Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
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.
In: BMC Research Notes, Vol. 1, 2008, p. 40.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
AU - Vives, Sergi
AU - Gilbert, M Thomas
AU - Arenas, Conchita
AU - Gigli, Elena
AU - Lao, Oscar
AU - Lalueza-Fox, Carles
PY - 2008
Y1 - 2008
N2 - ABSTRACT: 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.
AB - ABSTRACT: 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.
U2 - 10.1186/1756-0500-1-40
DO - 10.1186/1756-0500-1-40
M3 - Journal article
C2 - 18710493
VL - 1
SP - 40
JO - BMC Research Notes
JF - BMC Research Notes
SN - 1756-0500
ER -
ID: 10456849