Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis.

Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.

Using single molecule Molecular Inversion Probes as a cost-effective, high-throughput sequencing approach to target all genes and loci associated with macular diseases.

Macular degenerations (MDs) are a subgroup of retinal disorders characterized by central vision loss. Knowledge is still lacking on the extent of genetic and nongenetic factors influencing inherited MD (iMD) and age-related MD (AMD) expression. Single molecule Molecular Inversion Probes (smMIPs) have proven effective in sequencing the ABCA4 gene in patients with Stargardt disease to identify associated coding and noncoding variation, however many MD patients still remain genetically unexplained. We hypothesized that the missing heritability of MDs may be revealed by smMIPs-based sequencing of all MD-associated genes and risk factors. Using 17,394 smMIPs, we sequenced the coding regions of 105 iMD and AMD-associated genes and noncoding or regulatory loci, known pseudo-exons, and the mitochondrial genome in two test cohorts that were previously screened for variants in ABCA4. Following detailed sequencing analysis of 110 probands, a diagnostic yield of 38% was observed. This established an ''MD-smMIPs panel," enabling a genotype-first approach in a high-throughput and cost-effective manner, whilst achieving uniform and high coverage across targets. Further analysis will identify known and novel variants in MD-associated genes to offer an accurate clinical diagnosis to patients. Furthermore, this will reveal new genetic associations for MD and potential genetic overlaps between iMD and AMD.

Analysis of Small Area Environmental, Socioeconomic and Health Data in Collaboration with Local Communities to Target and Evaluate 'Triple Win' Interventions in a Deprived Community in Birmingham UK.

The contemporary environment is a complex of interactions between physical, biological and socioeconomic systems with major impacts on public health. It is well understood that deprived communities are more exposed to negative environmental and social factors, more susceptible to the effects of those exposures, more excluded from access to positive factors, less able to change their circumstances and consequently experience worse health, economic and social outcomes compared to the more affluent. Welsh House Farm estate in Birmingham is one of the most deprived areas in Europe. An alliance between a local charity, City Council Public Health and a University in collaboration with the local community has accessed, analysed and mapped a range of health, social and economic factors at small area level, identifying areas where the community experience is unacceptably worse than other parts of Birmingham and therefore requiring targeted interventions. We make specific recommendations for coordinated action addressing the living, moving and consuming domains of residents' lives and have also identified positive aspects of life on the estate to celebrate. This pilot demonstrates the utility and cost-effectiveness of local collaboration to identify and target health, environmental and social inequalities informed by local concerns.

Wider horizons, wiser choices: horizon scanning for public health protection and improvement.

Background: Systematic continuous thinking about the future helps organizations, professions and communities to both prepare for, and shape, the future. This becomes ever more critical given the accelerating rate at which new data emerge, and in some cases uncertainties around their reliability and interpretation. Businesses with the capability to filter and analyse vast volumes of data to create knowledge and insights requiring action have a competitive advantage. Similarly Government and the public sector, including public health can be more effective and efficient through the early identification of emerging issues (both threats and opportunities). Methods: Horizon scanning approaches, and the use of resulting intelligence related to health protection and improvement were reviewed. Results: Public health horizon scanning systems have to date focussed on health technologies and infectious diseases. While these have been successful there is a major gap in terms of non-infectious hazards and health improvement. Conclusion: Any system to meet this need must recognize the changed environment for delivering front line public health services and the critical role of local authorities and the local democratic process. This presents opportunities and challenges and this paper explores those dynamics describing an existing environment and health horizon scanning system which could readily and rapidly be re-engineered to provide a national service.

Next-generation carrier screening.

PURPOSE: Carrier screening for recessive Mendelian disorders traditionally employs focused genotyping to interrogate limited sets of mutations most prevalent in specific ethnic groups. We sought to develop a next-generation DNA sequencing-based workflow to enable analysis of a more comprehensive set of disease-causing mutations. METHODS: We utilized molecular inversion probes to capture the protein-coding regions of 15 genes from genomic DNA isolated from whole blood and sequenced those regions using the Illumina HiSeq 2000 (Illumina, San Diego, CA). To assess the quality of the resulting data, we measured both the fraction of the targeted region yielding high-quality genotype calls, and the sensitivity and specificity of those calls by comparison with conventional Sanger sequencing across hundreds of samples. Finally, to improve the overall accuracy for detecting insertions and deletions, we introduce a novel assembly-based approach that substantially increases sensitivity without reducing specificity. RESULTS: We generated high-quality sequence for at least 99.8% of targeted base pairs in samples derived from blood and achieved high concordance with Sanger sequencing (sensitivity >99.9%, specificity >99.999%). Our novel algorithm is capable of detecting insertions and deletions inaccessible by current methods. CONCLUSION: Our next-generation DNA sequencing-based approach yields the accuracy and completeness necessary for a carrier screening test.