Human Mutation Databases

Horaitis, Ourania; Cotton, Richard G.H.

doi:10.1002/0471142905.hg0711s37

Cited by 3 publications

(3 citation statements)

References 18 publications

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“…To facilitate scientific and especially diagnostic application, all variants detected should be submitted to a relevant public repository, preferably a gene variant database [Locus Specific DataBase (LSDB), UNIT here (Horaitis and Cotton, )]. Available databases can be found using the HGNC‐approved gene symbol, e.g., http://DMD.lovd.nl or http://TP53.lovd.nl, linking to a list of all available databases (http://www.lovd.nl/lsdbs).…”

Section: Recommendationsmentioning

confidence: 99%

Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer

Dunnen

2016

CP Human Genetics

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Consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome, in particular in DNA diagnostics. The HGVS nomenclature-recommendations for the description of sequence variants as originally proposed by the Human Genome Variation Society-has gradually been accepted as the international standard for variant description. In this unit, we describe the current recommendations (HGVS version 15.11) regarding how to describe variants at the DNA, RNA, and protein level. We explain the rationale and give example descriptions for all variant types: substitution, deletion, duplication, insertion, inversion, conversion, and complex, as well as special types occurring only on the RNA (splicing) or protein level (nonsense, frame shift, extension). Finally, we point users to available support tools and give examples for the use of the freely available Mutalyzer suite. An extensive version of the HGVS recommendations is available online at http://varnomen.hgvs.org/. © 2016 by John Wiley & Sons, Inc.

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Section: Recommendationsmentioning

confidence: 99%

Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer

Dunnen

2016

CP Human Genetics

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“…OMIM is an often‐overlooked resource that provides an incredible amount of genomic and clinical information, and should be considered the "first stop" when beginning to research a new genetic disease or disorder. UNIT here (Horaitis and Cotton, ) presents an overview of human mutation databases, presenting the reader with a brief history of mutation databases and a thorough discussion of the various types of mutation databases currently available. UNIT here (Stenson et al., ) covers the Human Gene Mutation Database (HGMD), a collection of information on published mutations responsible for human genetic diseases and disorders.…”

Section: Overviewmentioning

confidence: 99%

The Importance of Biological Databases in Biological Discovery

Baxevanis¹,

Bateman

2015

CP in Bioinformatics

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Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non‐sequence‐centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. © 2015 by John Wiley & Sons, Inc.

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“…However, challenges are presented in integrating these data into one single database, and/or graphical user interface such as a genome browser. Quality of information, data formats, and underlying sequences can differ, and the need for security in dealing with patient data present restrictions on data access (Horaitis and Cotton, 2005). The necessity of integrating information from disparate sources is clear, and projects are currently underway to standardize data formats (Dalgleish et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Disease and Phenotype Data at Ensembl

Spudich

Fernández‐Suárez

2011

CP Human Genetics

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Biological databases are an important resource for the life sciences community. Accessing the hundreds of databases supporting molecular biology and related fields is a daunting and time-consuming task. Integrating this information into one access point is a necessity for the life sciences community, which includes researchers focusing on human disease. Here we discuss the Ensembl genome browser, which acts as a single entry point with Graphical User Interface to data from multiple projects, including OMIM, dbSNP, and the NHGRI GWAS catalog. Ensembl provides a comprehensive source of annotation for the human genome, along with other species of biomedical interest. In this unit, we explore how to use the Ensembl genome browser in example queries related to human genetic diseases. Support protocols demonstrate quick sequence export using the BioMart tool.

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Human Mutation Databases

Abstract: The first part of this unit compares general and locus‐specific mutation databases. The second section deals with submitting data. The third part provides guidance for accessing mutation data. The final section offers advice on database construction.

Cited by 3 publications

References 18 publications

Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer

Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer

The Importance of Biological Databases in Biological Discovery

Disease and Phenotype Data at Ensembl

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