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Identification of RNA editing sites in the SNP database
The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of ident...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185576/ https://www.ncbi.nlm.nih.gov/pubmed/16100382 http://dx.doi.org/10.1093/nar/gki771 |
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author | Eisenberg, Eli Adamsky, Konstantin Cohen, Lital Amariglio, Ninette Hirshberg, Abraham Rechavi, Gideon Levanon, Erez Y. |
author_facet | Eisenberg, Eli Adamsky, Konstantin Cohen, Lital Amariglio, Ninette Hirshberg, Abraham Rechavi, Gideon Levanon, Erez Y. |
author_sort | Eisenberg, Eli |
collection | PubMed |
description | The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications. |
format | Text |
id | pubmed-1185576 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-11855762005-08-15 Identification of RNA editing sites in the SNP database Eisenberg, Eli Adamsky, Konstantin Cohen, Lital Amariglio, Ninette Hirshberg, Abraham Rechavi, Gideon Levanon, Erez Y. Nucleic Acids Res Article The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications. Oxford University Press 2005 2005-08-12 /pmc/articles/PMC1185576/ /pubmed/16100382 http://dx.doi.org/10.1093/nar/gki771 Text en © The Author 2005. Published by Oxford University Press. All rights reserved |
spellingShingle | Article Eisenberg, Eli Adamsky, Konstantin Cohen, Lital Amariglio, Ninette Hirshberg, Abraham Rechavi, Gideon Levanon, Erez Y. Identification of RNA editing sites in the SNP database |
title | Identification of RNA editing sites in the SNP database |
title_full | Identification of RNA editing sites in the SNP database |
title_fullStr | Identification of RNA editing sites in the SNP database |
title_full_unstemmed | Identification of RNA editing sites in the SNP database |
title_short | Identification of RNA editing sites in the SNP database |
title_sort | identification of rna editing sites in the snp database |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1185576/ https://www.ncbi.nlm.nih.gov/pubmed/16100382 http://dx.doi.org/10.1093/nar/gki771 |
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