ALBERT

Description: Background: Preterm delivery is the leading cause of neonatal morbidity and mortality. Two-thirds of preterm deliveries are idiopathic. The initiating molecular mechanisms behind spontaneous preterm delivery are unclear. Umbilical cord blood DNA samples are an easy source of material to study the neonatal state at birth. DNA methylation changes can be exploited as markers to identify spontaneous preterm delivery. To identify methylation differences specific to idiopathic preterm delivery, we assessed genome-wide DNA methylation changes in 24 umbilical cord blood samples (UCB) using the 450 K Illumina methylation array. After quality control, conclusions were based on 11 term and 11 idiopathic preterm born neonates. The differentially methylated positions (DMPs) specific for preterm/term delivery, neonatal sex, use of oxytocin and mode of initiation of labor were calculated by controlling the FDR p value at 0.05. Results: The analysis identifies 1855 statistically significant DMPs between preterm and term deliveries of which 508 DMPs are also attributable to clinical variables other than preterm versus term delivery.1347 DMPs are unique to term vs preterm delivery, of which 196 DMPs do not relate to gestational age as such. Pathway analysis indicated enrichment of genes involved in calcium signalling, myometrial contraction and relaxation pathways. The 1151 DMPs that correlate with advancing gestational age (p 

Description: Shared decision-making can improve patient satisfaction and outcomes. To participate in shared decision-making, patients need information about the potential risks and benefits of treatment options. Our team h...

Description: BioBin is a bioinformatics software package developed to automate the process of binning rare variants into groups for statistical association analysis using a biological knowledge-driven framework. BioBin col...

Description: Background: We present a compendium of N-ethyl-N-nitrosourea (ENU)-induced mouse mutations, identified in our laboratory over a period of 10 years either on the basis of phenotype or whole genome and/or whole exome sequencing, and archived in the Mutagenetix database. Our purpose is threefold: 1) to formally describe many point mutations, including those that were not previously disclosed in peer-reviewed publications; 2) to assess the characteristics of these mutations; and 3) to estimate the likelihood that a missense mutation induced by ENU will create a detectable phenotype.FindingsIn the context of an ENU mutagenesis program for C57BL/6J mice, a total of 185 phenotypes were tracked to mutations in 129 genes. In addition, 402 incidental mutations were identified and predicted to affect 390 genes. As previously reported, ENU shows strand asymmetry in its induction of mutations, particularly favoring T to A rather than A to T in the sense strand of coding regions and splice junctions. Some amino acid substitutions are far more likely to be damaging than others, and some are far more likely to be observed. Indeed, from among a total of 494 non-synonymous coding mutations, ENU was observed to create only 114 of the 182 possible amino acid substitutions that single base changes can achieve. Based on differences in overt null allele frequencies observed in phenotypic vs. non-phenotypic mutation sets, we infer that ENU-induced missense mutations create detectable phenotype only about 1 in 4.7 times. While the remaining mutations may not be functionally neutral, they are, on average, beneath the limits of detection of the phenotypic assays we applied. Conclusions: Collectively, these mutations add to our understanding of the chemical specificity of ENU, the types of amino acid substitutions it creates, and its efficiency in causing phenovariance. Our data support the validity of computational algorithms for the prediction of damage caused by amino acid substitutions, and may lead to refined predictions as to whether specific amino acid changes are responsible for observed phenotypes. These data form the basis for closer in silico estimations of the number of genes mutated to a state of phenovariance by ENU within a population of G3 mice.

Description: MotivationNext-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions. Ensuring appropriate accuracy and quality in variant calling can come at a computational cost. Results: We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study. Conclusions: We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging ‘big data’ problems in biomedical research brought on by the expansion of NGS technologies.

Description: Yarrowia lipolytica is an oleaginous ascomycete yeast that stores lipids in response to limitation of nitrogen. While the enzymatic pathways responsible for neutral lipid accumulation ...

Description: Background: Despite heritability estimates of 40–70 % for obesity, less than 2 % of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI. Methods: Using genotypic data from 18,686 individuals across five study cohorts – ARIC, CARDIA, FHS, CHS, MESA – we filtered SNPs (Single Nucleotide Polymorphisms) using two parallel approaches. SNPs were filtered either on the strength of their main effects of association with BMI, or on the number of knowledge sources supporting a specific SNP-SNP interaction in the context of BMI. Filtered SNPs were specifically analyzed for interactions that are highly associated with BMI using QMDR (Quantitative Multifactor Dimensionality Reduction). QMDR is a nonparametric, genetic model-free method that detects non-linear interactions associated with a quantitative trait. Results: We identified seven novel, epistatic models with a Bonferroni corrected p-value of association 

