Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies

Biochemical and Biophysical Research Communications

Volumn 333, Issue 1, 2005, Pages 122-130

  Bandelt, Hans Jürgen ^a   Achilli, Alessandro ^b   Kong, Qing Peng ^c   Salas, Antonio ^d   Lutz Bonengel, Sabine ^e   Sun, Chang ^c   Zhang, Ya Ping ^c   Torroni, Antonio ^b   Yao, Yong Gang ^c  

^a UNIVERSITY OF HAMBURG   (Germany)

^b UNIVERSITY OF PAVIA   (Italy)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

^d Hospital Clinico Universitario   (Spain)

^e UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Dilated cardiomyopathy; Documentation error; Mitochondrial disease; Mitochondrial DNA; Mitochondrial encephaloneuromyopathy; Nonsyndromic deafness; Phantom mutation; Phylogeny

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA DETERMINATION; DNA SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; MITOCHONDRIAL DNA DISORDER; MOLECULAR PHYLOGENY; PENETRANCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; VALIDATION PROCESS;

ARTIFACTS; BASE SEQUENCE; CHINA; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; DNA, MITOCHONDRIAL; DOCUMENTATION; EPIDEMIOLOGIC STUDIES; EUROPEAN UNION; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; GENETICS, POPULATION; HUMANS; INCIDENCE; MITOCHONDRIAL DISEASES; MOLECULAR SEQUENCE DATA; PENETRANCE; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 20444443621     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2005.04.055     Document Type: Article

References (43)

