Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman
<p>Abstract</p> <p>Background</p> <p>Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2009-06-01
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| Series: | BMC Genetics |
| Online Access: | http://www.biomedcentral.com/1471-2156/10/29 |
| _version_ | 1818229728436289536 |
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| author | Egarter-Vigl Eduard Brooks Jerome Brotherton Paul Pichler Irene Sanchez Juan J Endicott Phillip Cooper Alan Pramstaller Peter |
| author_facet | Egarter-Vigl Eduard Brooks Jerome Brotherton Paul Pichler Irene Sanchez Juan J Endicott Phillip Cooper Alan Pramstaller Peter |
| author_sort | Egarter-Vigl Eduard |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.</p> <p>Results</p> <p>The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.</p> <p>Conclusion</p> <p>The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of <it>a priori </it>risks would significantly improve the credibility of results.</p> |
| first_indexed | 2024-12-12T10:23:13Z |
| format | Article |
| id | doaj.art-c771ee2e6d5444b0acce1e573b82e209 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-12T10:23:13Z |
| publishDate | 2009-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-c771ee2e6d5444b0acce1e573b82e2092022-12-22T00:27:30ZengBMCBMC Genetics1471-21562009-06-011012910.1186/1471-2156-10-29Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean IcemanEgarter-Vigl EduardBrooks JeromeBrotherton PaulPichler IreneSanchez Juan JEndicott PhillipCooper AlanPramstaller Peter<p>Abstract</p> <p>Background</p> <p>Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.</p> <p>Results</p> <p>The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.</p> <p>Conclusion</p> <p>The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of <it>a priori </it>risks would significantly improve the credibility of results.</p>http://www.biomedcentral.com/1471-2156/10/29 |
| spellingShingle | Egarter-Vigl Eduard Brooks Jerome Brotherton Paul Pichler Irene Sanchez Juan J Endicott Phillip Cooper Alan Pramstaller Peter Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman BMC Genetics |
| title | Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman |
| title_full | Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman |
| title_fullStr | Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman |
| title_full_unstemmed | Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman |
| title_short | Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman |
| title_sort | genotyping human ancient mtdna control and coding region polymorphisms with a multiplexed single base extension assay the singular maternal history of the tyrolean iceman |
| url | http://www.biomedcentral.com/1471-2156/10/29 |
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