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- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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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. |
- Dong, Jiang, et al.
(författare)
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Millennial-scale interaction between the East Asian winter monsoon and El Niño-related tropical Pacific precipitation in the Holocene
- 2021
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Ingår i: Palaeogeography, Palaeoclimatology, Palaeoecology. - : Elsevier BV. - 0031-0182. ; 573
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Tidskriftsartikel (refereegranskat)abstract
- Both the East Asian winter monsoon (EAWM) and El Niño (EN) activities are vital climate modes that regulate the Pacific hydrologic cycle. However, the Holocene interactions among the EAWM, EN activities, and tropical Pacific precipitation remain unclear due to the lack of appropriate EAWM proxies. Here, we present high-resolution grain size records from the East China Sea shelf along with a transient climate model simulation to study the Holocene EAWM evolution and compare the findings with paleo-EN precipitation-related proxies records. The millennial-scale oscillations of grain size records, which are indicative of the intensity of the EAWM-driven coastal current, reveal an anti-phase coupling between the EAWM and EN-related tropical Pacific precipitation on a millennial timescale since 5.8 ka. These results, which are consistent with simulation results, indicate that the intensified EAWM could not only reduce equatorial western Pacific precipitation by reducing the sea surface temperature but also likely change boundary conditions in the tropical Pacific (i.e., the east-west Pacific temperature gradient and westerly anomaly) to favor the formation of subsequent intensive EN activities. The enhanced EN activities, inferred by the positive tropical eastern Pacific precipitation anomalies, could subsequently suppress the EAWM through anomalous low-level anticyclones and associated southerly anomalies, thereby generating intensified tropical western Pacific (mainly tropical monsoon areas) precipitation. Our study highlights these intrinsic interactions during the mid- to late Holocene and has useful implications for understanding this millennial-scale climate oscillation, which may represent periodic atmospheric exchange between high- and low-latitude climate systems by mediating the EAWM.
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