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- 2019
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Tidskriftsartikel (refereegranskat)
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- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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- Ademuyiwa, Adesoji O., et al.
(författare)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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- Ahrén, Bo, et al.
(författare)
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Albiglutide for the treatment of type 2 diabetes mellitus : An integrated safety analysis of the HARMONY phase 3 trials
- 2017
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Ingår i: Diabetes Research and Clinical Practice. - : Elsevier BV. - 0168-8227. ; 126, s. 230-239
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Tidskriftsartikel (refereegranskat)abstract
- Aims Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) stimulate the incretin system and lower glycaemic parameters in type 2 diabetes mellitus (T2DM). This analysis of clinical studies of up to 3 years evaluated the safety of albiglutide, a GLP-1 RA, in people with T2DM. Methods Integrated safety analysis included seven phase-3 T2DM studies of albiglutide compared with placebo and/or active comparators (a dipeptidyl peptidase-4 inhibitor, GLP-1 RA, insulin, sulphonylurea, and thiazolidinedione). Results Studies of 32 months (HARMONY 7), 1 year (HARMONY 6), and 3 years (HARMONY 1–5), reported similar rates of adverse events (AEs) (84.8%, 82.3%), and serious AEs (13.1%, 12.9%) between albiglutide and all comparators, respectively. AEs that did not differ between the groups included symptomatic or severe hypoglycaemia as well as nausea (12.0%, 11.3%) and vomiting (5.3%, 4.7%) for albiglutide and all comparators, respectively. According to the Medical Dictionary for Regulatory Activities preferred terms, only diarrhoea (13.7%, 9.9%), injection-site reaction (9.0%, 2.0%), and peripheral oedema (4.5%, 6.8%) had at least 2% difference between the albiglutide and all-comparator groups. In a similar integrated analysis, pancreatitis occurred more often with albiglutide (0.3%, 0.1%). Renal and cardiac function did not differ between the two groups. Conclusions In an integrated analysis of seven phase 3 clinical trials, albiglutide-treated patients experienced frequencies of AEs (including cardiovascular and renal) similar to the all-comparators group treated with other T2DM medications or placebo. Albiglutide treatment was associated with higher rates of diarrhoea and injection-site reactions, but not increased nausea and vomiting, versus all comparators.
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- Aken, Bronwen L., et al.
(författare)
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The Ensembl gene annotation system
- 2016
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Ingår i: Database. - : Oxford University Press (OUP). - 1758-0463.
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Tidskriftsartikel (refereegranskat)abstract
- The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.
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- Woolfenden, Susan, et al.
(författare)
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Who is our cohort: : recruitment, representativeness, baseline risk and retention in the 'Watch Me Grow' study?
- 2016
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Ingår i: BMC Pediatrics. - : Springer Science and Business Media LLC. - 1471-2431. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND The "Watch Me Grow" (WMG) study examines the current developmental surveillance system in South West Sydney. This paper describes the establishment of the study birth cohort, including the recruitment processes, representativeness, follow-up and participants’ baseline risk for future developmental risk. METHODS Newborn infants and their parents were recruited from two public hospital postnatal wards and through child health nurses during the years 2011-2013. Data was obtained through a detailed participant questionnaire and linked with the participant’s electronic medical record (EMR). Representativeness was determined by Chi-square analyses of the available clinical, psychosocial and sociodemographic EMR data, comparing the WMG participants to eligible non-participants. Reasons for non-participation were also elicited. Participant characteristics were examined in six, 12, and 18-month follow-ups. RESULTS The number of infants recruited totalled 2,025, with 50 % of those approached agreeing to participate. Reasons for parents not participating included: lack of interest, being too busy, having plans to relocate, language barriers, participation in other research projects, and privacy concerns. The WMG cohort was broadly representative of the culturally diverse and socially disadvantaged local population from which it was sampled. Of the original 2025 participants enrolled at birth, participants with PEDS outcome data available at follow-up were: 792 (39 %) at six months, 649 (32 %) at 12 months, and 565 (28 %) at 18 months. Participants with greater psychosocial risk were less likely to have follow-up outcome data. Almost 40 % of infants in the baseline cohort were exposed to at least two risk factors known to be associated with developmental risk. CONCLUSIONS The WMG study birth cohort is a valuable resource for health services due to the inclusion of participants from vulnerable populations, despite there being challenges in being able to actively follow-up this population.
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