Indel

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For the village on Kola Peninsula, see Indel, Murmansk Oblast.

Indel is a molecular biology term for the insertion or the deletion of bases in the DNA of an organism. It has slightly different definitions between its use in evolutionary studies and its use in germline and somatic mutation studies.

  • 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, and may not be related to each other in any way.[6]
  • In germline and somatic mutation studies, indel describes a special mutation class, defined as a mutation resulting in both an insertion of nucleotides and a deletion nucleotides which results in a net change in the total number of nucleotides, where both changes are nearby on the DNA. A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides.[7]

In coding regions of the genome, unless the length of an indel is a multiple of 3, it will 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. An indel inserts and deletes nucleotides from a sequence, while a point mutation is a form of substitution that replaces one of the nucleotides without changing the overall number in the DNA. 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] It has been shown that genomic regions with multiple indels can also be used for species-identification procedures.[13][14][15]

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.[citation needed] There are approximately 192-280 frameshifting indels in each person.[16] 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, one can not tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When one cannot infer the phylogenetic direction of the sequence change, the sequence change event is referred to as an "indel".[citation needed]

References

  1. ↑ Kondrashov AS, Rogozin IB (February 2004). "Context of deletions and insertions in human coding sequences". Hum. Mutat. 23 (2): 177–85. doi:10.1002/humu.10312. PMID 14722921. 
  2. ↑ Ogurtsov AY, Sunyaev S, Kondrashov AS (August 2004). "Indel-based evolutionary distance and mouse-human divergence". Genome Res. 14 (8): 1610–6. doi:10.1101/gr.2450504. PMC 509270. PMID 15289479. 
  3. ↑ William M. Gelbart; Lewontin, Richard C.; Griffiths, Anthony J. F.; Miller, Jeffrey H. (2002). Modern genetic analysis: integrating genes and genomes. New York: W.H. Freeman and CO. p. 736. ISBN 0-7167-4382-5. 
  4. ↑ Gregory TR (January 2004). "Insertion-deletion biases and the evolution of genome size". Gene 324: 15–34. doi:10.1016/j.gene.2003.09.030. PMID 14693368. 
  5. ↑ Halangoda A, Still JG, Hill KA, Sommer SS (2001). "Spontaneous microdeletions and microinsertions in a transgenic mouse mutation detection system: analysis of age, tissue, and sequence specificity". Environ. Mol. Mutagen. 37 (4): 311–23. doi:10.1002/em.1038. PMID 11424181. 
  6. ↑ Sachin apurwa, Wilson MD, Rubio JM, Post RJ (March 2004). "A molecular marker for the identification of Simulium squamosum (Diptera: Simuliidae)". Ann Trop Med Parasitol 98 (2): 197–208. doi:10.1179/000349804225003118. PMID 15035730. 
  7. ↑ Gonzalez KD, Hill KA, Li K et al. (January 2007). "Somatic microindels: analysis in mouse soma and comparison with the human germline". Hum. Mutat. 28 (1): 69–80. doi:10.1002/humu.20416. PMID 16977595. 
  8. ↑ Kaneko T, Tahara S, Matsuo M (May 1996). "Non-linear accumulation of 8-hydroxy-2'-deoxyguanosine, a marker of oxidized DNA damage, during aging". Mutat. Res. 316 (5–6): 277–85. doi:10.1016/S0921-8734(96)90010-7. PMID 8649461. 
  9. ↑ Hill KA, Wang J, Farwell KD, Sommer SS (January 2003). "Spontaneous tandem-base mutations (TBM) show dramatic tissue, age, pattern and spectrum specificity". Mutat. Res. 534 (1–2): 173–86. doi:10.1016/S1383-5718(02)00277-2. PMID 12504766. 
  10. ↑ Buettner VL, Hill KA, Halangoda A, Sommer SS. 1999. Tandem-based mutations occur in mouse liver and adipose tissue preferentially as G:C to T:A transversions and accumulate with age. Environ Mol Mutagen 33:320–324.
  11. ↑ Väli U, Brandström M, Johansson M, Ellegren H (2008). "Insertion-deletion polymorphisms (indels) as genetic markers in natural populations". BMC Genetic 9: 8. doi:10.1186/1471-2156-9-8. PMC 2266919. PMID 18211670. 
  12. ↑ Erixon P, Oxelman B (2008). "Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene". In Volff, Jean-Nicolas. PLoS ONE 3 (1): e1386. doi:10.1371/journal.pone.0001386. PMC 2148103. PMID 18167545. 
  13. ↑ Pereira, F.; Carneiro, J.; Matthiesen, R.; van Asch, B.; Pinto, N.; Gusmao, L.; Amorim, A. (4 October 2010). "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 (22): e203–e203. doi:10.1093/nar/gkq865. 
  14. ↑ Nakamura, H; Muro, T; Imamura, S; Yuasa, I (March 2009). "Forensic species identification based on size variation of mitochondrial DNA hypervariable regions.". International journal of legal medicine 123 (2): 177–84. doi:10.1007/s00414-008-0306-7. PMID 19052767. 
  15. ↑ Taberlet, P.; Coissac, E.; Pompanon, F.; Gielly, L.; Miquel, C.; Valentini, A.; Vermat, T.; Corthier, G.; Brochmann, C.; Willerslev, E. (26 January 2007). "Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding". Nucleic Acids Research 35 (3): e14–e14. doi:10.1093/nar/gkl938. 
  16. ↑ 1000 Genomes Project, Consortium; Durbin, RM, Abecasis, GR, Altshuler, DL, Auton, A, Brooks, LD, Durbin, RM, Gibbs, RA, Hurles, ME, McVean, GA (2010-10-28). "A map of human genome variation from population-scale sequencing". Nature 467 (7319): 1061–73. doi:10.1038/nature09534. PMC 3042601. PMID 20981092. 
Mechanisms of mutation
Mutation with respect to structure
Large-scale mutation
  • Chromosomal translocations
  • Chromosomal inversions
Mutation with respect to overall fitness
  • Deleterious mutation
  • Advantageous mutation
  • Neutral mutation
  • Nearly neutral mutation
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