title: Identical repeated backbone of the human genome.
abstract: BACKGROUND
  Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome.
  
  
  RESULTS
  The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to approximately 2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes.
  
  
  CONCLUSIONS
  In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México. czepeda@lcg.unam.mx
authors.forename: Cinthya J
authors.initials: CJ
authors.lastname: Zepeda-Mendoza
authors.forename: Tzitziki
authors.initials: T
authors.lastname: Lemus
authors.forename: Omar
authors.initials: O
authors.lastname: Yáñez
authors.forename: Delfino
authors.initials: D
authors.lastname: García
authors.forename: David
authors.initials: D
authors.lastname: Valle-García
authors.forename: Karla F
authors.initials: KF
authors.lastname: Meza-Sosa
authors.forename: María
authors.initials: M
authors.lastname: Gutiérrez-Arcelus
authors.forename: Yamile
authors.initials: Y
authors.lastname: Márquez-Ortiz
authors.forename: Rocío
authors.initials: R
authors.lastname: Domínguez-Vidaña
authors.forename: Claudia
authors.initials: C
authors.lastname: Gonzaga-Jauregui
authors.forename: Margarita
authors.initials: M
authors.lastname: Flores
authors.forename: Rafael
authors.initials: R
authors.lastname: Palacios
mesh_terms: D056915:DNA Copy Number Variations; D015894:Genome, Human; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA