Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP’02–03 proficiency testing trial

Salas, Antonio; Prieto, Lourdes; Montesino, M.; Albarrán, Cristina; Arroyo, Eduardo; Paredes-Herrera, Miguel Rafael; Lonardo, A.M. Di; Doutremépuich, Christian; Fernández-Fernández, I; Vega, Alberto González de la; Alves, Cı́ntia; Meza-López, Carlos; López-Soto, Manolo; Lorente, José A.; Picornell, A.; Espinheira, R.; Hernández, Alexis; Palacio, Ana; Espinoza, Marta; Londoño, Juan José Yunis; Pérez-Lezaun, Anna; Pestano, J.; Carril, Juan Carlos; Corach, Daniel; Vide, M.C.; Álvarez-Iglesias, Vanesa; Pinheiro, M.F.; Whittle, M.R.; Brehm, António; Gómez, Josefina

doi:10.1016/j.forsciint.2004.06.008

Cited by 40 publications

(16 citation statements)

References 12 publications

(10 reference statements)

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“…Forensic studies (which comprise a significant portion of the existing dataset) and many population studies published before 2002 have predicted Hgs based on the HVS-I motif alone, thereby ignoring the occurrence of homoplasy and back mutations [2,9]. Moreover, it has been shown that many published mtDNA databases contain errors that distort phylogenetic and medical conclusions [10–15]. Therefore, it has become abundantly clear that a phylogenetically reliable and systematically quality-controlled database is needed to serve as a standard for the comparison of any newly reported data whether medical, forensic, or anthropological [7].…”

Section: Introductionmentioning

confidence: 99%

The Genographic Project Public Participation Mitochondrial DNA Database

Rosset²,

et al. 2007

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The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

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Section: Introductionmentioning

confidence: 99%

The Genographic Project Public Participation Mitochondrial DNA Database

Rosset²,

et al. 2007

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“…It seems that a Electrophoresis 2005, 26, 3414-3429 nonoptimized sequencing setup can induce an elevated level of phantom mutations. Most phantom mutations so far have been pinpointed in analyses of hypervariable segments I and II (HVS-I and HVS-II)-simply because these parts of the control region (CR) were most popular in large-scale mtDNA sequencing efforts of anthropology and forensics [2][3][4]. The coding region, mainly targeted in medical studies, is, however, not exempt of such problems [5].…”

Section: Introductionmentioning

confidence: 99%

Phantom mutation hotspots in human mitochondrial DNA

Brandstätter¹,

Sänger²,

Lutz-Bonengel³

et al. 2005

Electrophoresis

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Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

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“…The number of participating laboratories has slightly increased with respect to the last exercise [6], but this circumstance has not involved a decrease in the quality of the results. The main causes of error were documentation mistakes and nomenclature deficiencies.…”

Section: Final Remarksmentioning

confidence: 99%

“…Parti- cularly important were the good results obtained for the hair shafts (M7) since most of the laboratories (only one exception) reported the consensus results. It is worth mentioning that a scrutiny of the results using a phylogenetic approach [6,12,[16][17][18][19] could easily recognize most of the causes of errors.…”

Section: Final Remarksmentioning

confidence: 99%