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"reference database"
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Predicting disease genes using protein–protein interactions
Background: The responsible genes have not yet been identified for many genetically mapped disease loci. Physically interacting proteins tend to be involved in the same cellular process, and mutations in their genes may lead to similar disease phenotypes. Objective: To investigate whether protein–protein interactions can predict genes for genetically heterogeneous diseases. Methods: 72 940 protein–protein interactions between 10 894 human proteins were used to search 432 loci for candidate disease genes representing 383 genetically heterogeneous hereditary diseases. For each disease, the protein interaction partners of its known causative genes were compared with the disease associated loci lacking identified causative genes. Interaction partners located within such loci were considered candidate disease gene predictions. Prediction accuracy was tested using a benchmark set of known disease genes. Results: Almost 300 candidate disease gene predictions were made. Some of these have since been confirmed. On average, 10% or more are expected to be genuine disease genes, representing a 10-fold enrichment compared with positional information only. Examples of interesting candidates are AKAP6 for arrythmogenic right ventricular dysplasia 3 and SYN3 for familial partial epilepsy with variable foci. Conclusions: Exploiting protein–protein interactions can greatly increase the likelihood of finding positional candidate disease genes. When applied on a large scale they can lead to novel candidate gene predictions.
Journal Article
Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y‐STRs
Background Dalian is a city formed in the 1880s in Liaoning province, Northeastern China with a population of 6.69 million now. Han is the largest ethnic group not only across Mainland China (92%) and Taiwan (97%) but also considered to be the largest ethnic group of the world contributing to above 18% of world's population. Methods In the current study, we genotyped Goldeneye® 20Y System loci in 879 unrelated male individuals from the Han ethnic group in Dalian city and calculated the forensic parameters of the 20 Y‐STR loci. Results In total, we observed 855 haplotypes, among which 835 (94.99%) were unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is 97.27% and it slightly reduces to 96.93% when only Y‐filer® set of 17 Y‐STRs were used, which mitigates using the extended set of markers in this population. We found DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed the highest gene diversity (0.7621) in single copy Y‐STR, and DYS385 showed the highest gene diversity (0.9683) among all. Conclusion Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic distance showed difference among Han population from the east to the west and from the north to the south. We also predicted haplogroups using Y‐STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a null allele at the DYS448 in our samples. We also performed linear discriminatory analysis (LDA) between Han and other prominent Chinese minority ethnic groups. We presented Y‐STRs data in the Y‐Chromosome Haplotype Reference Database (YHRD) for the future forensic and other usage. Our analysis showed difference among Han population from east to west and north to south. We also predicted haplogroups using Y‐STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han. Moreover, we found 10 individuals showed a null allele at DYS448 in our samples.
Journal Article
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on
k
-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.
Journal Article
GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding
Aim: Environmental DNA metabarcoding has recently emerged as a non-invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. The major limitation currently impairing the large-scale application of eDNA-based inventories is the lack of species sequences available in public genetic databases. Unfortunately, these gaps are still unknown spatially and taxonomically, hindering targeted future sequencing efforts. Innovation: We propose GAPeDNA, a user-friendly web interface that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of eDNA inventories at larger scale. This tool is flexible and can be expanded to other taxa and primers upon data availability. Main conclusions: Using our global fish case study, we show that gaps increase towards the tropics where species diversity and the number of threatened species are the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non-sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non-sequenced threatened species. By presenting the global genetic database completeness for several primers on any taxa and building an open-access, updatable and flexible tool, GAPeDNA appears as a valuable contribution to support any kind of eDNA metabarcoding study.
