DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

Investigative Genetics

Volumn 4, Issue 1, 2013, Pages

  Templeton, Jennifer E L ^a,b   Brotherton, Paul M ^a,c   Llamas, Bastien ^a   Soubrier, Julien ^a   Haak, Wolfgang ^a   Cooper, Alan ^a   Austin, Jeremy J ^a,d  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

^c UNIVERSITY OF HUDDERSFIELD   (United Kingdom)

^d MUSEUM VICTORIA   (Australia)

Author keywords

Ancient DNA; Degraded DNA; DNA enrichment; DNA hybridisation; Forensic science; Mitochondrial DNA; Next generation sequencing

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; CONTROLLED STUDY; DNA DEGRADATION; DNA EXTRACTION; DNA FRAGMENTATION; DNA HYBRIDIZATION; DNA LIBRARY; FORENSIC GENETICS; FORENSIC IDENTIFICATION; GENE DOSAGE; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN TISSUE; MITOCHONDRIAL GENOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84888595248     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/2041-2223-4-26     Document Type: Article

References (59)

1. Butler JM. Advanced Topics in Forensic DNA Typing: Methodology 2011, London: Academic.
2. Nandineni MR, Vedanayagam JP. Selective enrichment of human DNA from non-human DNAs for DNA typing of decomposed skeletal remains. Forensic Sci Int-Gen Supplement Series 2009, 2:520-521.
3. Alonso A, Martín P, Albarrán C, García P, Primorac D, García O, de Fernández Simón L, García-Hirschfeld J, Sancho M, Fernández-Piqueras J. Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies. Croat Med J 2003, 44:273-280.
4. van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 2009, 30:E386-E394. 10.1002/humu.20921, 18853457.
5. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajković D, Kućan Z, Gušić I, Schmitz R, Doronichev VB, Golovanova LV, Rasilla M, Fortea J, Rosas A, Pääbo S. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 2009, 325:318-321. 10.1126/science.1174462, 19608918.
6. Anderung C, Persson P, Bouwman A, Elburg R, Götherström A. Fishing for ancient DNA. Forensic Sci Int-Gen 2008, 2:104-107.
7. Brotherton P, Sanchez JJ, Cooper A, Endicott P. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX. Nucleic Acids Res. 2010, 38:e7. 10.1093/nar/gkp897, 2811011, 19864251.
8. Parsons TJ, Huel R, Davoren J, Katzmarzyk C, Miloš A, Selmanović A, Smajlović L, Coble MD, Rizvić A. Application of novel 'mini-amplicon' STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int-Gen 2007, 1:175-179.
9. Bright J-A, Taylor D, Curran JM, Buckleton JS. Developing allelic and stutter peak height models for a continuous method of DNA interpretation. Forensic Sci Int-Gen 2013, 7:296-304.
10. Hill CR, Kline MC, Coble MD, Butler JM. Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J Forensic Sci 2008, 53:73-80.
11. Lee HY, Park MJ, Kim NY, Sim JE, Yang WI, Shin K-J. Simple and highly effective DNA extraction methods from old skeletal remains using silica columns. Forensic Sci Int-Gen 2010, 4:275-280.
12. Fregeau CJ, De Moors A. Competition for DNA binding sites using Promega DNA IQ (TM) paramagnetic beads. Forensic Sci Int-Gen 2012, 6:511-522.
13. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 2001, 114:204-210. 10.1007/s004149900117, 11355396.
14. Budowle B, Wilson MR, DiZinno JA, Stauffer C, Fasano MA, Holland MM, Monson KL. Mitochondrial DNA regions HVI and HVII population data. Forensic Sci Int 1999, 103:23-35. 10.1016/S0379-0738(99)00042-0, 10464936.
15. Allen M, Engström AS, Meyers S, Handt O, Saldeen T, Von Haeseler A, Pääbo S, Gyllensten U. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J Forensic Sci 1998, 43:453-464.
16. Boles TC, Snow CC, Stover E. Forensic DNA testing on skeletal remains from mass graves: a pilot project in Guatemala. J Forensic Sci 1995, 40:349-355.
17. Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, Hagelberg E, Sullivan K. Identification of the remains of the Romanov family by DNA analysis. Nat Genet 1994, 6:130-135. 10.1038/ng0294-130, 8162066.
18. Ginther C, Issel-Tarver L, King M-C. Identifying individuals by sequencing mitochondrial DNA from teeth. Nat Genet 1992, 2:135-138. 10.1038/ng1092-135, 1303263.
19. Butler JM, Levin BC. Forensic applications of mitochondrial DNA. Trends Biotechnol 1998, 16:158-162. 10.1016/S0167-7799(98)01173-1, 9586238.
20. Just RS, Loreille OM, Molto JE, Merriwether AD, Woodward SR, Matheson C, Creed J, McGrath SE, Sturk-Andreaggi K, Coble MD, Irwin JA, Ruffman A, Parr RL. Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort. Forensic Sci Int-Gen 2011, 5:231-235.
21. Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Adler CJ, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar D, Meller H, Alt KW, Cooper A,. the Genographic Consortium Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 2013, 4:1764. the Genographic Consortium.
22. Melton T, Clifford S, Kayser M, Nasidze I, Batzer M, Stoneking M. Diversity and heterogeneity in mitochondrial DNA of North American populations. J Forensic Sci 2001, 46:46-52.
23. Grubwieser P, Mühlmann R, Parson W. New sensitive amplification primers for the STR locus D2S1338 for degraded casework DNA. Int J Legal Med 2003, 117:185-188.