Description: Background: B cell lymphoma 2 (Bcl-2) proteins are the central regulators of apoptosis. The two bcl-2 genes in Drosophila modulate the response to stress-induced cell death, but not developmental cell death. Because null mutants are viable, Drosophila provides an optimum model system to investigate alternate functions of Bcl-2 proteins. In this report, we explore the role of one bcl-2 gene in nutrient stress responses. Results: We report that starvation of Drosophila larvae lacking the bcl-2 gene, buffy, decreases survival rate by more than twofold relative to wild-type larvae. The buffy null mutant reacted to starvation with the expected responses such as inhibition of target of rapamycin (Tor) signaling, autophagy initiation and mobilization of stored lipids. However, the autophagic response to starvation initiated faster in larvae lacking buffy and was inhibited by ectopic buffy. We demonstrate that unusually high basal Tor signaling, indicated by more phosphorylated S6K, was detected in the buffy mutant and that removal of a genomic copy of S6K, but not inactivation of Tor by rapamycin, reverted the precocious autophagy phenotype. Instead, Tor inactivation also required loss of a positive nutrient signal to trigger autophagy and loss of both was sufficient to activate autophagy in the buffy mutant even in the presence of enforced phosphoinositide 3-kinase (PI3K) signaling. Prior to starvation, the fed buffy mutant stored less lipid and glycogen, had high lactate levels and maintained a reduced pool of cellular ATP. These observations, together with the inability of buffy mutant larvae to adapt to nutrient restriction, indicate altered energy metabolism in the absence of buffy. Conclusions: All animals in their natural habitats are faced with periods of reduced nutrient availability. This study demonstrates that buffy is required for adaptation to both starvation and nutrient restriction. Thus, Buffy is a Bcl-2 protein that plays an important non-apoptotic role to promote survival of the whole organism in a stressful situation.

Description: Background: NICE recommends computerised cognitive behavioural therapy (cCBT) for the treatment of several mental health problems such as anxiety and depression. cCBT may be one way that services can reduce waiting lists and improve capacity and efficiency. However, there is some doubt about the extent to which the National Health Service (NHS) in the UK is embracing this new health technology in practice. This study aimed to investigate Scottish health service infrastructure and policies that promote or impede the implementation of cCBT in the NHS. Methods: A telephone survey of lead IT staff at all health board areas across Scotland to systematically enquire about the ability of local IT infrastructure and IT policies to support delivery of cCBT. Results: Overall, most of the health boards possess the required software to use cCBT programmes. However, the majority of NHS health boards reported that they lack dedicated computers for patient use, hence access to cCBT at NHS sites is limited. Additionally, local policy in the majority of boards prevent staff from routinely contacting patients via email, skype or instant messenger, making the delivery of short, efficient support sessions difficult. Conclusions: Conclusions: Overall most of the infrastructure is in place but is not utilised in ways that allow effective delivery. For cCBT to be successfully delivered within a guided support model, as recommended by national guidelines, dedicated patient computers should be provided to allow access to online interventions. Additionally, policy should allow staff to support patients in convenient ways such as via email or live chat. These measures would increase the likelihood of achieving Scottish health service targets to reduce waiting time for psychological therapies to 18 weeks.

Description: Background: Interoperable electronic health record (EHR) solutions are currently being implemented in Canada, as in many other countries. Understanding EHR users' perspectives is key to the success of EHR implementation projects. This Delphi study aimed to assess in the Canadian context the applicability, the importance, and the priority of pre-identified factors from a previous mixed-methods systematic review of international literature. Methods: A three-round Delphi study was held with representatives of 4 Canadian EHR user groups defined as partners of the implementation process who use or are expected to use EHR in their everyday activity. These groups are: non-physician healthcare professionals, health information professionals, managers, and physicians. Four bilingual online questionnaire versions were developed from factors identified by the systematic review. Participants were asked to rate the applicability and the importance of each factor. The main outcome measures were consensus and priority. Consensus was defined a priori as strong (〉= 75 %) or moderate (〉= 60-74 %) according to user groups' level of agreement on applicability and importance, partial (〉= 60 %) when participants agreed only on applicability or importance, or as no consensus ( 〈 60 %). Priority for decision-making was defined as factors with strong consensus with scores of 4 or 5 on a five-point Likert scale for applicability and importance. Results: Three Delphi rounds were completed by 64 participants. Levels of consensus of 100 %, 64 %, 64 %, and 44 % were attained on factors submitted to non-physician healthcare professionals, health information professionals, managers, and physicians, respectively. While agreement between and within user groups varied, key factors were prioritized if they were classified as strong (〉= 75 % from questionnaire answers of user groups), for decision-making concerning EHR implementation. The10 factors that were prioritized are perceived usefulness, productivity, motivation, participation of end-users in the implementation strategy, patient and health professional interaction, lack of time and workload, resources availability, management, outcome expectancy, and interoperability. Conclusions: Amongst all factors influencing EHR implementation identified in a previous systematic review, ten were prioritized through this Delphi study. The varying levels of agreement between and within user groups could mean that users' perspectives of each factor are complex and that each user group has unique professional priorities and roles in the EHR implementation process. As more EHR implementations in Canada are completed it will be possible to corroborate this preliminary result with a larger population of EHR users.