Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism

Background: The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should...

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Autores: Bosch Pagès, Nina, Morell, Marta, Ponsa, Immaculada, Mercader Bigas, Josep Maria, Armengol i Dulcet, Lluís, Estivill, Xavier, 1955-
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2009
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/16437
Acesso em linha:http://hdl.handle.net/10230/16437
http://dx.doi.org/10.1371/journal.pone.0008269
Access Level:acceso abierto
Palavra-chave:Cromosomes humans
Genoma humà
Citogenètica
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spelling Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphismBosch Pagès, NinaMorell, MartaPonsa, ImmaculadaMercader Bigas, Josep MariaArmengol i Dulcet, LluísEstivill, Xavier, 1955-Cromosomes humansGenoma humàCitogenèticaBackground: The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results: We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH). The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples. Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p<0.0005) according to the orientation of the 8p23.1 region. Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion: By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred. Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status. FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.Public Library of Science (PLoS)201220122009info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/16437http://dx.doi.org/10.1371/journal.pone.0008269reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésPLoS ONE. 2009;4(12):e8269© 2009 Bosch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://creativecommons.org/licenses/by/2.5/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/164372026-05-29T05:05:01Z
dc.title.none.fl_str_mv Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
title Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
spellingShingle Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
Bosch Pagès, Nina
Cromosomes humans
Genoma humà
Citogenètica
title_short Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
title_full Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
title_fullStr Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
title_full_unstemmed Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
title_sort Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism
dc.creator.none.fl_str_mv Bosch Pagès, Nina
Morell, Marta
Ponsa, Immaculada
Mercader Bigas, Josep Maria
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author Bosch Pagès, Nina
author_facet Bosch Pagès, Nina
Morell, Marta
Ponsa, Immaculada
Mercader Bigas, Josep Maria
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author_role author
author2 Morell, Marta
Ponsa, Immaculada
Mercader Bigas, Josep Maria
Armengol i Dulcet, Lluís
Estivill, Xavier, 1955-
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Cromosomes humans
Genoma humà
Citogenètica
topic Cromosomes humans
Genoma humà
Citogenètica
description Background: The human chromosome 8p23.1 region contains a 3.8–4.5 Mb segment which can be found in different orientations (defined as genomic inversion) among individuals. The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results: We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH). The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples. Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p<0.0005) according to the orientation of the 8p23.1 region. Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion: By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred. Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status. FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.
publishDate 2009
dc.date.none.fl_str_mv 2009
2012
2012
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/16437
http://dx.doi.org/10.1371/journal.pone.0008269
url http://hdl.handle.net/10230/16437
http://dx.doi.org/10.1371/journal.pone.0008269
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS ONE. 2009;4(12):e8269
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/2.5/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/2.5/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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