Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)

Forensic Science International: Genetics - Tập 7 - Trang 632-639 - 2013
Walther Parson1,2, Christina Strobl1, Gabriela Huber1, Bettina Zimmermann1, Sibylle M. Gomes3, Luis Souto3, Liane Fendt1,4, Rhena Delport5, Reina Langit6, Sharon Wootton6, Robert Lagacé6, Jodi Irwin7
1Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
2Penn State Eberly College of Science, University Park, PA, USA
3Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
4Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria
5Department of Chemical Pathology, School of Medicine, University of Pretoria, South Africa
6Life Technologies, Foster City, CA, USA
7FBI Laboratory, Quantico, VA, USA

Tài liệu tham khảo

Brown, 1980, Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis, Proc. Natl. Acad. Sci. U.S.A., 77, 3605, 10.1073/pnas.77.6.3605 Parson, 2007, EMPOP—a forensic mtDNA database, Forensic Sci. Int. Genet., 1, 88, 10.1016/j.fsigen.2007.01.018 van Oven, 2009, Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum. Mutat., 30, E386, 10.1002/humu.20921 Bandelt, 2012, Haplogrouping mitochondrial DNA sequences in legal medicine/forensic genetics, Int. J. Legal Med., 126, 901, 10.1007/s00414-012-0762-y Röck, 2013, Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA), Forensic Sci. Int. Genet., 10.1016/j.fsigen.2013.07.005 Yao, 2009, mtDNA data mining in GenBank needs surveying, Am. J. Hum. Genet., 85, 929, 10.1016/j.ajhg.2009.10.023 Bandelt, 2009, Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies, J. Hum. Genet., 54, 174, 10.1038/jhg.2009.9 Zimmermann, 2011, Application of a west Eurasian-specific filter for quasi-median network analysis: sharpening the blade for mtDNA error detection, Forensic Sci. Int. Genet., 2, 133, 10.1016/j.fsigen.2010.10.003 Fendt, 2009, Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences, BMC Genomics, 10, 139, 10.1186/1471-2164-10-139 Irwin, 2011, mtGenome reference population databases and the future of forensic mtDNA analysis, Forensic Sci. Int. Genet., 5, 222, 10.1016/j.fsigen.2010.02.008 Bandelt, 2012, Current next generation sequencing technology may not meet forensic standards, Forensic Sci. Int. Genet., 6, 143, 10.1016/j.fsigen.2011.04.004 Mikkelsen, 2009, Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing, Forensic Sci. Int.: Genet. Suppl. Series, 2, 518 Holland, 2011, Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy, Croat. Med. J., 52, 299, 10.3325/cmj.2011.52.299 Loreille, 2011, Application of next generation sequencing technologies to the identification of highly degraded unknown soldiers’ remains, Forensic Sci. Int.: Genet. Suppl. Series, 3, e540 Rothberg, 2011, An integrated semiconductor device enabling non-optical genome sequencing, Nature, 475, 348, 10.1038/nature10242 Fendt, 2012, Mitochondrial DNA control region data from indigenous Angolan Khoe-San lineages, Forensic Sci. Int. Genet., 6, 662, 10.1016/j.fsigen.2012.02.010 Fendt, 2011, Accumulation of mutations over the entire mitochondrial genome of breast cancer cells obtained by tissue microdissection, Breast Cancer Res. Treat., 128, 327, 10.1007/s10549-010-1092-8 Walsh, 1991, Chelex-100 as a medium for simple extraction of DNA for PCR-based typing from forensic material, Biotechniques, 10, 506 Parson, 2000, Species identification by means of the cytochrome b gene, Int. J. Legal Med., 114, 23, 10.1007/s004140000134 Andrews, 1999, Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat. Genet., 23, 147, 10.1038/13779 Bandelt, 2008, Consistent treatment of length variants in the human mtDNA control region: a reappraisal, Int. J. Legal Med., 122, 11, 10.1007/s00414-006-0151-5 Li, 2010, A survey of sequence alignment algorithms for next-generation sequencing, Brief. Bioinform., 11, 473, 10.1093/bib/bbq015 Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754 Berger, 2011, Evaluating sequence-derived mtDNA length heteroplasmy by amplicon size analysis, Forensic Sci. Int. Genet., 5, 142, 10.1016/j.fsigen.2010.10.002 Carracedo, 2000, DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing, Forensic Sci. Int., 110, 79, 10.1016/S0379-0738(00)00161-4 Mayr-Eduardoff, 2013, Mass spectrometric base composition profiling: implications for forensic mtDNA databasing, Forensic Sci. Int. Genet. Tully, 2001, Considerations by the European DNA profiling (EDNAP) group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles, Forensic Sci. Int., 124, 83, 10.1016/S0379-0738(01)00573-4 Eichmann, 2007, Molecular characterization of the canine mitochondrial DNA control region for forensic applications, Int. J. Legal Med., 121, 411, 10.1007/s00414-006-0143-5