1. V. Macaulay, M. Richards, and B. Sykes Mitochondrial DNA recombination-no need to panic Proc. R. Soc. London Ser. B 266 1999 2037 2039
2. T. Kivisild, H.V. Tolk, J. Parik, Y. Wang, S.S. Papiha, H.-J. Bandelt, and R. Villems The emerging limbs and twigs of the East Asian mtDNA tree Mol. Biol. Evol. 19 2002 1737 1751 erratum in: Mol. Biol. Evol. 20 (2002) 162
3. T. Ozawa, M. Tanaka, H. Ino, K. Ohno, T. Sano, Y. Wada, M. Yoneda, Y. Tanno, T. Miyatake, T. Tanaka, S. Itoyama, S. Ikebe, T. Kondo, and Y. Mizuno Distinct clustering of point mutations in mitochondrial DNA among patients with mitochondrial encephalomyopathies and with Parkinson's disease Biochem. Biophys. Res. Commun. 176 1991 938 946
4. T. Ozawa, M. Tanaka, S. Sugiyama, H. Ino, K. Ohno, K. Hattori, T. Ohbayashi, T. Ito, H. Deguchi, K. Kawamura, Y. Nakane, and K. Hashiba Patients with idiopathic cardiomyopathy belong to the same mitochondrial DNA gene family of Parkinson's disease and mitochondrial encephalomyopathy Biochem. Biophys. Res. Commun. 177 1991 518 525
5. T. Ozawa Mechanism of somatic mitochondrial DNA mutations associated with age and diseases Biochem. Biophys. Acta 1271 1995 177 189
6. R.M. Andrews, I. Kubacka, P.F. Chinnery, R.N. Lightowlers, D.M. Turnbull, and N. Howell Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat. Genet. 23 1999 147
7. H.-J. Bandelt, L. Quintana-Murci, A. Salas, and V. Macaulay The fingerprint of phantom mutations in mitochondrial DNA data Am. J. Hum. Genet. 71 2002 1150 1160
8. H.-J. Bandelt, A. Salas, and C. Bravi Problems in FBI mtDNA database Science 305 2004 1402 1404
9. H.-J. Bandelt, A. Salas, and S. Lutz-Bonengel Artificial recombination in forensic mtDNA population databases Int. J. Legal Med. 118 2004 267 273
10. H.-J. Bandelt, P. Lahermo, M. Richards, and V. Macaulay Detecting errors in mtDNA data by phylogenetic analysis Int. J. Legal. Med. 115 2001 64 69
11. M.g. Palanichamy, C. Sun, S. Agrawal, H.-J. Bandelt, Q.-P. Kong, F. Khan, C.-Y. Wang, T.K. Chaudhuri, V. Palla, and Y.-P. Zhang Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia Am. J. Hum. Genet. 75 2004 966 978
12. A. Achilli, C. Rengo, C. Magri, V. Battaglia, A. Olivieri, R. Scozzari, F. Cruciani, M. Zeviani, E. Briem, V. Carelli, P. Moral, J.M. Dugoujon, U. Roostalu, E.L. Loogvali, T. Kivisild, H.-J. Bandelt, M. Richards, R. Villems, A.S. Santachiara-Benerecetti, O. Semino, and A. Torroni The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool Am. J. Hum. Genet. 75 2004 910 918
13. A. Achilli, C. Rengo, V. Battaglia, M. Pala, A. Olivieri, S. Fornarino, C. Magri, R. Scozzari, N. Babudri, A.S. Santachiara-Benerecetti, H.-J. Bandelt, O. Semino, and A. Torroni Saami and Berbers-an unexpected mitochondrial DNA link Am. J. Hum. Genet. 76 2005 883 886
14. Q.-P. Kong, Y.-G. Yao, C. Sun, H.-J. Bandelt, C.-L. Zhu, and Y.-P. Zhang Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences Am. J. Hum. Genet. 73 2003 671 676 erratum in: Am. J. Hum. Genet. 75 (2004) 157
15. M. Tanaka, V.M. Cabrera, A.M. González, J.M. Larruga, T. Takeyas, N. Fuku, L.J. Guo, R. Hirose, Y. Fujita, M. Kurata, K. Shinoda, K. Umetsu, Y. Yamada, Y. Oshida, Y. Sato, N. Hattori, Y. Mizuno, Y. Arai, N. Hirose, S. Ohta, O. Ogawa, Y. Tanaka, R. Kawamori, M. Shamoto-Nagai, W. Maruyama, H. Shimokata, R. Suzuki, and H. Shimodaira Mitochondrial genome variation in eastern Asia and the peopling of Japan Genome Res. 14 2004 1832 1850
16. C. Herrnstadt, J.L. Elson, E. Fahy, G. Preston, D.M. Turnbull, C. Anderson, S.S. Ghosh, J.M. Olefsky, M.F. Beal, R.E. Davis, and N. Howell Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups Am. J. Hum. Genet. 70 2002 1152 1171 erratum in: Am. J. Hum. Genet. 71 (2002) 448-449
17. C. Herrnstadt, G. Preston, and N. Howell Errors, phantom and otherwise, in human mtDNA sequences Am. J. Hum. Genet. 72 2003 1585 1586
18. B.A. Malyarchuk, and I.B. Rogozin Mutagenesis by transient misalignment in the human mitochondrial DNA control region Ann. Hum. Genet. 68 2004 324 339
19. K.L. Monson, K.W.P. Miller, M.R. Wilson, J.A. DiZinno, and B. Budowle The mtDNA population database: an integrated software and database resource for forensic comparison Forensic Sci. Comm. 4 2002 no. 2
20. B. Budowle, D. Polanskey, M.W. Allard, and R. Chakraborty Addressing the use of phylogenetics for identification of sequences in error in the SWGDAM mitochondrial DNA database J Forensic Sci. 49 2004 1 6
