Genomic Insertions and Deletions (Indels)

Indels are insertions and deletions in the genome; 40% of indels are single nucleotide changes, while 98% consist of changes fewer than 100 bps. Mechanisms for small indel events are replication slippage (as seen in STR regions), recombination, unequal crossing over, and tandem duplication caused by imperfect repair of double strand breaks. Larger indels may be caused by segmental duplications and transposable elements. Humans have an expanded genome compared to great apes due in part to insertions resulting from retrotransposon activity. Indels that are due to repetitive sequence-mediated deletions, and indels that are not associated with repeat sequences, do not differ significantly by species. Retrotransposon-produced insertions are lineage specific and the increased insertions in humans are caused by younger retrotransposons (Alu, L1, LTR), not ancient ones (L2, L3, DNA transposons). Intergenic indels are more common than intragenic indels; intragenic indels account for 0.21% of human sequence uniqueness, whereas intragenic indels account for 1.4%. A recent study identified 844,552 human-specific indels of segments shorter than 100 base pairs, and of genes with known function, those most affected by indels in a human-specific fashion are involved in transcription and translation regulatory activities.