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- Foox, Jonathan, et al.
(författare)
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The SEQC2 epigenomics quality control (EpiQC) study
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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| 2. |
- Van Loon, Anne F., et al.
(författare)
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Review article: Drought as a continuum: memory effects in interlinked hydrological, ecological, and social systems
- 2024
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Droughts are often long lasting phenomena, without a distinct start or end, and with impacts cascading across sectors and systems, creating long-term legacies. Nevertheless, our current perception and management of droughts and their impacts is often event-based, which can limit the effective assessment of drought risks and reduction of drought impacts. Here, we advocate for changing this perspective and viewing drought as a hydro-eco-social continuum. We take a systems theory perspective and focus on how “memory” causes feedback and interactions between parts of the interconnected systems at different time scales. We first discuss the characteristics of the drought continuum with a focus on the hydrological, ecological, and social systems separately; and then study the system of systems. Our analysis is based on a review of the literature and a study of five cases: Chile, the Colorado River Basin in the US, Northeast Brazil, Kenya, and the Rhine River Basin in Northwest Europe. We find that the memories of past dry and wet periods, carried by both bio-physical (e.g. groundwater, vegetation) and social systems (e.g. people, governance), influence how future drought risk manifests. We identify four archetypes of drought dynamics: Impact & recovery; Slow resilience-building; Gradual collapse; and High resilience, big shock. The interactions between the hydrological, ecological and social systems result in systems shifting between these types, which plays out differently in the five case studies. We call for more research on drought preconditions and recovery in different systems, on dynamics cascading between systems and triggering system changes, and on dynamic vulnerability and maladaptation. Additionally, we argue for more continuous monitoring of drought hazards and impacts, modelling tools that better incorporate memories and adaptation responses, and management strategies that increase social and institutional memory to better deal with the complex hydro-eco-social drought continuum and identify effective pathways to adaptation.
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