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Identical repeated backbone of the human genome
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 remodel...
Autores principales: | , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845111/ https://www.ncbi.nlm.nih.gov/pubmed/20096123 http://dx.doi.org/10.1186/1471-2164-11-60 |
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author | Zepeda-Mendoza, Cinthya J Lemus, Tzitziki Yáñez, Omar García, Delfino Valle-García, David Meza-Sosa, Karla F Gutiérrez-Arcelus, María Márquez-Ortiz, Yamile Domínguez-Vidaña, Rocío Gonzaga-Jauregui, Claudia Flores, Margarita Palacios, Rafael |
author_facet | Zepeda-Mendoza, Cinthya J Lemus, Tzitziki Yáñez, Omar García, Delfino Valle-García, David Meza-Sosa, Karla F Gutiérrez-Arcelus, María Márquez-Ortiz, Yamile Domínguez-Vidaña, Rocío Gonzaga-Jauregui, Claudia Flores, Margarita Palacios, Rafael |
author_sort | Zepeda-Mendoza, Cinthya J |
collection | PubMed |
description | 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 ~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. |
format | Text |
id | pubmed-2845111 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-28451112010-03-26 Identical repeated backbone of the human genome Zepeda-Mendoza, Cinthya J Lemus, Tzitziki Yáñez, Omar García, Delfino Valle-García, David Meza-Sosa, Karla F Gutiérrez-Arcelus, María Márquez-Ortiz, Yamile Domínguez-Vidaña, Rocío Gonzaga-Jauregui, Claudia Flores, Margarita Palacios, Rafael BMC Genomics Research Article 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 ~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. BioMed Central 2010-01-23 /pmc/articles/PMC2845111/ /pubmed/20096123 http://dx.doi.org/10.1186/1471-2164-11-60 Text en Copyright ©2010 Zepeda-Mendoza et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Zepeda-Mendoza, Cinthya J Lemus, Tzitziki Yáñez, Omar García, Delfino Valle-García, David Meza-Sosa, Karla F Gutiérrez-Arcelus, María Márquez-Ortiz, Yamile Domínguez-Vidaña, Rocío Gonzaga-Jauregui, Claudia Flores, Margarita Palacios, Rafael Identical repeated backbone of the human genome |
title | Identical repeated backbone of the human genome |
title_full | Identical repeated backbone of the human genome |
title_fullStr | Identical repeated backbone of the human genome |
title_full_unstemmed | Identical repeated backbone of the human genome |
title_short | Identical repeated backbone of the human genome |
title_sort | identical repeated backbone of the human genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845111/ https://www.ncbi.nlm.nih.gov/pubmed/20096123 http://dx.doi.org/10.1186/1471-2164-11-60 |
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