Biology:Indel

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Short description: Insertions and deletions in a genome

Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. Indels ≥ 50 bases in length are classified as structural variants.[1][2]

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 Jewish or Japanese population.[3] Indels can be contrasted with a point mutation. An indel inserts or 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.[4] 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).[5]

Indels, being either insertions, or deletions, can be used as genetic markers in natural populations, especially in phylogenetic studies.[6][7] It has been shown that genomic regions with multiple indels can also be used for species-identification procedures.[8][9][10]

An indel change of a single base pair in the coding part of an mRNA results in a frameshift during mRNA translation that could lead 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.[11][12] There are approximately 192-280 frameshifting indels in each person.[13] Indels are likely to represent between 16% and 25% of all sequence polymorphisms in humans.[14] In most known genomes, including humans, indel frequency tends to be markedly lower than that of single nucleotide polymorphisms (SNP), except near highly repetitive regions, including homopolymers and microsatellites.[15]

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]

Using passenger-immunoglobulin mouse models, a study found that the most prevalent indel events are the activation-induced cytidine deaminase (AID)-dependent ±1-base pair (bp) indels, which can lead to deleterious outcomes, whereas longer in-frame indels were rare outcomes.[16]

See also

References

  1. ↑ Mahmoud, Medhat; Gobet, Nastassia; Cruz-Dávalos, Diana Ivette; Mounier, Ninon; Dessimoz, Christophe; Sedlazeck, Fritz J. (2019). "Structural variant calling: the long and the short of it". Genome Biology 20. doi:10.1186/s13059-019-1828-7. 
  2. ↑ Ebert, Peter et al. (2021). "Haplotype-resolved diverse human genomes and integrated analysis of structural variation". Science 372 (6537). doi:10.1126/science.abf7117. PMC 8026704. https://www.science.org/doi/10.1126/science.abf7117. 
  3. ↑ "Non-linear accumulation of 8-hydroxy-2'-deoxyguanosine, a marker of oxidized DNA damage, during aging". Mutation Research 316 (5–6): 277–285. May 1996. doi:10.1016/S0921-8734(96)90010-7. PMID 8649461. 
  4. ↑ "Spontaneous tandem-base mutations (TBM) show dramatic tissue, age, pattern and spectrum specificity". Mutation Research 534 (1–2): 173–186. January 2003. doi:10.1016/S1383-5718(02)00277-2. PMID 12504766. 
  5. ↑ "Tandem-base mutations occur in mouse liver and adipose tissue preferentially as G:C to T:A transversions and accumulate with age". Environmental and Molecular Mutagenesis 33 (4): 320–324. 1999. doi:10.1002/(SICI)1098-2280(1999)33:4<320::AID-EM9>3.0.CO;2-S. PMID 10398380. 
  6. ↑ "Insertion-deletion polymorphisms (indels) as genetic markers in natural populations". BMC Genetics 9: 8. January 2008. doi:10.1186/1471-2156-9-8. PMID 18211670. 
  7. ↑ "Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene". PLOS ONE 3 (1): e1386. January 2008. doi:10.1371/journal.pone.0001386. PMID 18167545. Bibcode: 2008PLoSO...3.1386E. 
  8. ↑ "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 (22): e203. December 2010. doi:10.1093/nar/gkq865. PMID 20923781. 
  9. ↑ "Forensic species identification based on size variation of mitochondrial DNA hypervariable regions". International Journal of Legal Medicine 123 (2): 177–184. March 2009. doi:10.1007/s00414-008-0306-7. PMID 19052767. 
  10. ↑ "Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding". Nucleic Acids Research 35 (3): e14. 26 January 2007. doi:10.1093/nar/gkl938. PMID 17169982. 
  11. ↑ "Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a Landrace cultivar of foxtail millet". PLOS ONE 8 (9): e73514. 2013. doi:10.1371/journal.pone.0073514. PMID 24039970. Bibcode: 2013PLoSO...873514B. 
  12. ↑ "Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)". Genome Biology 12 (11): R114. November 2011. doi:10.1186/gb-2011-12-11-r114. PMID 22104744. 
  13. ↑ "A map of human genome variation from population-scale sequencing". Nature 467 (7319): 1061–1073. October 2010. doi:10.1038/nature09534. PMID 20981092. Bibcode: 2010Natur.467.1061T. 
  14. ↑ "An initial map of insertion and deletion (INDEL) variation in the human genome". Genome Research 16 (9): 1182–1190. September 2006. doi:10.1101/gr.4565806. PMID 16902084. 
  15. ↑ Lodish, H (2021). Molecular Cell Biology (9th ed.). W. H. Freeman. pp. 726–892. 
  16. ↑ Hao, Qian; Zhan, Chuanzong; Lian, Chaoyang; Luo, Simin; Cao, Wenyi; Wang, Binbin; Xie, Xia; Ye, Xiaofei et al. (2023-03-31). "DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification" (in en). Science Immunology 8 (81): eade1167. doi:10.1126/sciimmunol.ade1167. ISSN 2470-9468. PMID 36961908. 



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