Low copy repeats (LCRs), also known as segmental duplications (SDs), 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 owing to a significant expansion during
primate evolution.[1] In humans,
chromosomes Y and
22 have the greatest proportion of SDs: 50.4% and 11.9% respectively.[2]
The two widely accepted methods for SD detection[7] 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.