Low copy repeats (LCRs), also known as segmental duplications (SDs), or duplicons, are DNA sequences present in multiple locations within a genome that share high levels of sequence identity.

Repeats

The repeats, or duplications, are typically 10–300 kb in length, and bear greater than 95% sequence identity. Though rare in most mammals, LCRs comprise a large portion of the

human genome The human genome is a complete set of nucleic acid sequences for humans, encoded as the DNA within each of the 23 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual Mitochondrial DNA, mitochondria. These ar ...

owing to a significant expansion during primate evolution. In humans, chromosomes Y and 22 have the greatest proportion of SDs: 50.4% and 11.9% respectively. SRGAP2 is an SD. Misalignment of LCRs during

non-allelic homologous recombination Non-allelic homologous recombination (NAHR) is a form of homologous recombination that occurs between two lengths of DNA that have high sequence similarity, but are not alleles. It usually occurs between sequences of DNA that have been previously ...

(NAHR) is an important mechanism underlying the chromosomal microdeletion disorders as well as their reciprocal duplication partners. Many LCRs are concentrated in "hotspots", such as the 17p11-12 region, 27% of which is composed of LCR sequence. NAHR and

non-homologous end joining Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. It is called "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair ...

(NHEJ) within this region are responsible for a wide range of disorders, including Charcot–Marie–Tooth syndrome type 1A, hereditary neuropathy with liability to pressure palsies,

Smith–Magenis syndrome Smith–Magenis syndrome (SMS), also known as 17p-microdeletion syndrome, is a microdeletion syndrome characterized by an abnormality in the short (p) arm of chromosome 17. It has features including intellectual disability, facial abnormalities, ...

, and Potocki–Lupski syndrome.

Detection

The two widely accepted methods for SD detection are: *1. Whole-genome assembly comparison (WGAC), in which regions of homology within the assembly are identified. *2. Whole-genome shotgun sequence detection (WSSD), in which the duplication of regions is inferred by increased read coverage at the site of segmental duplication.

References

{{Repeated sequence Molecular genetics Mutation

Repeats

Detection

See also

References