24. Maricic T, Whitten M, Pääbo S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 2010, 5:e14004. 10.1371/journal.pone.0014004, 2982832, 21103372.
25. Knapp M, Stiller M, Meyer M. Generating barcoded libraries for multiplex high-throughput sequencing. Edited by Shapiro B, Hofreiter M 2012, 155-170. Humana Press: New York, Ancient DNA.
26. Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 2013, 23:553-559. 10.1016/j.cub.2013.02.044, 23523248.
27. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR. Genome-wide in situ exon capture for selective resequencing. Nat Genet 2007, 39:1522-1527. 10.1038/ng.2007.42, 17982454.
28. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nussbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27:182-189. 10.1038/nbt.1523, 2663421, 19182786.
29. Cooper A, Poinar HN. Ancient DNA: do it right or not at all. Science 2000, 289:1139-1139.
30. Swango KL, Timken MD, Chong MD, Buoncristiani MR. A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci Int 2006, 158:14-26. 10.1016/j.forsciint.2005.04.034, 15936161.
31. Adler CJ, Haak W, Donlon D, Cooper A,. the Genographic Consortium Survival and recovery of DNA from ancient teeth and bones. J Archaeol Sci 2011, 38:956-964. the Genographic Consortium.
32. FASTX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit/index.html.
33. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal 2011, 1:1-10.
34. Andrews S. FastQC. A quality control tool for high throughput sequence data. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc.
35. Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli E-L, Silva NM, Kivisild T, Torroni A, Villems R. A 'Copernican' reassessment of the human mitochondrial DNA tree from its root. Am J Hum Gen 2012, 90:675-684.
36. TMAP v3.2.1. https://github.com/nh13/TMAP.
37. Merriman B, Torrent I, Rothberg JM. Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 2012, 33:3397-3417. 10.1002/elps.201200424, 23208921.
38. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
39. Picard Tools. http://picard.sourceforge.net.
40. Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011, 27:2153-2155. 10.1093/bioinformatics/btr347, 21659319.
41. Geneious v6.0 created by Biomatters. http://www.geneious.com/.
42. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tanzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 2005, 310:1016-1018.
43. Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, der Sarkissian C, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A,. the Genographic Consortium Ancient DNA from European early Neolithic farmers reveals their near eastern affinities. PLoS Biol. 2010, 8:e1000536. 10.1371/journal.pbio.1000536, 2976717, 21085689, the Genographic Consortium.
44. Sánchez-Quinto F, Schroeder H, Ramirez O, Ávila-Arcos MC, Pybus M, Olalde I, Velazquez A, Marcos MEP, Encinas JMV, Bertranpetit J, Orlando L, Gilbert MTP, Lalueza-Fox C. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr Biol 2012, 22:1494-1499. 10.1016/j.cub.2012.06.005, 22748318.
45. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 2010, 20:231-236. 10.1016/j.cub.2009.11.068, 20045327.
46. Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković, Kućan Z, Gušić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008, 134:416-426. 10.1016/j.cell.2008.06.021, 2602844, 18692465.
47. Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee ASG. Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. PLoS One 2012, 7:e45798. 10.1371/journal.pone.0045798, 3446914, 23029247.
48. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC genomics 2012, 13:341. 10.1186/1471-2164-13-341, 3431227, 22827831.
49. Golan D, Medvedev P. Using state machines to model the Ion Torrent sequencing process and to improve read error rates. Bioinformatics 2013, 29:i344-i351. 10.1093/bioinformatics/btt212, 3694666, 23813003.
50. Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW. Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput Biol 2013, 9:e1003031. 10.1371/journal.pcbi.1003031, 3623719, 23592973.
51. Koehnemann S, Pfeiffer H. Application of mtDNA SNP analysis in forensic casework. Forensic Sci Int-Gen 2011, 5:216-221.
52. Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Roy Soc B: Biol Sci 2012, 279:4724-4733.
53. Irwin JA, Parson W, Coble MD, Just RS. mtGenome reference population databases and the future of forensic mtDNA analysis. Forensic Sci Int-Gen 2011, 5:222-225.
54. Just RS, Leney MD, Barritt SM, Los CW, Smith BC, Holland TD, Parsons TJ. The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases. J Forensic Sci 2009, 54:887-891. 10.1111/j.1556-4029.2009.01069.x, 19486251.
55. 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, 118:137-146. 10.1007/s00414-004-0427-6, 14760490.
56. Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RAH, Kayser M. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int-Gen 2012, 6:425-436.
57. van Oven M, Vermeulen M, Kayser M. Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution. Invest Genet 2011, 2:6-6.
58. Quintans B, Alvarez-Iglesias V, Salas A, Phillips C, Lareu MV, Carracedo A. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci Int 2004, 140:251-257. 10.1016/j.forsciint.2003.12.005, 15036446.
59. 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, 8547161.