BMC Cancer Correspondence Contamination and sample mix-up can best explain some patterns of mtDNA instabilities in buccal cells and oral squamous cell carcinoma Hans-Jürgen Bandelt1 and Antonio Salas*2 BioMed Central Open Access Address: 1Department of Mathematics, University of Hamburg, 20146 Hamburg, Germany and 2Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica e Ciencias Forenses, Facultad de Medicina, Universidade de Santiago de Compostela, 15782; Galicia, Spain Email: Hans-Jürgen Bandelt - bandelt@math.uni-hamburg.de; Antonio Salas* - antonio.salas@usc.es * Corresponding author Published: 16 April 2009 BMC Cancer 2009, 9:113 doi:10.1186/1471-2407-9-113 This article is available from: http://www.biomedcentral.com/1471-2407/9/113 Received: 22 May 2008 Accepted: 16 April 2009 © 2009 Bandelt and Salas; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The study of somatic DNA instabilities constitutes a debatable topic because different causes can lead to seeming DNA alteration patterns between different cells or tissues from the same individual. Carcinogenesis or the action of a particular toxic could generate such patterns, and this is in fact the leitmotif of a number of studies on mitochondrial DNA (mtDNA) instability. Patterns of seeming instabilities could also arise from technical errors at any stage of the analysis (DNA extraction, amplification, mutation screening/sequencing, and documentation). Specifically, inadvertent DNA contamination or sample mixing would yield mosaic variation that could be erroneously interpreted as real mutation differences (instabilities) between tissues from the same individual. From the very beginning, mtDNA studies comparing cancerous to non-cancerous tissues have suffered from such mosaic results. We demonstrate here that the phylogenetic linkage of whole arrays of mtDNA mutations provides strong evidence of artificial recombination in previous studies on buccal cells and oral squamous cell carcinoma. Background Mitochondrial DNA analysis of different tissues and cells from an individual is often carried out in order to learn more about the distribution of some minor variation (het- eroplasmy) of mtDNA molecules within an organism and about spontaneous somatic mutations that could play a role in carcinogenesis, in particular. Such analysis is, more often than generally believed, beset with problems related to the quality of mtDNA samples, DNA extraction, PCR and sequencing protocols, and the omnipresent risk of contamination and documentation errors [1-8]. A careful design of experiments and optimal laboratory conditions will prevent most of the potential artifacts before they occur, but there can never be a full guarantee that the per- formed mutation screening eventually represents authen- tic variation. Data analysis of the fully documented screening and sequencing results should therefore be employed a posteriori, by using all available database and phylogenetic information [9,10]. A previous study [11] on mtDNA alterations in oral squamous cell carcinoma and a most recent study [12] on mtDNA abnormalities in buc- cal cells of smokers then do not seem to be exempt from the notorious problems of sample mixing and contamina- tion. Page 1 of 8 (page number not for citation purposes)