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Sökning: WFRF:(Torkamani A)

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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: Genome Biology. - 1465-6906 .- 1474-760X. ; 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.
  • Dewan, Ramita, et al. (författare)
  • Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis
  • 2020
  • Ingår i: Neuron. - : Cell Press. - 0896-6273. ; 109:3, s. 448-460.e4
  • Tidskriftsartikel (refereegranskat)abstract
    • Using large-scale whole-genome sequencing, Dewan et al. identify pathogenic HTT repeat expansions in patients diagnosed with FTD/ALS neurodegenerative disorders. Autopsies confirm the TDP-43 pathology expected in FTD/ALS and show polyglutamine inclusions within the frontal cortices but no striatal degeneration. These data broaden the phenotype resulting from HTT repeat expansions.
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4.
  • Schork, Andrew J, et al. (författare)
  • All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.
  • 2013
  • Ingår i: PLoS genetics. - 1553-7404. ; 9:4
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci.
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7.
  • Banijamali, S. M., et al. (författare)
  • Effect of Ce Addition on the Tribological Behavior of ZK60 Mg-Alloy
  • 2020
  • Ingår i: Metals and Materials International. - : Springer. - 1598-9623 .- 2005-4149.
  • Tidskriftsartikel (refereegranskat)abstract
    • The present work aims to study the tribological behavior of an extruded ZK60 alloy in the presence of Ce; in a previous study, among ZK60 alloys with different Ce addition rates, an alloy with 3 wt% of Ce was found to exhibit the most promising mechanical (e.g., hardness and strengths) properties, while its wear behavior remained unknown. The results of microstructural examinations by optical and electron microscopes show that Ce addition reduces the grain size from 6.1 to 2.0 μm. Besides, in addition to the precipitates already distributed in the base alloy (Mg7Zn3), Ce could promote the formation of a new precipitate (MgZn2Ce), increasing the total fraction of the precipitates. These microstructural evolutions enhance the strengths of the studied ZK60 alloy, as the yield and tensile strengths increase from 212 to 308 MPa and from 297 to 354 MPa, respectively. A pin on disc tribometer was employed to study the wear behavior of the developed alloy under different normal loads (5, 20, 40, and 60 N). The results show that the base and Ce-added alloys exhibit almost a similar frictional behavior, while the wear resistance of the Ce-added alloy is higher within the load ranges applied: (i) in low load conditions (5 and 20 N), where the abrasive wear is the active mechanism, the precipitates in the Ce-added alloy could enhance the wear resistance. (ii) Under the load of 40 N, oxidative wear is also an operative wear mechanism, leading to a sharp increase in the wear rate of the alloys. In this condition, Ce could provide a protective oxide layer, which could improve the wear resistance of the alloy. (iii) At a load of 60 N, both studied alloys exhibit a similar wear rate due to a severe oxidation condition. Therefore, beyond this loading condition, the microstructural evolutions (e.g., change in precipitation behavior) caused by Ce addition can no longer contribute to the enhancement of wear resistance.
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