Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation

Chunn, Lauren M.; Nefcy, Diane C.; Scouten, Rachel W.; Tarpey, Ryan P.; Chauhan, Gurinder; Lim, Megan S.; Elenitoba-Johnson, Kojo S.J.; Schwartz, Steven H.; Kiel, Mark J.

doi:10.3389/fgene.2020.577152

Cited by 63 publications

(46 citation statements)

References 26 publications

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“…A comprehensive literature review was performed using Mastermind, a database of variants with evidence cited in the medical literature (Genomenon Inc.) (Chunn et al, 2020 ) and considered all publications indexed in PubMed as of April 7, 2020. We followed stated guidelines for performing meta‐analyses from biomedical literature.…”

Section: Methodsmentioning

confidence: 99%

Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH)

et al. 2021

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X‐linked hypophosphatemia (XLH), the most common form of hereditary hypophosphatemia, is caused by disrupting variants in the PHEX gene, located on the X chromosome. XLH is inherited in an X‐linked pattern with complete penetrance observed for both males and females. Patients experience lifelong symptoms resulting from chronic hypophosphatemia, including impaired bone mineralization, skeletal deformities, growth retardation, and diminished quality of life. This chronic condition requires life‐long management with disease‐specific therapies, which can improve patient outcomes especially when initiated early in life. To centralize and disseminate PHEX variant information, we have established a new PHEX gene locus‐specific database, PHEX LSDB. As of April 30, 2021, 870 unique PHEX variants, compiled from an older database of PHEX variants, a comprehensive literature search, a sponsored genetic testing program, and XLH clinical trials, are represented in the PHEX LSDB. This resource is publicly available on an interactive, searchable website (https://www.rarediseasegenes.com/), which includes a table of variants and associated data, graphical/tabular outputs of genotype‐phenotype analyses, and an online submission form for reporting new PHEX variants. The database will be updated regularly with new variants submitted on the website, identified in the published literature, or shared from genetic testing programs.

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Section: Methodsmentioning

confidence: 99%

Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH)

et al. 2021

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“…This is not trivial to extract, and different text mining and curation approaches enable access to different information. Mastermind Genomic Search Engine ( 26 ) mines full text articles and supplementary information for variants, described as protein or transcript changes. It has over 7.5 million full-text articles and 2.5 million supplemental datasets.…”

Section: Comprehensive Genome Annotation For Reference Vertebrate Speciesmentioning

confidence: 99%

Ensembl 2022

Cunningham

Allen

et al. 2021

Nucleic Acids Research

1,474

938

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Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

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“…The database HGMD 19 (http://www.hgmd.cf.ac.uk/ac/index.php), Ensembl Variation 20 , VarSome 21 (https://varsome.com/), ClinVar 22 (https://www.ncbi.nlm.nih.gov/clinvar/) and Genomenon Mastermind 23 (https://mastermind.genomenon.com/) were used alongside literature retrieval to identify additional ADAMTS13 variants with published reports of pathogenicity.…”

Section: Methodsmentioning

confidence: 99%

“…All paper were saved in Medline format and stored in NoSQL database MongoDB documents using NCBI Entrez Programming Utilities 17 (E-utilities) with Python package biopython 18 and pymongo implementation. The database HGMD 19 (http://www.hgmd.cf.ac.uk/ac/index.php), Ensembl Variation 20 , VarSome 21 (https://varsome.com/), ClinVar 22 (https://www.ncbi.nlm.nih.gov/clinvar/) and Genomenon Mastermind 23 (https://mastermind.genomenon.com/) were used alongside literature retrieval to identify additional ADAMTS13 variants with published reports of pathogenicity. A list of all single nucleotide variants (SNVs) for ADAMTS13 was compiled using Ensembl Variant Simulator.…”

Section: Materials and Methods Identification Of Known Disease-causing Variantsmentioning

confidence: 99%

The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome

Zhao

Fan

Sun³

2021

Preprint

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Purpose: Upshaw-Schulman syndrome (USS) is an autosomal recessive disease of thrombotic microangiopathy, caused by pathogenic variants in ADAMTS13. We aimed to (1) perform data mining pathogenicity of ADAMTS13 variants, (2) estimate carrier frequency and genetic prevalence of USS from gnomAD data, and (3) curated ADAMTS13 gene pathogenic variants database. Methods: PubMed and Scopus were comprehensive retrieved. All previously reported pathogenic ADAMTS13 variants were compiled and annotated with gnomAD allele frequencies. Pooled global and population-specific carrier frequency and genetic prevalence for USS were calculated using Hardy-Weinberg equation. Results: we mined reported disease-causing variants, of these were present in gnomAD exomes v2.1.1, filtering by allele frequency, pathogenicity of variants were classified by American College of Medical Genetics and Genomics criteria. The genetic prevalence and carrier frequency of USS was 0.43 per 1 million (95% CI: [0.36, 0.55]) and 1.31 per thousand, respectively. Combining known with novel pathogenic/likely pathogenic variants, the genetic prevalence and carrier frequency are 1 per 1 million (95% CI: [0.89, 1.37]) and 2.1 per thousand, respectively. Conclusion: the genetic prevalence and carrier frequency of Upshaw-Schulman syndrome are within range of previously rough estimated.

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Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation

Cited by 63 publications

References 26 publications

Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH)

Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH)

Ensembl 2022

The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome

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