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Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

BACKGROUND: We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C→...

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Autores principales: Vives, Sergi, Gilbert, M Thomas, Arenas, Conchita, Gigli, Elena, Lao, Oscar, Lalueza-Fox, Carles
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547106/
https://www.ncbi.nlm.nih.gov/pubmed/18710493
http://dx.doi.org/10.1186/1756-0500-1-40
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author Vives, Sergi
Gilbert, M Thomas
Arenas, Conchita
Gigli, Elena
Lao, Oscar
Lalueza-Fox, Carles
author_facet Vives, Sergi
Gilbert, M Thomas
Arenas, Conchita
Gigli, Elena
Lao, Oscar
Lalueza-Fox, Carles
author_sort Vives, Sergi
collection PubMed
description BACKGROUND: We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C→T and G→A miscoding lesions (the predominant manifestation of post mortem damage) that are seen at a frequency of more than one clone among sequences from a single PCR, but do not represent the true endogenous sequence. FINDINGS: The data indicates an extreme bias towards C→T over G→A miscoding lesions (observed ratio of 67:2 compared to an expected ratio of 7:2), implying that the mtDNA Light strand molecule suffers proportionally more damage-derived miscoding lesions than the Heavy strand. CONCLUSION: The clustering of Cs in the Light strand as opposed to the singleton pattern of Cs in the Heavy strand could explain the observed bias, a phenomenon that could be further tested with non-PCR based approaches. The characterization of the HVS1 hotspots will be of use to future Neandertal mtDNA studies, with specific regards to assessing the authenticity of new positions previously unknown to be polymorphic.
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spelling pubmed-25471062008-09-23 Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA Vives, Sergi Gilbert, M Thomas Arenas, Conchita Gigli, Elena Lao, Oscar Lalueza-Fox, Carles BMC Res Notes Short Report BACKGROUND: We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C→T and G→A miscoding lesions (the predominant manifestation of post mortem damage) that are seen at a frequency of more than one clone among sequences from a single PCR, but do not represent the true endogenous sequence. FINDINGS: The data indicates an extreme bias towards C→T over G→A miscoding lesions (observed ratio of 67:2 compared to an expected ratio of 7:2), implying that the mtDNA Light strand molecule suffers proportionally more damage-derived miscoding lesions than the Heavy strand. CONCLUSION: The clustering of Cs in the Light strand as opposed to the singleton pattern of Cs in the Heavy strand could explain the observed bias, a phenomenon that could be further tested with non-PCR based approaches. The characterization of the HVS1 hotspots will be of use to future Neandertal mtDNA studies, with specific regards to assessing the authenticity of new positions previously unknown to be polymorphic. BioMed Central 2008-07-10 /pmc/articles/PMC2547106/ /pubmed/18710493 http://dx.doi.org/10.1186/1756-0500-1-40 Text en Copyright © 2008 Vives et al; licensee BioMed Central Ltd. 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 Short Report
Vives, Sergi
Gilbert, M Thomas
Arenas, Conchita
Gigli, Elena
Lao, Oscar
Lalueza-Fox, Carles
Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title_full Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title_fullStr Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title_full_unstemmed Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title_short Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
title_sort statistical analysis of post mortem dna damage-derived miscoding lesions in neandertal mitochondrial dna
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2547106/
https://www.ncbi.nlm.nih.gov/pubmed/18710493
http://dx.doi.org/10.1186/1756-0500-1-40
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