Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

Melton, 2012, Forensic mitochondrial DNA analysis: current practice and future potential, Forensic Sci. Rev., 24, 101 Just, 2009, The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases, J. Forensic Sci., 54, 887, 10.1111/j.1556-4029.2009.01069.x Payne, 2013, Universal heteroplasmy of human mitochondrial DNA, Hum. Mol. Genet., 22, 384, 10.1093/hmg/dds435 Salas, 2001, Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report, Int. J. Legal Med., 114, 186, 10.1007/s004140000164 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 Berglund, 2011, Next-generation sequencing technologies and applications for human genetic history and forensics, Invest. Genet., 2, 23, 10.1186/2041-2223-2-23 Fisher, 2011, A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries, Genome Biol., 12, R1, 10.1186/gb-2011-12-1-r1 Kircher, 2012, Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform, Nucleic Acids Res., 40, e3, 10.1093/nar/gkr771 Lennon, 2010, A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454, Genome Biol., 11, R15, 10.1186/gb-2010-11-2-r15 Bornman, 2012, Short-read, high-throughput sequencing technology for STR genotyping, Biotechniques Rapid Dispatches, April, 1 Fordyce, 2011, High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform, Biotechniques, 51, 127, 10.2144/000113721 Caporaso, 2012, Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J., 6, 1621, 10.1038/ismej.2012.8 Kirsch, 2012, Sequence error storms and the landscape of mutations in cancer, PNAS, 109, 14289, 10.1073/pnas.1212246109 Schmitt, 2012, Detection of ultra-rare mutations by next-generation sequencing, PNAS, 109, 14508, 10.1073/pnas.1208715109 Zaragoza, 2010, Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing, PLoS ONE, 5, e12295, 10.1371/journal.pone.0012295 Goto, 2011, Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study, Genome Biol., 12, R59, 10.1186/gb-2011-12-6-r59 He, 2010, Heteroplasmic mitochondrial DNA mutations in normal turmour cells, Nature, 464, 610, 10.1038/nature08802 Li, 2010, Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes, Am. J. Hum. Genet., 87, 237, 10.1016/j.ajhg.2010.07.014 Tang, 2013, Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects, Hum. Mutat., 34, 882, 10.1002/humu.22307 Parson, 2013, Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM), Forensic Sci. Int. Genet., 7, 543, 10.1016/j.fsigen.2013.06.003 Loman, 2012, Performance comparison of benchtop high-throughput sequencing platforms, Nat. Biotechnol., 30, 434, 10.1038/nbt.2198 Quail, 2012, A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers, BMC Genomics, 13, 341, 10.1186/1471-2164-13-341 Illumina Inc., 2011 Lander, 1988, Genomic mapping by fingerprinting random clones: a mathematical analysis, Genomics, 2, 231, 10.1016/0888-7543(88)90007-9 Freeman, 2003, DNA from buccal swabs recruited by mail: evaluation of storage effects on long-term stability and suitability for multiplex polymerase chain reaction genotyping, Behav. Genet., 33, 67, 10.1023/A:1021055617738 Fendt, 2009, Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences, BMC Genomics, 10, 139, 10.1186/1471-2164-10-139 Tanaka, 1996, Automated sequencing of mitochondrial DNA, Methods Enzymol., 264, 407, 10.1016/S0076-6879(96)64037-3 Illumina Inc., 2012 Anderson, 1981, Sequence and organization of the human mitochondrial genome, Nature, 290, 457, 10.1038/290457a0 Andrews, 1999, Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat. Genet., 23, 147, 10.1038/13779 Li, 2009, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Smith, 1981, Identification of common molecular subsequences, J. Mol. Biol., 147, 195, 10.1016/0022-2836(81)90087-5 Bland, 1986, Statistical methods for assessing agreement between two methods of clinical measurement, Lancet, 1, 307, 10.1016/S0140-6736(86)90837-8 Bland, 1999, Measuring agreement in method comparison studies, Stat Methods Med. Res., 8, 135, 10.1191/096228099673819272 Harismendy, 2009, Evaluation of next generation sequencing platforms for population targeted sequencing studies, Genome Biol., 10, R32, 10.1186/gb-2009-10-3-r32 Dohm, 2008, Substantial biases in ultra-short read data sets from high-throughput DNA sequencing, Nucleic Acids Res., 36, e105, 10.1093/nar/gkn425 Teytelman, 2009, Impact of chromatin structures on DNA processing for genomic analyses, PLoS ONE, 4, e6700, 10.1371/journal.pone.0006700 Bentley, 2008, Accurate whole human genome sequencing using reversible terminator chemistry, Nature, 456, 53, 10.1038/nature07517 Minoche, 2011, Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems, Genome Biol., 12, R112, 10.1186/gb-2011-12-11-r112 Qu, 2009, Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing, Genome Res., 19, 1309, 10.1101/gr.089151.108 Forster, 2010, Evaluating length heteroplasmy in human mitochondrial DNA control region, Int. J. Legal Med., 124, 133, 10.1007/s00414-009-0385-0 Irwin, 2009, Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples, J. Mol. Evol., 68, 516, 10.1007/s00239-009-9227-4 Strouss, 2006 Tamura, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol., 10, 512 Vigilant, 1991, African populations and the evolution of human mitochondrial DNA, Science, 253, 1503, 10.1126/science.1840702 Wakeley, 1993, Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA, J. Mol. Evol., 37, 613, 10.1007/BF00182747 Pavel, 1996, Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II, Nat. Genet., 12, 417, 10.1038/ng0496-417