Mutalyzer is a web-based software tool which was primarily developed to check the description of sequence variants identified in a

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

during

genetic testing Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or ...

. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a

DNA sequence A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nu ...

record containing the transcript and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

feature annotation as a reference. Mutalyzer 2 accepts

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...

and Locus Reference Genomic (LRG) records. The annotation is also used to apply the correct codon translation tables and generate DNA and protein variant descriptions for any organism. The Mutalyzer server supports programmatic access via a

SOAP Soap is a salt (chemistry), salt of a fatty acid (sometimes other carboxylic acids) used for cleaning and lubricating products as well as other applications. In a domestic setting, soaps, specifically "toilet soaps", are surfactants usually u ...

Web service A web service (WS) is either: * a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or * a server running on a computer device, listening for requests at a particular port over a n ...

described in the

Web Services Description Language The Web Services Description Language (WSDL ) is an XML-based interface description language that is used for describing the functionality offered by a web service. The acronym is also used for any specific WSDL description of a web service (also ...

(WSDL) and an

HTTP HTTP (Hypertext Transfer Protocol) is an application layer protocol in the Internet protocol suite model for distributed, collaborative, hypermedia information systems. HTTP is the foundation of data communication for the World Wide Web, wher ...

/ RPC+

JSON JSON (JavaScript Object Notation, pronounced or ) is an open standard file format and electronic data interchange, data interchange format that uses Human-readable medium and data, human-readable text to store and transmit data objects consi ...

web service.

Background

Genetic testing Genetic testing, also known as DNA testing, is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression, or ...

is generally performed in families with hereditary disease. Any sequence variant identified in a gene can be described in test reports using the position of the change and the

nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

involved. With this simple rule, a deletion of the nucleotide

guanine Guanine () (symbol G or Gua) is one of the four main nucleotide bases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine ( uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside ...

(G) in a stretch of 4 G nucleotides might be described in 4 different ways, when each of the G positions is used. Although different descriptions do not affect the functional consequences of the change, they may obfuscate the fact that two persons share the same variant or the real frequency of a variant in the population. The standard human sequence variant nomenclature proposed by the Human Genome Variation Society was developed to solve this problem. Proper variant descriptions are expected to facilitate searches for more information about the functional consequences in the literature and in gene variant or locus-specific databases (LSDBs). Mutalyzer is used by the Leiden Open Variation Database ( LOVD), which stores sequence variant information for many human genes, to check variant descriptions before submission of new data. This helps data sharing, display and integration with other

genetic resources Genetic resources are genetic material of actual or potential value, where genetic material means any material of plant, animal, microbial genetics, microbial or other origin containing functional units of heredity. Genetic resources is one of the ...

(e.g.,

Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other v ...

, UCSC Genome Browser, NCBI sequence viewer)

References

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External links

Mutalyzer website

HGVS sequence variant nomenclature website

LOVD 2.0 website

GenBank website

Locus Reference Genomic website

RefSeq website
Medical genetics