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Genetic Marker

Source: vignettes/articles/genetic_marker.Rmd
genetic_marker.Rmd

The genetic marker is the central concept in all MGI reports. Some of the reports made accessible with this package are about characterizing a subset of mouse genetic markers, whereas others are about their relationships to other similar genetic entities in other databases.

Put simply, a marker is the means by which a gene or a locus is identified.

Genetic marker definition

In the context of Mouse Gene Informatics (MGI), a genetic marker is defined as any biological feature that can be used to identify a specific position on a chromosome through various mapping methods such as genetic, physical, or other forms of mapping. These features include genes, anonymous DNA segments, mutations, or phenotypes.

Defining features of genetic markers

  1. Positional reference: They serve as points of reference for locating other genetic features on chromosomes.

  2. Assay dependence: The identification of markers depends on specific assays that detect genetic variation.

  3. Biological significance: Markers can distinguish particular biological states, such as gene expression profiles or characteristic morphologies.

Marker types

  • Gene: A functional unit of inheritance, usually encoding a protein or RNA.
  • DNA Segment: Mapped anonymous DNA segments used for generating genetic maps.
  • Cytogenetic Marker: Identified through cytogenetic techniques, visible under a microscope.
  • Quantitative Trait Locus (QTL): Polymorphic loci associated with the variation in phenotypic traits.
  • Transgene: Genes that have been transferred naturally or by any of a number of genetic engineering techniques.
  • Pseudogene: Non-functional sequences that resemble functional genes.
  • BAC/YAC Ends: Ends of Bacterial Artificial Chromosomes (BACs) or Yeast Artificial Chromosomes (YACs) used in mapping.
  • Other Genome Features: Any other identified features within the genome.
  • Complex/Cluster/Region: Grouped genomic entities located closely on a chromosome.

These marker types are retrievable with marker_types().

Markers as database entities

Markers provide a framework for organizing and communicating genetic information, facilitating the mapping of genetic features, and helping in the identification of genes responsible for phenotypic traits.

In Mouse Genome Informatics (MGI), a marker is an object for which unique official nomenclature is assigned, i.e. an accession identifier: a unique alphanumeric character string that is used to unambiguously identify a particular record in the MGI database. In report data returned by read_report() this variable is called marker_id. Other common accompanying variables include:

  • marker_status: marker status, indicating whether a currently in-use genetic marker, or if it has been withdrawn .
  • marker_type: the type of genetic marker, as discussed above.
  • marker_name: word or phrase that uniquely identifies the genetic marker, e.g. a gene or allele name.
  • marker_symbol: a unique abbreviation of the marker name.

References