Collins PJ, Hennessy LK, Leibelt CS, Roby RK, Reeder DJ, Foxall PA: Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFISTR Identifiler PCR Amplificaiton Kit. J Forensic Sci. 2004, 49: 1265-1277.
Article
CAS
PubMed
Google Scholar
Oostdik K, French J, Yet D, Smalling B, Nolde C, Vallone PM, Butts EL, Hill CR, Kline MC, Rinta T, Gerow AM, Allen SR, Huber CK, Teske J, Krenke B, Ensenberger M, Fulmer P, Sprecher C: Developmental validation of the PowerPlex® 18D System, a rapid STR multiplex for analysis of reference samples. Forensic Sci Int Genet. 2013, 7: 129-135. 10.1016/j.fsigen.2012.07.008.
Article
CAS
PubMed
Google Scholar
Budowle B, van Daal A: Extracting evidence from forensic DNA analyses: future molecular biology directions. Biotechniques. 2009, 46: 339-340. 10.2144/000113136. 342-350
Article
CAS
PubMed
Google Scholar
Budowle B, Planz JV, Campbell RS, Eisenberg AJ: Single nucleotide polymorphisms and microarray technology in forensic genetics — Development and application to mitochondrial DNA. Forensic Sci Rev. 2004, 16: 21-36.
CAS
PubMed
Google Scholar
Budowle B, van Daal A: Forensically relevant SNP classes. Biotechniques. 2008, 44: 603-608. 610
Article
CAS
PubMed
Google Scholar
Wilson MR, Polanskey D, Butler J, DiZinno JA, Replogle J, Budowle B: Extraction, PCR amplification and sequencing of mitochondrial DNA from human hair shafts. Biotechniques. 1995, 18: 662-629.
CAS
PubMed
Google Scholar
Kayser M, Kittler R, Erler A, Hedman M, Lee AC, Mohyuddin A, Mehdi SQ, Rosser Z, Stoneking M, Jobling MA, Sajantila A, Tyler-Smith C: A comprehensive survey of human Y-chromosomal microsatellites. Am J Hum Genet. 2004, 74: 1183-1197. 10.1086/421531.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sanger F, Nicklen S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci. 1977, 74: 5463-5467. 10.1073/pnas.74.12.5463.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilson MR, DiZinno JA, Polanskey D, Replogle J, Budowle B: Validation of mitochondrial DNA sequencing for forensic casework analysis. Int J Legal Med. 1995, 108: 68-74. 10.1007/BF01369907.
Article
CAS
PubMed
Google Scholar
Ginther C, Issel-Tarver L, King MC: Identifying individuals by sequencing mitochondrial DNA from teeth. Nat Genet. 1992, 2: 135-138. 10.1038/ng1092-135.
Article
CAS
PubMed
Google Scholar
Cann RL, Stoneking M, Wilson AC: Mitochondrial DNA and human evolution. Nature. 1987, 325: 31-36. 10.1038/325031a0.
Article
CAS
PubMed
Google Scholar
Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, Muzny DM, Gibbs RA: Whole-genome sequencing in a patient with Charcot-Marie-Tooth Neuropathy. N Engl J Med. 2010, 362: 1181-1191. 10.1056/NEJMoa0908094.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tucker T, Marra M, Friedman JM: Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet. 2009, 85: 142-154. 10.1016/j.ajhg.2009.06.022.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cummings CA, Bormann Chung CA, Fang R, Barker M, Brzoska P, Williamson PC, Beaudry J, Matthews M, Schupp J, Wagner DM, Birdsell D, Vogler AJ, Furtado MR, Keim P, Budowle B: Accurate, rapid, and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet. 2010, 1: 5-10.1186/2041-2223-1-5.
Article
PubMed Central
PubMed
Google Scholar
Gilad Y, Pritchard JK, Thornton K: Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 2009, 25: 463-471. 10.1016/j.tig.2009.09.003.
Article
PubMed Central
CAS
PubMed
Google Scholar
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
Google Scholar
Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagacé R, Irwin J: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci Int Genet. 2013, 7: 543-549. 10.1016/j.fsigen.2013.06.003.
Article
PubMed Central
CAS
PubMed
Google Scholar
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA: Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009, 10: R32-10.1186/gb-2009-10-3-r32.
Article
PubMed Central
PubMed
Google Scholar
King J, LaRue B, Novroski N, Stoljarova M, Seo SB, Zeng X, Warshauer DH, Davis CP, Parson W, Sajantila A, Budowle B: High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet.
McElroy K, Thomas T, Luciani F: Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatics solutions. Microb Inform Exp. 2014, 4: 1-10.1186/2042-5783-4-1.
Article
PubMed Central
PubMed
Google Scholar
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S: Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011, 39: e90-10.1093/nar/gkr344.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L: Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics. 2011, 12: 451-10.1186/1471-2105-12-451.
Article
PubMed Central
PubMed
Google Scholar
Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T: Discovering motifs that induce sequencing errors. BMC Bioinformatics. 2013, 14 (Suppl 5): S1-10.1186/1471-2105-14-S5-S1.
Article
PubMed Central
PubMed
Google Scholar
SWGDAM Mitochondrial DNA Analysis Interpretation Guidelines. [http://swgdam.org/docs.html]
Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo-Smith EA: From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics. 2014, 15: 68-10.1186/1471-2164-15-68.
Article
PubMed Central
PubMed
Google Scholar
Part II: Overview of Torrent Sequencing and Alignment (v4.x). [http://ioncommunity.lifetechnologies.com/docs/DOC-3266]
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics. 2010, 26: 589-595. 10.1093/bioinformatics/btp698.
Article
PubMed Central
PubMed
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, Kronenberg F: HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat. 2011, 32: 25-32. 10.1002/humu.21382.
Article
PubMed
Google Scholar
Levin L, Zhidkov I, Gurman Y, Hawlena H, Mishmar D: Functional Recurrent Mutations in the Human Mitochondrial Phylogeny: Dual Roles in Evolution and Disease. Genome Biol Evol. 2013, 5: 876-890. 10.1093/gbe/evt058.
Article
PubMed Central
PubMed
Google Scholar
XXX X: Qubit® 2.0 Fluorometer. [http://www.ebc.uu.se/digitalAssets/120/120360_qubit2fluorometerusermannual.pdf]
Gunnarsdóttir ED, Li M, Bauchet M, Finstermeier K, Stoneking M: High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res. 2011, 21: 1-11. 10.1101/gr.107615.110.
Article
PubMed Central
PubMed
Google Scholar
Ion PGM™ Sequencing 200 Kit v2. [http://ioncommunity.lifetechnologies.com/docs/DOC-6775]
Integrative Genomics Viewer. [http://www.broadinstitute.org/igv/]
Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, Horsman D, et al: Circos: An information aesthetic for comparative genomics. Genome Res. 2009
Google Scholar