Characterization of Genetic Miscoding Lesions Caused by Postmortem Damage

Abstract

The spectrum of postmortem damage in mitochondrial DNA was analyzed in a large data set of cloned sequences from ancient human specimens. The most common forms of damage observed are two complementary groups of transitions, termed "type 1" (adenine-->guanine/thymine-->cytosine) and "type 2" (cytosine-->thymine/guanine-->adenine). Single-primer extension PCR and enzymatic digestion with uracil-N-glycosylase confirm that each of these groups of transitions result from a single event, the deamination of adenine to hypoxanthine, and cytosine to uracil, respectively. The predominant form of transition-manifested damage varies by sample, though a marked bias toward type 2 is observed with increasing amounts of damage. The two transition types can be used to identify the original strand, light (L) or heavy (H), on which the initial damage event occurred, and this can increase the number of detected jumping-PCR artifacts by up to 80%. No bias toward H-strand-specific damage events is noted within the hypervariable 1 region of human mitochondria, suggesting the rapid postmortem degradation of the secondary displacement (D-loop) H strand. The data also indicate that, as damage increases within a sample, fewer H strands retain the ability to act as templates for enzymatic amplification. Last, a significant correlation between archaeological site and sample-specific level of DNA damage was detected.

Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims

“…Lastly, the techniques used here include the use of the modified PCR enzyme Platinum Taq Hifidelity (as opposed to 'standard' Taq polymerases). The increased yields and successes of aDNA amplifications performed using this enzyme have been noted previously (Willerslev et al, 1999;Hansen et al, 2001;Gilbert et al, 2003a) especially in amplifying low-copy-number DNA.…”

“…The human DNA bears characteristics that suggest authenticity, including the observed consistency of amplified sequences and the observed spectrum of damage within the human cloned sequences (Pääbo, 1989;Gilbert et al, 2003a), the pattern of nuclear to mitochondrial DNA survival (Hofreiter et al, 2001) and the appropriate behaviour of negative controls and extraction blanks (Cooper & Poinar, 2000). However, it is very difficult to guarantee the authenticity of aDNA from human samples (cf.…”

Detection of the A189G mtDNA heteroplasmic mutation in relation to age in modern and ancient bones

“…Actually, modifications of transition types could occur at death in certain sites known to have high mutation rates [25]. In addition, by providing new indicators for age evaluation, this mutation study could also be very helpful during anthropological studies.…”

Evaluating bacterial pathogen DNA preservation in museum osteological collections

“…In the remaining five samples, both the lab contaminant and 1-2 other sequences were identified. Where two non-IB sequences were identified from the same sample, the differences between them were sufficiently slight (2-4 transitions) that they could be attributed to template damage (Gilbert et al 2003a). A range of results, including template damage and contamination, is common in amplifications of degraded human material (e.g.…”