Low copy repeats

Low copy repeats (LCRs), also known as segmental duplications (SDs), are highly homologous sequence elements within the eukaryotic genome. They are typically 10–300 kb in length, and bear >95% sequence identity. Though rare in most mammals, LCRs comprise a large portion of the human genome due to a significant expansion during primate evolution.

Misalignment of LCRs during non-allelic homologous recombination (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 (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, and Potocki-Lupski syndrome.