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Large-scale inference of the point mutational spectrum in human segmental duplications
BACKGROUND: Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene evolution and genomic disease. The DNA sequence differences between copies of a segmental dupl...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640414/ https://www.ncbi.nlm.nih.gov/pubmed/19161616 http://dx.doi.org/10.1186/1471-2164-10-43 |
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author | Nakken, Sigve Rødland, Einar A Rognes, Torbjørn Hovig, Eivind |
author_facet | Nakken, Sigve Rødland, Einar A Rognes, Torbjørn Hovig, Eivind |
author_sort | Nakken, Sigve |
collection | PubMed |
description | BACKGROUND: Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene evolution and genomic disease. The DNA sequence differences between copies of a segmental duplication represent the result of various mutational events over time, since any two duplication copies originated from the same ancestral DNA sequence. Based on this fact, we have developed a computational scheme for inference of point mutational events in human segmental duplications, which we collectively term duplication-inferred mutations (DIMs). We have characterized these nucleotide substitutions by comparing them with high-quality SNPs from dbSNP, both in terms of sequence context and frequency of substitution types. RESULTS: Overall, DIMs show a lower ratio of transitions relative to transversions than SNPs, although this ratio approaches that of SNPs when considering DIMs within most recent duplications. Our findings indicate that DIMs and SNPs in general are caused by similar mutational mechanisms, with some deviances at the CpG dinucleotide. Furthermore, we discover a large number of reference SNPs that coincide with computationally inferred DIMs. The latter reflects how sequence variation in duplicated sequences can be misinterpreted as ordinary allelic variation. CONCLUSION: In summary, we show how DNA sequence analysis of segmental duplications can provide a genome-wide mutational spectrum that mirrors recent genome evolution. The inferred set of nucleotide substitutions represents a valuable complement to SNPs for the analysis of genetic variation and point mutagenesis. |
format | Text |
id | pubmed-2640414 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26404142009-02-12 Large-scale inference of the point mutational spectrum in human segmental duplications Nakken, Sigve Rødland, Einar A Rognes, Torbjørn Hovig, Eivind BMC Genomics Research Article BACKGROUND: Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene evolution and genomic disease. The DNA sequence differences between copies of a segmental duplication represent the result of various mutational events over time, since any two duplication copies originated from the same ancestral DNA sequence. Based on this fact, we have developed a computational scheme for inference of point mutational events in human segmental duplications, which we collectively term duplication-inferred mutations (DIMs). We have characterized these nucleotide substitutions by comparing them with high-quality SNPs from dbSNP, both in terms of sequence context and frequency of substitution types. RESULTS: Overall, DIMs show a lower ratio of transitions relative to transversions than SNPs, although this ratio approaches that of SNPs when considering DIMs within most recent duplications. Our findings indicate that DIMs and SNPs in general are caused by similar mutational mechanisms, with some deviances at the CpG dinucleotide. Furthermore, we discover a large number of reference SNPs that coincide with computationally inferred DIMs. The latter reflects how sequence variation in duplicated sequences can be misinterpreted as ordinary allelic variation. CONCLUSION: In summary, we show how DNA sequence analysis of segmental duplications can provide a genome-wide mutational spectrum that mirrors recent genome evolution. The inferred set of nucleotide substitutions represents a valuable complement to SNPs for the analysis of genetic variation and point mutagenesis. BioMed Central 2009-01-22 /pmc/articles/PMC2640414/ /pubmed/19161616 http://dx.doi.org/10.1186/1471-2164-10-43 Text en Copyright © 2009 Nakken 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 Nakken, Sigve Rødland, Einar A Rognes, Torbjørn Hovig, Eivind Large-scale inference of the point mutational spectrum in human segmental duplications |
title | Large-scale inference of the point mutational spectrum in human segmental duplications |
title_full | Large-scale inference of the point mutational spectrum in human segmental duplications |
title_fullStr | Large-scale inference of the point mutational spectrum in human segmental duplications |
title_full_unstemmed | Large-scale inference of the point mutational spectrum in human segmental duplications |
title_short | Large-scale inference of the point mutational spectrum in human segmental duplications |
title_sort | large-scale inference of the point mutational spectrum in human segmental duplications |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640414/ https://www.ncbi.nlm.nih.gov/pubmed/19161616 http://dx.doi.org/10.1186/1471-2164-10-43 |
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