Low copy repeats

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]

Misalignment of LCRs during non-allelic homologous recombination (NAHR)[3] is an important mechanism underlying the chromosomal microdeletion disorders as well as their reciprocal duplication partners.[4] 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,[5] hereditary neuropathy with liability to pressure palsies,[5] Smith–Magenis syndrome,[6] and Potocki–Lupski syndrome.[3]

Detection

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.

See also

References
  1. Johnson, M.E. (2008). Primate Gene and Genome Evolution Driven by Segmental Duplication of Chromosome 16 (PDF) (Ph.D.). Case Western Reserve University.
  2. Bailey, Jeffrey A.; Eichler, EE (2006). "Primate segmental duplications: crucibles of evolution, diversity and disease". Nature Reviews Genetics. 7 (7): 552–64. doi:10.1038/nrg1895. PMID 16770338. S2CID 3203768.
  3. Zhang, F; Potocki, L; Sampson, JB; Liu, P; Sanchez-Valle, A; Robbins-Furman, P; Navarro, AD; Wheeler, PG; Spence, JE; Brasington, CK; Withers, MA; Lupski, JR (12 March 2010). "Identification of uncommon recurrent Potocki-Lupski syndrome-associated duplications and the distribution of rearrangement types and mechanisms in PTLS". American Journal of Human Genetics. 86 (3): 462–70. doi:10.1016/j.ajhg.2010.02.001. PMC 2833368. PMID 20188345.
  4. Shaikh, TH; Kurahashi, H; Saitta, SC; O'Hare, AM; Hu, P; Roe, BA; Driscoll, DA; McDonald-McGinn, DM; Zackai, EH; Budarf, ML; Emanuel, BS (1 March 2000). "Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis". Human Molecular Genetics. 9 (4): 489–501. doi:10.1093/hmg/9.4.489. PMID 10699172.
  5. Inoue, K; Dewar, K; Katsanis, N; Reiter, LT; Lander, ES; Devon, KL; Wyman, DW; Lupski, JR; Birren, B (June 2001). "The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes". Genome Research. 11 (6): 1018–33. doi:10.1101/gr.180401. PMC 311111. PMID 11381029.
  6. Shaw, CJ; Withers, MA; Lupski, JR (July 2004). "Uncommon deletions of the Smith-Magenis syndrome region can be recurrent when alternate low-copy repeats act as homologous recombination substrates". American Journal of Human Genetics. 75 (1): 75–81. doi:10.1086/422016. PMC 1182010. PMID 15148657.
  7. "Genome-wide detection of segmental duplications".
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