Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. Zebrafish is a popular model organism, which is widely used in developmental biology research. Finally, we present an example of a real-life case where the use of evolutionary genetics information facilitated the discovery of disease-causing variants in medical genomics. Then, we review how evolutionary principles can be integrated into the prioritization schemes of analyzed variants. In this chapter, we first provide an overview of NGS analysis workflow.
Incorporating information from healthy population databases, other organisms’ databases, and computational prediction tools are evolution-based strategies that give valuable insight to interpret the variant pathogenicity. Several strategies are used to discover the causative mutations among hundreds of variants of uncertain significance. However, identifying the potential effects of the variations and their association with a particular disease phenotype is the main challenge in this field. In recent years, next-generation sequencing (NGS) platforms that facilitate generation of a vast amount of genomic variation data have become widely used for diagnostic purposes in medicine. Researchers benefit from being able to assess the quality of data prior to the data access decision and thereby, increasing the reusability of data (). QC reports allow anonymous EGA users to view summary-level information regarding the files within a specific dataset, such as quality of reads, alignment quality, number and type of variants and other features.
Here, we present a new File QC Portal developed at EGA, along with QC reports performed and created for 1 694 442 files submitted at EGA. In this regard, one of the community concerns is the potential usability of the stored data, as of now, data submitters are not mandated to perform any quality control (QC) before uploading their data and associated metadata information.
#QCTOOLS ALTERNATIVE ARCHIVE#
Since its launch in 2008, the European Genome–Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data.
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