Journal Article
Metabarcoding of soil nematodes: the importance of taxonomic coverage and availability of reference sequences in choosing suitable marker(s)
For many organisms, there is agreement on the specific genomic region used for developing barcode markers. With nematodes, however, it has been found that the COI region designated for most animals lacks the taxonomic coverage (ability to amplify a diverse group of taxa) required of a metabarcoding marker. For that reason, studies on metabarcoding of nematodes thus far have utilized primarily regions within the highly conserved 18S ribosomal DNA. Two popular markers within this region are the ones flanked by the primer pairs NF1-18Sr2b and SSUF04-SSUR22. The NF1-18Sr2b primer pair, especially, has been critiqued as not being specific enough for nematodes leading to suggestions for other candidate markers while the SSUF04-SSUR22 region has hardly been tested on soil nematodes. The current study aimed to evaluate these two markers against other alternative ones within the 28S rDNA and the COI region for their suitability for nematode metabarcoding. The results showed that the NF1-18Sr2b marker could offer wide coverage and good resolution for characterizing soil nematodes. Sufficient availability of reference sequences for this region was found to be a significant factor that resulted in this marker outperforming the other markers, particularly the 18S-based SSUFO4-SSUR22 marker. None of the other tested regions compared with this marker in terms of the proportion of the taxa recovered. The COI-based marker had the lowest number of taxa recovered, and this was due to the poor performance of its primers and the insufficient number of reference sequences in public databases. In summary, this study highlights how dependent the success of metabarcoding is on the availability of a good reference sequence collection for the marker of choice as well as its taxonomic coverage.
Journal Article
RefXAS: an open access database of X‐ray absorption spectra
Under DAPHNE4NFDI, the X‐ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user‐friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server‐side automatic authentication and (meta‐) data storage via MongoDB, PostgreSQL and (data‐) files via relevant APIs. The RefXAS database under DAPHNE4NFDI enables users to access quality‐controlled, curated X‐ray absorption spectra of references along with important metadata and to share their data with the research community in easy steps.
Journal Article
Increasing African genomic data generation and sharing to resolve rare and undiagnosed diseases in Africa: a call-to-action by the H3Africa rare diseases working group
The rich and diverse genomics of African populations is significantly underrepresented in reference and in disease-associated databases. This renders interpreting the Next Generation Sequencing (NGS) data and reaching a diagnostic more difficult in Africa and for the African diaspora. It increases chances for false positives with variants being misclassified as pathogenic due to their novelty or rarity. We can increase African genomic data by (1) making consent for sharing aggregate frequency data an essential component of research toolkit; (2) encouraging investigators with African data to share available data through public resources such as gnomAD, AVGD, ClinVar, DECIPHER and to use MatchMaker Exchange; (3) educating African research participants on the meaning and value of sharing aggregate frequency data; and (4) increasing funding to scale-up the production of African genomic data that will be more representative of the geographical and ethno-linguistic variation on the continent. The RDWG of H3Africa is hereby calling to action because this underrepresentation accentuates the health disparities. Applying the NGS to shorten the diagnostic odyssey or to guide therapeutic options for rare diseases will fully work for Africans only when public repositories include sufficient data from African subjects.
Journal Article
Random impact force localisation enabled by the weighted reference database method
The mechanical properties of an engineering structure can be substantially influenced by a random impact force (RIF), which may compromise the integrity and safety of the structure. Nevertheless, accurately localising the RIF applied to a structure presents a significant challenge. To address this issue, this study introduces a novel method known as the weighted reference database method (WRDM). Its innovations are reflected in three aspects: (i) constrained by the sparse construction of a reference database, bicubic interpolation is utilised to increase the reference impact point density and improve the localisation accuracy; (ii) a weighted random impact localisation framework is constructed, in which a cosine distance variant is chosen as the weight to further improve the localisation accuracy; and (iii) to overcome the region limitation of interpolation, the boundary range of the WRDM is extended. Experiments on a suspended rectangular plate were conducted to validate and demonstrate the effectiveness of the WRDM in terms of localisation accuracy. The experimental results indicate that the average absolute error of the method is 16.67 mm (the interpolation interval size is 2 mm and the prioritisation point number (PPN) is 108), and its localisation accuracy is higher than that of previously published methods (21.54 mm for PRMCSM; 20.80 mm for the hybrid method).
Journal Article