A high-throughput Sanger strategy for human mitochondrial genome sequencing

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Lyons, Elizabeth A ^a,b,c   Scheible, Melissa K ^a,b   Sturk Andreaggi, Kimberly ^a,b   Irwin, Jodi A ^a,b,d   Just, Rebecca S ^a,b,e  

^a American Registry of Pathology   (United States)

^b Dover AFB   (United States)

^c Michigan State Police   (United States)

^d Federal Bureau of Investigation   (United States)

^e UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AMPLICON; ARTICLE; DNA BASE COMPOSITION; ELECTROPHORESIS; GENE AMPLIFICATION; GENE SEQUENCE; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; MITOCHONDRIAL GENOME; POLYMERASE CHAIN REACTION; SANGER SEQUENCE; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT;

GENOME, MITOCHONDRIAL; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; ROBOTICS; SEQUENCE ANALYSIS, DNA;

EID: 84890286468     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-881     Document Type: Article

References (31)

1. Andreasson H, Nilsson M, Styrman H, Pettersson U, Allen M. Forensic mitochondrial coding region analysis for increased discrimination using pyrosequencing technology. Forensic Sci Int Genet 2007, 1(1):35-43. 10.1016/j.fsigen.2006.10.002, 19083726.
2. Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int J Legal Med 2004, 118(3):147-157. 10.1007/s00414-004-0428-5, 14760491.
3. Salas A, Quintans B, Alvarez-Iglesias V. SNaPshot typing of mitochondrial DNA coding region variants. Methods Mol Biol 2005, 297:197-208.
4. Calloway C, Stuart S, Erlich HA. Development of a multiplex PCR and linear array probe assay targeting informative polymorphisms within the entire mitochondrial genome. NIJ Grant Final Report 2009, http://www.ncjrs.gov/pdffiles1/nij/grants/228279.pdf.
5. Irwin JA, Parson W, Coble MD, Just RS. mtGenome reference population databases and the future of forensic mtDNA analysis. Forensic Sci Int Genet 2011, 5(3):222-225. 10.1016/j.fsigen.2010.02.008, 20457096.
6. Vallone PM, Jakupciak JP, Coble MD. Forensic application of the Affymetrix human mitochondrial resequencing array. Forensic Sci Int Genet 2007, 1(2):196-198. 10.1016/j.fsigen.2007.01.016, 19083755.
7. Loreille O, Koshinsky H, Fofanov VY, Irwin JA. Application of next generation sequencing technologies to the identification of highly degraded unknown soldiers' remains. Forensic Sci Int Genet Suppl Ser 2011, 3:e540-e541.
8. Irwin J, Just R, Scheible M, Loreille O. Assessing the potential of next generation sequencing technologies for missing persons identification efforts. Forensic Sci Int Genet Suppl Ser 2011, 3:e447-e448.
9. Kong QP, Salas A, Sun C, Fuku N, Tanaka M, Zhong L, Wang CY, Yao YG, Bandelt HJ. Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS One 2008, 3(8):e3016. 10.1371/journal.pone.0003016, 2515346, 18714389.
10. Bandelt HJ, Yao YG, Bravi CM, Salas A, Kivisild T. Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies. J Hum Genet 2009, 54(3):174-181. 10.1038/jhg.2009.9, 19322152.
11. Bandelt HJ, Salas A. Current next generation sequencing technology may not meet forensic standards. Forensic Sci Int Genet 2012, 6:143-145. 10.1016/j.fsigen.2011.04.004, 21565569.
12. Fendt L, Zimmermann B, Daniaux M, Parson W. Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences. BMC Genomics 2009, 10:139. 10.1186/1471-2164-10-139, 2669098, 19331681.
13. Irwin JA, Saunier JL, Strouss KM, Sturk KA, Diegoli TM, Just RS, Coble MD, Parson W, Parsons TJ. Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation. Forensic Sci Int Genet 2007, 1(2):154-157. 10.1016/j.fsigen.2007.01.019, 19083747.
14. van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 2009, 30(2):E386-E394. 10.1002/humu.20921, 18853457.
15. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Rohl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 2009, 84(6):740-759. 10.1016/j.ajhg.2009.05.001, 2694979, 19500773.
16. Levin BC, Cheng H, Reeder DJ. A human mitochondrial DNA standard reference material for quality control in forensic identification, medical diagnosis, and mutation detection. Genomics 1999, 55(2):135-146. 10.1006/geno.1998.5513, 9933560.
17. Levin BC, Holland KA, Hancock DK, Coble M, Parsons TJ, Kienker LJ, Williams DW, Jones M, Richie KL. Comparison of the complete mtDNA genome sequences of human cell lines-HL-60 and GM10742A-from individuals with pro-myelocytic leukemia and leber hereditary optic neuropathy, respectively, and the inclusion of HL-60 in the NIST human mitochondrial DNA standard reference material-SRM 2392-I. Mitochondrion 2003, 2(6):387-400. 10.1016/S1567-7249(03)00010-2, 16120335.
18. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 2004, 118(3):137-146. 10.1007/s00414-004-0427-6, 14760490.
19. Parsons TJ. Mitochondrial DNA genome sequencing and SNP assay development for increased power of discrimination. NIJ Grant Final Report 2006, http://www.ncjrs.gov/pdffiles1/nij/grants/213502.pdf.
20. Just RS, Diegoli TM, Saunier JL, Irwin JA, Parsons TJ. Complete mitochondrial genome sequences for 265 African American and U.S " Hispanic" individuals. Forensic Sci Int Genet 2008, 2(3):e45-e48. 10.1016/j.fsigen.2007.12.001, 19083815.
21. Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365-386. Humana Press, Krawetz S, Misener S, Totowa NJ.
22. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 1999, 23(2):147. 10.1038/13779, 10508508.
23. Goios A, Prieto L, Amorim A, Pereira L. Specificity of mtDNA-directed PCR-influence of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques. Int J Legal Med 2008, 122(4):341-345. 10.1007/s00414-007-0191-5, 17874117.
24. Primer-BLAST: Finding primers specific to your PCR template (using Primer3 and BLAST). http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?.
25. Herrnstadt C, Clevenger W, Ghosh SS, Anderson C, Fahy E, Miller S, Howell N, Davis RE. A novel mitochondrial DNA-like sequence in the human nuclear genome. Genomics 1999, 60(1):67-77. 10.1006/geno.1999.5907, 10458912.
26. Ravard-Goulvestre C, Crainic K, Guillon F, Paraire F, Durigon M, de Mazancourt P. Successful extraction of human genomic DNA from serum and its application to forensic identification. J Forensic Sci 2004, 49(1):60-63.
27. Parson W, Bandelt HJ. Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci Int Genet 2007, 1(1):13-19. 10.1016/j.fsigen.2006.11.003, 19083723.
28. Scientific Working Group on DNA Analysis Methods (SWGDAM) Interpretation guidelines for mitochondrial DNA analysis by forensic DNA testing laboratories. 2013, http://swgdam.org/SWGDAM%20mtDNA_Interpretation_Guidelines_APPROVED_073013.pdf, Scientific Working Group on DNA Analysis Methods (SWGDAM).
29. Carracedo A, Bar W, Lincoln P, Mayr W, Morling N, Olaisen B, Schneider P, Budowle B, Brinkmann B, Gill P, Holland M, Tully G, Wilson M. DNA commission of the international society for forensic genetics: guidelines for mitochondrial DNA typing. Forensic Sci Int 2000, 110(2):79-85. 10.1016/S0379-0738(00)00161-4, 10808096.
30. Salas A, Carracedo A, Macaulay V, Richards M, Bandelt HJ. A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 2005, 335(3):891-899. 10.1016/j.bbrc.2005.07.161, 16102729.
31. Carracedo A, Butler JM, Gusmao L, Linacre A, Parson W, Roewer L, Schneider PM. New guidelines for the publication of genetic population data. Forensic Sci Int Genet 2013, 7(2):217-220. 10.1016/j.fsigen.2013.01.001, 23375886.