scholarly journals Leiden open variation database of the MUTYH gene

2010 ◽  
Vol 31 (11) ◽  
pp. 1205-1215 ◽  
Author(s):  
Astrid A. Out ◽  
Carli M.J. Tops ◽  
Maartje Nielsen ◽  
Marjan M. Weiss ◽  
Ivonne J.H.M. van Minderhout ◽  
...  
Keyword(s):  
Mutyh Gene ◽  
Variation Database

scholarly journals A novel nonsense variant of the AGXT identified in a Chinese family: special variant research in the Chinese reference genome

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chang Bao Xu ◽  
Xu Dong Zhou ◽  
Hong En Xu ◽  
Yong Li Zhao ◽  
Xing Hua Zhao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Genetic Diagnosis ◽  
Primary Hyperoxaluria ◽  
Missense Variant ◽  
Population Heterogeneity ◽  
Chinese Family ◽  
Pathogenic Variants ◽  
Variation Database ◽  
Genetic Level

Abstract Background Primary hyperoxaluria(PH)is a rare autosomal recessive genetic disease that contains three subtypes (PH1, PH2 and PH3). Approximately 80% of PH patients has been reported as subtype PH1, this subtype of PH has been related to a higher risk of renal failure at any age. Several genetic studies indicate that the variants in gene AGXT are responsible for the occurrence of PH1. However, the population heterogeneity of the variants in AGXT makes the genetic diagnosis of PH1 more challenging as it is hard to locate each specific variant. It is valuable to have a complete spectrum of AGXT variants from different population for early diagnosis and clinical treatments of PH1. Case presentation In this study, We performed high-throughput sequencing and genetic analysis of a 6-year-old male PH1 patient from a Chinese family. Two variants (c.346G > A: p.Gly116Arg; c.864G > A: p.Trp288X) of the gene AGXT were identified. We found a nonsense variant (c.864G > A: p.Trp288X) that comes from the proband’s mother and has never been reported previously. The other missense variant (c.346G > A: p.Gly116Arg) was inherited from his father and has been found previously in a domain of aminotransferase, which plays an important role in the function of AGT protein. Furthermore, we searched 110 pathogenic variants of AGXT that have been reported worldwide in healthy local Chinese population, none of these pathogenic variants was detected in the local genomes. Conclusions Our research provides an important diagnosis basis for PH1 on the genetic level by updating the genotype of PH1 and also develops a better understanding of the variants in AGXT by broadening the variation database of AGXT according to the Chinese reference genome.

scholarly journals Allele frequency of variants reported to cause adenine phosphoribosyltransferase deficiency

2021 ◽  
Author(s):  
Hrafnhildur L. Runolfsdottir ◽  
John A. Sayer ◽  
Olafur S. Indridason ◽  
Vidar O. Edvardsson ◽  
Brynjar O. Jensson ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Autosomal Recessive Disorder ◽  
European Population ◽  
Adenine Phosphoribosyltransferase ◽  
Genomic Databases ◽  
Pathogenic Variants ◽  
Adenine Phosphoribosyltransferase Deficiency ◽  
Variation Database ◽  
The Uk ◽  
Aprt Deficiency

AbstractAdenine phosphoribosyltransferase deficiency is a rare, autosomal recessive disorder of purine metabolism that causes nephrolithiasis and progressive chronic kidney disease. The small number of reported cases indicates an extremely low prevalence, although it has been suggested that missed diagnoses may play a role. We assessed the prevalence of APRT deficiency based on the frequency of causally-related APRT sequence variants in a diverse set of large genomic databases. A thorough search was carried out for all APRT variants that have been confirmed as pathogenic under recessive mode of inheritance, and the frequency of the identified variants examined in six population genomic databases: the deCODE genetics database, the UK Biobank, the 100,000 Genomes Project, the Genome Aggregation Database, the Human Genetic Variation Database and the Korean Variant Archive. The estimated frequency of homozygous genotypes was calculated using the Hardy-Weinberg equation. Sixty-two pathogenic APRT variants were identified, including six novel variants. Most common were the missense variants c.407T>C (p.(Met136Thr)) in Japan and c.194A>T (p.(Asp65Val)) in Iceland, as well as the splice-site variant c.400 + 2dup (p.(Ala108Glufs*3)) in the European population. Twenty-nine variants were detected in at least one of the six genomic databases. The highest cumulative minor allele frequency (cMAF) of pathogenic variants outside of Japan and Iceland was observed in the Irish population (0.2%), though no APRT deficiency cases have been reported in Ireland. The large number of cases in Japan and Iceland is consistent with a founder effect in these populations. There is no evidence for widespread underdiagnosis based on the current analysis.

