Talk:Indel

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Definition of Microindel

I believe the definition of "microindel" here is misleading. This article suggests that microindel is specifically defined as an indel ranging from 1-50bp in size:

A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides.

This is not a general rule. The reference it goes back to self-defines "microindel" in this way:

The term ‘‘indel’’ has different definitions in different fields. In evolutionary studies, ‘‘indel’’ is used to mean an insertion or a deletion [Kondrashov and Rogozin, 2004; Ogurtsov et al., 2004] and ‘‘indels’’ simply refers to the mutation class that includes both insertions, deletions, and the combination thereof [Halangoda et al., 2001; Griffiths et al., 2002; Gregory, 2004], including insertion and deletion events that may be separated by many years [Mank et al., 2004]. In germline and somatic mutation studies, however, ‘‘indel’’ describes a special mutation class, defined as a colocalized insertion and deletion [Halangoda et al., 2001], and is sometimes defined to include cases in which the insertion and deletion are the same size (tandem base mutations [TBMs]). However, inclusion of TBMs, as in Chuzhanova et al. [2003], may confound an analysis since TBMs may result from fundamentally different mechanisms [Hill et al., 2003]. Herein, the term ‘‘indel’’ is 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 from 1 to 50 nucleotides.
— Gonzalez et al., Somatic Microindels: Analysis in Mouse Soma and Comparison With the Human Germline, HUMAN MUTATION 28(1), 69-80, 2007

As the source article states, they are defining the terms "indel" and "microindel" in particular ways for the sake of that article.

The reason I bring this up is because recently I have been considering the use of the term "microindels" to refer to the set of microdeletions and microduplications (or "microinsertions" if you will) in a genome. In the genome sequencing and medical genetics world, a microdeletion can be up to 50Mb in size, so it seems inconsistent with the definition of "microindel" presented in this article, which appears to be solely based on this one source. A source that was not attempting to define the term for all fields, but for the particular article within which the term was being used.

In the sequencing world, at least, "indel" is common shorthand for "small indel" or "short indel", which would be generally defined as an insertion or deletion from 0-50bp or 0-100bp in size. "Microdeletion" and "microduplication" are referring to larger events--commonly thought of as at least tens of kilobases in size, and ranging well into the megabase range. Therefore, in this community at least, a "microindel" seems to logically follow the definition of a larger insertion or deletion.

That said, I have difficulty coming up with a source defining the term "microindel" in this way. I would therefore suggest that at the very least this article be changed to reflect that the definition given for "microindel" was particular to that study, e.g. "Gonzalez et al., 2007 defined microindel as "an indel that results in a net gain or loss of from 1 to 50 nucleotides."

Mjatucla (talk) 18:18, 18 October 2013 (UTC)[reply]

Needs Updating

I think the information presented here is a bit out of date. The article states: "The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above." I would argue that in the past five years, not only has "indel" been co-opted, but it is now more commonly used to refer to one of the following:

An insertion or deletion detected by array CGH, commonly in the hundreds of kilobases to megabases in size.
A small insertion or deletion detected by next generation sequencing.

Mjatucla (talk) 18:18, 18 October 2013 (UTC)[reply]

Wiki Education assignment: Bioinformatics

This article was the subject of a Wiki Education Foundation-supported course assignment, between 29 August 2022 and 15 December 2022. Further details are available on the course page. Student editor(s): Dzapb (article contribs).

— Assignment last updated by SmolKraken (talk) 23:54, 11 October 2022 (UTC)[reply]