Abstract
Nuclear mitochondrial insertions (NUMTs) are sequences homologous to mtDNA, which are present throughout the human nuclear genome. The possibility that these sequences may be accidentally amplified in reactions directed to mtDNA has been raised and evaluated by different groups and by different means. Despite that, data is still missing on the specificity of PCRs in routine procedures in what concerns contamination with nuclear mtDNA insertions (NUMTs). In this work, we performed PCR sequencing reactions with primers directed either to mitochondrial or to NUMT DNA with different annealing temperatures and in different tissues. We observed that (a) contamination with NUMTs depends on the sample and tissue, and (b) employing routine techniques, there is no risk of co-amplification. Only when mtDNA is almost completely removed from the samples does the number of NUMT copies exceed mitochondrial sequences, i.e., only in samples with virtually no mtDNA, such as those resulting from preferential semen lysis, is there a risk of accidental amplification of NUMTs. We suggest that to evaluate a possible co-amplification of NUMT DNA, it is more relevant to take into account sample processing and original tissue of the samples, and consequently the relative proportions of NUMT and mtDNA, rather than the presence of NUMTs by itself, irrespectively of its proportion.
References
Bandelt HJ, Salas A, Lutz-Bonengel S (2004) Artificial recombination in forensic mtDNA population databases. Int J Legal Med 118:267–273
Pereira L, Richards M, Goios A et al (2006) Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale. Forensic Sci Int 159:43–50
Pereira L, Richards M, Goios A et al (2005) High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res 15:19–24
Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ (2006) Harvesting the fruit of the human mtDNA tree. Trends Genet 22:339–345
Wallace DC (1999) Mitochondrial diseases in man and mouse. Science 283:1482–1488
Herrnstadt C, Howell N (2004) An evolutionary perspective on pathogenic mtDNA mutations: haplogroup associations of clinical disorders. Mitochondrion 4:791–798
Goios A, Nogueira C, Pereira C, Vilarinho L, Amorim A, Pereira L (2005) mtDNA single macrodeletions associated with myopathies: absence of haplogroup-related increased risk. J Inherit Metab Dis 28:769–778
Davis RE, Miller S, Herrnstadt C et al (1997) Mutations in mitochondrial cytochrome c oxidase genes segregate with late-onset Alzheimer disease. Proc Natl Acad Sci U S A 94:4526–4531
Wallace DC, Stugard C, Murdock D, Schurr T, Brown MD (1997) Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. Proc Natl Acad Sci U S A 94:14900–14905
Hirano M, Shtilbans A, Mayeux R, Davidson MM, DiMauro S, Knowles JA, Schon EA (1997) Apparent mtDNA heteroplasmy in Alzheimer’s disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. Proc Natl Acad Sci U S A 94:14894–14899
Bravi CM, Parson W, Bandelt HJ (2006) Numts revisited. In: Bandelt HJ, Macaulay V, Richards M (eds) Human mitochondrial DNA and the evolution of Homo sapiens. Springer, Berlin, pp 31–46
Thangaraj K, Joshi MB, Reddy AG, Rasalkar AA, Singh L (2003) Sperm mitochondrial mutations as a cause of low sperm motility. J Androl 24:388–392
May-Panloup P, Chrétien MF, Savagner F, Vasseur C, Jean M, Malthiery Y, Reynier P (2003) Increased sperm mitochondrial DNA content in male infertility. Hum Reprod 18:550–556
Pereira L, Gonçalves J, Goios A, Rocha T, Amorim A (2005) Increased sperm mitochondrial DNA content in male infertility. Int J Androl 28:241–247
Roth DB, Porter TN, Wilson JH (1985) Mechanisms of nonhomologous recombination in mammalian cells. Mol Cell Biol 5:2599–2697
Woischnik M, Moraes CT (2002) Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res 12:885–893
Zischler H, Geisert H, von Haeseler A, Paabo S (1995) A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans. Nature 378:489–492
Mishmar D, Ruiz-Pesini E, Brandon M, Wallace DC (2004) Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration. Hum Mutat 23:125–133
Ricchetti M, Tekaia F, Dujon B (2004) Continued colonization of the human genome by mitochondrial DNA. PLoS Biol 2:E273
Parr RL, Maki J, Reguly B et al (2006) The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation. BMC Genomics 7:185–197
Goios A, Amorim A, Pereira L (2006) Mitochondrial DNA pseudogenes in the nuclear genome as possible sources of contamination. International Congress Series 1288. Elsevier, Amsterdam, pp 697–699
Bensasson D, Zhang D, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16:314–321
Behar DM, Metspalu E, Kivisild T et al (2006) The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78:487–497
Macaulay V, Hill C, Achilli A et al (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036
Montesino M, Salas A, Crespillo M et al (2006) Analysis of body fluid mixtures by mtDNA sequencing: An inter-laboratory study of the GEP-ISFG working group. Forensic Sci Int 168:42–56
Álvarez-Iglesias V, Jaime JC, Carracedo A, Salas A (2007) Coding region mitochondrial DNA SNPs: targeting east Asian and Native American haplogroups. Forensic Sci Int Genetics 1:44–55
Acknowledgements
We wish to thank the donors of the samples used in this study. We are also very grateful to Marta Montesino for the technical support. This work was partially supported by Fundação para a Ciência e a Tecnologia through a research grant to A.G. (SFRH/BD/16518/2004) and by “Programa Operacional Ciência, e Inovação 2010” (POCI 2010), VI Programa-Quadro (2002–2006).
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Fig. S1
Target sequence used in the NUMT analysis. Sequence on top is mtDNA and the dotted sequence is the corresponding region in NUMT AL359496.30. Primers used are marked. DP1 and DP2 are diagnostic positions used to distinguish mtDNA from NUMT (JPEG 166 kb)
Fig. S2
Electropherograms (forward and reverse sequencing) obtained for diagnostic position 1 when the amplification produced: a pure mtDNA, b a mixture of NUMT and mtDNA or c pure NUMT DNA (JPEG 656 kb)
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Goios, A., Prieto, L., Amorim, A. et al. Specificity of mtDNA-directed PCR—influence of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques. Int J Legal Med 122, 341–345 (2008). https://doi.org/10.1007/s00414-007-0191-5
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DOI: https://doi.org/10.1007/s00414-007-0191-5