ArticleNucleic acids research2005
How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence?
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Advanced molecular surveillance of hepatitis C virus.Viruses · 2015Review
- Pet fur or fake fur? A forensic approach.Investigative genetics · 2014Article
- The genetic origin and history of speed in the Thoroughbred racehorse.Nature communications · 2012Article
- Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach.Journal of molecular evolution · 2011Article
- To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.PloS one · 2011Article
- Accurate determination of phenotypic information from historic thoroughbred horses by single base extension.PloS one · 2010Article
- RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus.BMC evolutionary biology · 2009Article
- A statistical approach to identify ancient template DNA.Journal of molecular evolution · 2007Article
- Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs.Proceedings. Biological sciences · 2007Article
- Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations.PloS one · 2006Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.
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