Indel

Indel is a molecular biology term that has different definitions in different fields:

• In evolutionary studies, indel is used to mean an insertion or a deletion^[1][2] and indels simply refers to the mutation class that includes both insertions, deletions, and the combination thereof,^[3][4][5] including insertion and deletion events that may be separated by many years.^[6]
• In germline and somatic mutation studies, however, indel describes a special mutation class, defined as a mutation resulting in a colocalized insertion and deletion and a net gain or loss in nucleotides, and microindel is defined as an indel that results in a net gain or loss of 1 to 50 nucleotides.^[7]

In coding regions of the genome, unless the length of an indel is a multiple of 3, they produce a frameshift mutation. For example, a common microindel which results in a frameshift causes Bloom syndrome in the Japanese population.^[8] Indels can be contrasted with a point mutation; where an Indel inserts and deletes nucleotides from a sequence, a point mutation is a form of substitution that replaces one of the nucleotides. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms.^[9] A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed.^[10]

Indels, as defined as either an insertion or deletion, can be used as genetic markers in natural populations, especially in phylogenetic studies.^[11][12]

An indel change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) stop codon in a different frame. Indels that are not multiples of 3 are particularly uncommon in coding regions but relatively common in non-coding regions. There are approximately 192-280 frameshifting indels in each person ^[13] . Note, however, the absolute rate of indels in most known genomes, including humans, tends to be markedly lower than base substitutions, except near highly repetitive regions, including homopolymers and microsatellites.

The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above. This is a change from its original use and meaning, which arose from systematics. In systematics, researchers could find differences between sequences, such as from two different species. But it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 G nucleotides at a locus and species B has 5 G's at the same locus. If the mode of selection is unknown, we can't tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When we cannot infer the phylogenetic direction of the sequence change, the sequence change event is referred to as an "indel".

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