scholarly journals RETRACTION: CGVD: a genomic variation database for Chinese populations

2019 ◽  
Author(s):  
Jingyao Zeng ◽  
Na Yuan ◽  
Junwei Zhu ◽  
Mengyu Pan ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Genomic Variation ◽  
Chinese Populations ◽  
Variation Database

scholarly journals The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures

2019 ◽  
Author(s):  
Ningbo Chen ◽  
Weiwei Fu ◽  
Jianbang Zhao ◽  
Jiafei Shen ◽  
Qiuming Chen ◽  
...  
Keyword(s):  
Bovine Genome ◽  
Distribution Patterns ◽  
Global Scale ◽  
Genomic Region ◽  
Genome Browser ◽  
Web Database ◽  
Genome Variation ◽  
Gene Search ◽  
Variation Database ◽  
Coordinate Conversion

AbstractNext-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.

scholarly journals Ebola Outbreak Response: The Role of Information Resources and the National Library of Medicine

2014 ◽  
Vol 9 (1) ◽  
pp. 82-85 ◽  
Author(s):  
Cynthia B. Love ◽  
Stacey J. Arnesen ◽  
Steven J. Phillips
Keyword(s):  
Social Media ◽  
Information Resources ◽  
Free Access ◽  
Outbreak Response ◽  
National Library ◽  
Online Data ◽  
Journal Literature ◽  
The Us ◽  
Variation Database ◽  
Disaster Event

AbstractThe US National Library of Medicine (NLM) offers Internet-based, no-cost resources useful for responding to the 2014 West Africa Ebola outbreak. Resources for health professionals, planners, responders, and researchers include PubMed, Disaster Lit, the Web page “Ebola Outbreak 2014: Information Resources,” and the Virus Variation database of sequences for Ebolavirus. In cooperation with participating publishers, NLM offers free access to full-text articles from over 650 biomedical journals and 4000 online reference books through the Emergency Access Initiative. At the start of a prolonged disaster event or disease outbreak, the documents and information of most immediate use may not be in the peer-reviewed biomedical journal literature. To maintain current awareness may require using any of the following: news outlets; social media; preliminary online data, maps, and situation reports; and documents published by nongovernmental organizations, international associations, and government agencies. Similar to the pattern of interest shown in the news and social media, use of NLM Ebola-related resources is also increasing since the start of the outbreak was first reported in March 2014 (Disaster Med Public Health Preparedness. 2014;0:1-4)

The effect of drone transport on the stability of biochemical, coagulation and hematological parameters in healthy individuals

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Desirée Perlee ◽  
Klaas Henk van der Steege ◽  
Gijs den Besten
Keyword(s):  
Hematological Parameters ◽  
Blood Parameters ◽  
Control Group ◽  
Healthy Individuals ◽  
Glucose Phosphate ◽  
Relevant Effect ◽  
Novel Approach ◽  
Variation Database ◽  
Allowable Error ◽  
The Stability

