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Sökning: WFRF:(Llorca Javier)

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1.
  • Brownstein, Catherine A., et al. (författare)
  • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
  • 2014
  • Ingår i: ; 15:3, s. R53-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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2.
  • Dadaev, Tokhir, et al. (författare)
  • Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.
  • 2018
  • Ingår i: ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.
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5.
  • Ortiz, J.L., et al. (författare)
  • Detection of sporadic impact flashes on the Moon : Implications for the luminous efficiency of hypervelocity impacts and derived terrestrial impact rates
  • 2006
  • Ingår i: Icarus (New York, N.Y. 1962). - 0019-1035 .- 1090-2643. ; 184:2, s. 319-326
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the first redundant detection of sporadic impact flashes on the Moon from a systematic survey performed between 2001 and 2004. Our wide-field lunar monitoring allows us to estimate the impact rate of large meteoroids on the Moon as a function of the luminous energy received on Earth. It also shows that some historical well-documented mysterious lunar events fit in a clear impact context. Using these data and traditional values of the luminous efficiency for this kind of event we obtain that the impact rate on Earth of large meteoroids (0.1–10 m) would be at least one order of magnitude larger than currently thought. This discrepancy indicates that the luminous efficiency of the hypervelocity impacts is higher than 10−2, much larger than the common belief, or the latest impact fluxes are somewhat too low, or, most likely, a combination of both. Our nominal analysis implies that on Earth, collisions of bodies with masses larger than 1 kg can be as frequent as 80,000 per year and blasts larger than 15-kton could be as frequent as one per year, but this is highly dependent on the exact choice of the luminous efficiency value. As a direct application of our results, we expect that the impact flash of the SMART-1 spacecraft should be detectable from Earth with medium-sized telescopes.
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