21. D. Polanskey, and B. Budowle Summary of the findings of a quality review of the Scientific Working Group on DNA analysis methods mitochondrial DNA database Forensic Sci. Comm. 7 2005 no. 1
22. P. Da Pozzo, E. Cardaioli, E. Radi, and A. Federico Sequence analysis of the complete mitochondrial genome in patients with mitochondrial encephaloneuromyopathies lacking the common pathogenic DNA mutations Biochem. Biophys. Res. Commun. 324 2004 360 364
23. S. Anderson, A.T. Bankier, B.G. Barrell, M.H. de Bruijn, A.R. Coulson, J. Drouin, I.C. Eperon, D.P. Nierlich, B.A. Roe, F. Sanger, P.H. Schreier, A.J. Smith, R. Staden, and I.G. Young Sequence and organization of the human mitochondrial genome Nature 290 1981 457 465
24. N. Maca-Meyer, A.M. González, J.M. Larruga, C. Flores, and V.M. Cabrera Major genomic mitochondrial lineages delineate early human expansions BMC Genet. 2 2001 13
25. M. Ingman, and U. Gyllensten Mitochondrial genome variation and evolutionary history of Australian and New Guinean Aborigines Genome Res. 13 2003 1600 1606
26. S. Finnilä, M.S. Lehtonen, and K. Majamaa Phylogenetic network for European mtDNA Am. J. Hum. Genet. 68 2001 1475 1484
27. Y.-G. Yao, V. Macauley, T. Kivisild, Y.-P. Zhang, and H.-J. Bandelt To trust or not to trust an idiosyncratic mitochondrial data set Am. J. Hum. Genet. 72 2003 1341 1346
28. V. Ruppert, D. Nolte, T. Aschenbrenner, S. Pankuweit, R. Funck, and B. Maisch Novel point mutations in the mitochondrial DNA detected in patients with dilated cardiomyopathy by screening the whole mitochondrial genome Biochem. Biophys. Res. Commun. 318 2004 535 543
29. M. Ingman, H. Kaessmann, S. Pääbo, and U. Gyllensten Mitochondrial genome variation and the origin of modern humans Nature 408 2000 708 713
30. V. Macaulay, M. Richards, E. Hickey, E. Vega, F. Cruciani, V. Guida, R. Scozzari, B. Bonné-Tamir, B. Sykes, and A. Torroni The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs Am. J. Hum. Genet. 64 1999 232 249 erratum in: Am. J. Hum. Genet. 64 (1999) 918-919
31. S. Lutz, H.-J. Weisser, J. Heizmann, and S. Pollak Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany Int. J. Legal Med. 111 1998 67 77 errata in: Int. J. Legal Med. 111 (1998) 286, and 112 (1999) 145-150. [Corrected data table available from the author.]
32. A.M. Gibson, J.A. Edwardson, D.M. Turnbull, I.G. McKeith, C.M. Morris, and P.F. Chinnery No evidence of an association between the T16189C mtDNA variant and late onset dementia J. Med. Genet. 41 2004 e7
33. S.M. Keers, A.M. Gibson, D.M. Turnbull, and P.F. Chinnery No evidence of an association between the mtDNA 16184-93 polyC tract and late onset dementia J. Med. Genet. 41 2004 957 958
34. R. Piercy, K.M. Sullivan, N. Benson, and P. Gill The application of mitochondrial sequence DNA typing to the study of white Caucasian genetic identification Int. J. Leg. Med. 106 1993 85 90
35. S.S. Khogali, B.M. Mayosi, J.M. Beattie, W.J. McKenna, H. Watkins, and J. Poulton A common mitochondrial DNA variant associated with susceptibility to dilated cardiomyopathy in two different populations Lancet 357 2001 1265 1267
36. J. Poulton, and S. Das Correction: no evidence of an association between the T16189C mtDNA variant and late onset dementia (Gibson et al) J. Med. Genet. 41 2004 957
37. W.Y. Young, L. Zhao, Y. Qian, Q. Wang, N. Li, J.H. Greinwald Jr., and M.X. Guan Extremely low penetrance of hearing loss in four Chinese families with the mitochondrial 12S rRNA A1555G mutation Biochem. Biophys. Res. Commun. 328 2005 1244 1251
38. Y.-G. Yao, Q.-P. Kong, H.-J. Bandelt, T. Kivisild, and Y.-P. Zhang Phylogeographic differentiation of mitochondrial DNA in Han Chinese Am. J. Hum. Genet. 70 2002 635 651
39. Y.-G. Yao, C.M. Bravi, and H.-J. Bandelt A call for mtDNA data quality control in forensic science Forensic Sci. Int. 141 2004 1 6
40. H.-J. Bandelt, Y.-G. Yao, and T. Kivisild Mitochondrial genes and schizophrenia Schizophr. Res. 72 2005 267 269
41. C. Herrnstadt, and N. Howell An evolutionary perspective on pathogenic mtDNA mutations: haplogroup associations of clinical disorders Mitochondrion 4 2004 791 798
42. M. Poetsch, H. Wittig, D. Krause, and E. Lignitz Corrigendum to "Mitochondrial diversity of a northeast German population sample" Forensic Sci. Int. 145 2004 73 77
43. B.A. Malyarchuk, T. Grzybowski, M.V. Derenko, J. Czarny, M. Wonźiak, and D. Miścicka-Śliwka Mitochondrial DNA variability in Poles and Russians Ann. Hum. Genet. 66 2002 261 283