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 (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
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
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The ...
record containing the
transcript and
protein 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 part ...
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 of a fatty acid used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are used ...
Web service 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
The Hypertext Transfer Protocol (HTTP) 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, w ...
/
RPC+
JSON
JSON (JavaScript Object Notation, pronounced ; also ) is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other se ...
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
A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosomal abnormality. Although polygenic disorders ...
. 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 molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules with ...
or
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
involved. With this simple rule, a deletion of the nucleotide
guanine
Guanine () (symbol G or Gua) is one of the four main nucleobases 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 is called ...
(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 (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
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate spe ...
, NCBI sequence viewer)
References
{{Reflist
External links
Mutalyzer websiteHGVS sequence variant nomenclature websiteLOVD 2.0 websiteGenBank websiteLocus Reference Genomic websiteRefSeq website
Medical genetics