comprise highly connected nodes in cellular pathways such as the focal adhesion, the axon guidance pathway and the autoimmune disease pathways. Statistical enrichment of domain/motif signatures in interacting protein pairs indicates extensive loss of connectivity of cell signaling pathways due to domain-altering SNPs, potentially leading to hereditary disorders

Interpretable machine learning models for classifying low back pain status using functional physiological variables.

PURPOSE:To evaluate the predictive performance of statistical models which distinguishes different low back pain (LBP) sub-types and healthy controls, using as input predictors the time-varying signals of electromyographic and kinematic variables, collected during low-load lifting. METHODS:Motion capture with electromyography (EMG) assessment was performed on 49 participants [healthy control (con) = 16, remission LBP (rmLBP) = 16, current LBP (LBP) = 17], whilst performing a low-load lifting task, to extract a total of 40 predictors (kinematic and electromyographic variables). Three statistical models were developed using functional data boosting (FDboost), for binary classification of LBP statuses (model 1: con vs. LBP; model 2: con vs. rmLBP; model 3: rmLBP vs. LBP). After removing collinear predictors (i.e. a correlation of > 0.7 with other predictors) and inclusion of the covariate sex, 31 predictors were included for fitting model 1, 31 predictors for model 2, and 32 predictors for model 3. RESULTS:Seven EMG predictors were selected in model 1 (area under the receiver operator curve [AUC] of 90.4%), nine predictors in model 2 (AUC of 91.2%), and seven predictors in model 3 (AUC of 96.7%). The most influential predictor was the biceps femoris muscle (peak [Formula: see text]  = 0.047) in model 1, the deltoid muscle (peak [Formula: see text] =  0.052) in model 2, and the iliocostalis muscle (peak [Formula: see text] =  0.16) in model 3. CONCLUSION:The ability to transform time-varying physiological differences into clinical differences could be used in future prospective prognostic research to identify the dominant movement impairments that drive the increased risk. These slides can be retrieved under Electronic Supplementary Material

The Feasibility of performing resistance exercise with acutely ill hospitalized older adults

BACKGROUND: For older adults, hospitalization frequently results in deterioration of mobility and function. Nevertheless, there are little data about how older adults exercise in the hospital and definitive studies are not yet available to determine what type of physical activity will prevent hospital related decline. Strengthening exercise may prevent deconditioning and Pilates exercise, which focuses on proper body mechanics and posture, may promote safety. METHODS: A hospital-based resistance exercise program, which incorporates principles of resistance training and Pilates exercise, was developed and administered to intervention subjects to determine whether acutely-ill older patients can perform resistance exercise while in the hospital. Exercises were designed to be reproducible and easily performed in bed. The primary outcome measures were adherence and participation. RESULTS: Thirty-nine ill patients, recently admitted to an acute care hospital, who were over age 70 [mean age of 82.0 (SD= 7.3)] and ambulatory prior to admission, were randomized to the resistance exercise group (19) or passive range of motion (ROM) group (20). For the resistance exercise group, participation was 71% (p = 0.004) and adherence was 63% (p = 0.020). Participation and adherence for ROM exercises was 96% and 95%, respectively. CONCLUSION: Using a standardized and simple exercise regimen, selected, ill, older adults in the hospital are able to comply with resistance exercise. Further studies are needed to determine if resistance exercise can prevent or treat hospital-related deterioration in mobility and function

A comparative genomics multitool for scientific discovery and conservation

A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.Peer reviewe

Older People, Sense of Coherence and Community

Population ageing is a global trend and even though years added to life often are lived in good health; it will have an impact on healthcare, housing and facilities, and social security costs. Healthy ageing in place, especially in one’s own home and community, increasingly receives attention from health professionals, researchers, and policymakers. In this chapter, we first discuss the meaning of the concept of healthy ageing, and how Sense of Coherence contributes to this process. Next, we discuss the characteristics of the community in which older people live their lives and how the community can provide resources (GRR and SRR) to strengthen Sense of Coherence and hence perceived well-being and quality of life