Abstract Objectives Transport of blood tubes is mainly by car or pneumatic transport. The transportation of blood tubes by drones is a novel approach for rapid transportation of blood tubes over long distances. However, limited data on the stability of biochemical, coagulation and hematological parameters is available after transport of blood tubes by drone. Methods To investigate the effect of drone transport on the stability of blood parameters, four test flights were performed. Blood was drawn from 20 healthy individuals and 39 of the most frequently measured blood parameters were compared between 4 groups; immediate measurement (control), late measurement, transport by car and transport by drone. Total Allowable Error (TAE) of the EFLM Biological Variation Database was used to determine the clinical relevance of significant differences. Results The majority of blood parameters were not affected by drone transport. Eight of the measured parameters showed significant differences between all the groups; glucose, phosphate, potassium, chloride, hemoglobin, platelet count, APTT and Lactate dehydrogenase (LD). A clinically relevant increase for LD after transport and a decrease for glucose values in time and after transport compared with the control group was shown. Conclusions Transportation of blood tubes from healthy individuals by drones has a limited clinically relevant effect. From the 39 investigated blood parameters only LD and glucose showed a clinically relevant effect.

Biological variation database: structure and criteria used for generation and update

2015 ◽  
Vol 53 (2) ◽  
Author(s):  
Carmen Perich ◽  
Joana Minchinela ◽  
Carmen Ricós ◽  
Pilar Fernández-Calle ◽  
Virtudes Alvarez ◽  
...  
Keyword(s):  
Numerical Data ◽  
Relevant Information ◽  
Laboratory Medicine ◽  
Biological Variation ◽  
The Internet ◽  
Analytical Quality ◽  
Database Structure ◽  
Variation Database ◽  
Quality Specifications ◽  
Allowable Error

AbstractNumerical data on the components of biological variation (BV) have many uses in laboratory medicine, including in the setting of analytical quality specifications, generation of reference change values and assessment of the utility of conventional reference values.Generation of a series of up-to-date comprehensive database of components of BV was initiated in 1997, integrating the more relevant information found in publications concerning BV. A scoring system was designed to evaluate the robustness of the data included. The database has been updated every 2 years, made available on the Internet and derived analytical quality specifications for imprecision, bias and total allowable error included in the tabulation of data.Our aim here is to document, in detail, the methodology we used to evaluate the reliability of the included data compiled from the published literature. To date, our approach has not been explicitly documented, although the principles have been presented at many symposia, courses and conferences.

scholarly journals HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

2010 ◽  
Vol 63 (3) ◽  
pp. 143-153 ◽  
Author(s):  
Harm Nijveen ◽  
Michel G. D. Kester ◽  
Chopie Hassan ◽  
Aurélie Viars ◽  
Arnoud H. de Ru ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Short Peptide ◽  
Variation Database ◽  
Hla Ligands

Common Genetic Variants of MUTYH are not Associated with Cutaneous Malignant Melanoma: Application of Molecular Screening by Means of High-Resolution Melting Technique in a Pilot Case-Control Study

2011 ◽  
Vol 26 (1) ◽  
pp. 37-42 ◽  
Author(s):  
Concetta Santonocito ◽  
Andrea Paradisi ◽  
Rodolfo Capizzi ◽  
Eleonora Torti ◽  
Sara Lanza-Silveri ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Direct Sequencing ◽  
Strong Association ◽  
Laboratory Data ◽  
Gene Mutations ◽  
Case Control ◽  
Common Genetic Variants ◽  
Mutyh Gene ◽  
Embryonic Origin

MUTYH glycosylase recognizes the 8-oxoG:A mismatch and is able to excise the adenine base using proofreading mechanisms. Some papers have reported a strong association between cancer development or aggressiveness and MUTYH gene mutations. The aim of this study was to find a possible association between the most frequent MUTYH mutations and melanoma in the context of a case-control pilot study. One hundred ninety-five melanoma patients and 195 healthy controls were matched for sex and age. Clinical and laboratory data were collected in a specific database and all individuals were analyzed for MUTYH mutations by high-resolution melting and direct sequencing techniques. Men and women had significantly different distributions of tumor sites and phototypes. No significant associations were observed between the Y165C, G382D and V479F MUTYH mutations and risk of melanoma development or aggressiveness. Our preliminary findings therefore do not confirm a role for MUTYH gene mutations in the melanoma risk. Further studies are necessary for the assessment of MUTYH not only in melanoma but also other cancer types with the same embryonic origin, in the context of larger arrays studies of genes involved in DNA stability or integrity.

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