Impacts of low coverage depths and post-mortem DNA damage on variant calling: A simulation study

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Parks, Matthew ^a   Lambert, David ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

Ancient DNA; Coverage depth; Next generation sequencing; Variant calling

Indexed keywords

ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DNA BASE COMPOSITION; DNA DAMAGE; DNA FRAGMENTATION; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; HETEROZYGOSITY; MEASUREMENT ACCURACY; PHASE TRANSITION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; COMPUTER SIMULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM;

DNA;

BASE COMPOSITION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA; DNA DAMAGE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84924339734     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1219-8     Document Type: Article

References (66)

1. Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM: Ancient population genomics and the study of evolution. Philos Trans R Soc London Ser B, doi:10.1098/rstb.2013.0381.
2. Shapiro B, Hofreiter M. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science. 2014;343:6169.
3. Pääbo S, Poinar H, Serre D, Jaenicke-Després V, Hebler J, Rohland N, et al. Genetic analyses from ancient DNA. Annu Rev Genet. 2004;38(1):645-79.
4. Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Gen Sel Evol. 2013;2013(45):4.
5. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A Draft sequence of the Neandertal genome. Science. 2010;328(5979):710-22.
6. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008;456(7220):387-90.
7. Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, et al. Genomic sequencing of Pleistocene cave bears. Science. 2005;309(5734):597-9.
8. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010;463(7282):757-62.
9. Rohland N, Reich D, Mallick S, Meyer M, Green RE, Georgiadis NJ, et al. Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and Savanna elephants. PLOS Biol. 2010;8:e1000564.
10. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, et al. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun. 2012;3:698.
11. Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, et al. A high-coverage genome sequence from an Archaic Denisovan individual. Science. 2012;338(6104):222-6.
12. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013;499(7456):74-8.
13. Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM. New developments in ancient genomics. Trends Ecol Evol. 2008;23(7):386-93.
14. Overballe-Petersen S, Orlando L, Willerslev E. Next-generation sequencing offers new insights into DNA degradation. Trends Biotechnol. 2012;30(7):364-8.
15. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, et al. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 2007;35(17):5717-28.
16. Prufer K, Stenzel U, Hofreiter M, Paabo S, Kelso J, Green RE. Computational challenges in the analysis of ancient DNA. Genome Biol. 2010;11:R47.
17. Le SQ, Durbin R. SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res. 2011;21(6):952-60.
18. Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011;27(15):2153-5.
19. Sánchez-Quinto F, Schroeder H, Ramirez O, Ávila-Arcos María C, Pybus M, Olalde I, et al. Genomic affinities of Two 7,000-year-Old Iberian hunter-gatherers. Curr Biol. 2012;22(16):1494-9.
20. Knapp M, Horsburgh KA, Prost S, Stanton J-A, Buckley HR, Walter RK, et al. Complete mitochondrial DNA genome sequences from the first New Zealanders. Proc Acad Nat Sci Phila. 2012;109(45):18350-4.
21. Avila-Arcos MC, Cappellini E, Romero-Navarro JA, Wales N, Moreno-Mayar JV, Rasmussen M, et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci Rep. 2011;1:74. doi:10.1038/srep00074.
22. Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE, Buigues B, et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science. 2006;311(5759):392-4.
23. Molak M, Ho SW. Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach. J Mol Evol. 2011;73(3-4):244-55.
24. Dabney J, Meyer M, Pääbo S. Ancient DNA damage. Cold Spring Harbor Perspectives in Biology. 2013;5:7.
25. Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res. 2011;21(10):1705-19.
26. Sawyer S, Krause J, Guschanksi K, Savolainen V, Pääbo S. Temporal Patterns of Nucleotide Misincorporations and DNA fragmentation in Ancient DNA. PLoS ONE. 2012;7(3):e34131.
27. Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Acad Nat Sci Phila. 2007;104(37):14616-21.
28. Sequin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, Prado JL, et al. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS ONE. 2013;8(10):e78575.
29. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24(5):713-4.
30. Kerpedjiev P, Frellsen J, Lindgreen S, Krogh A. Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC Bioinformatics. 2014;15:100.
31. Ruffalo M, LaFramboise T, Koyutürk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011;27(20):2790-6.
32. Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics. 2012;13:178.
33. Hatem A, Bozdag D, Toland AE, Catalyurek UV. Benchmarking short sequence mapping tools. BMC Bioinformatics. 2013;14:184.
34. Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y. Steps to ensure accuracy in genotype and SNP calling from illumina sequencing data. BMC Genomics. 2014;13 Suppl 8:S8.
35. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinf. 2010;11(5):473-83.
36. Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, et al. The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet. 2013;1:11.
37. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 2009;461(7268):1243-7.
38. Ben Rhouma F, Azzouz H, Petit F, Khelifa M, Chehida A, Nasrallah F, et al. Molecular and biochemical characterization of a novel intronic single point mutation in a Tunisian family with glycogen storage disease type III. Mol Biol Rep. 2013;1:6.
39. Nicholson SJ, Hoecker U, Srivastava V. A novel phytochrome B allele in Arabidopsis thaliana exhibits partial mutant phenotype: a short deletion in N-terminal extension reduces phytochrome B activity. Plant Growth Regulation. 2011;65:207-12.
40. Solomon DA, Kim T, Diaz-Martinez LA, Fair J, Elkahloun AG, Harris BT, et al. Mutational inactivation of STAG2 causes aneuplooidy in human cancer. Science. 2011;333:1039-43.
41. Vidal O, Araguas RM, Fernández R, Heras S, Sanz N, Pla C. Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine-256 in the MC1R gene. Animal Gen. 2010;41(6):656-8.
42. Vital A, Sole G, Casenave P, Magdelaine C, Ferrer X, Vital C, et al. Severe Charcot-Marie-Tooth disease type 1E caused by a novel p.Phe84Leufs*24 PMP22 point mutation. J Peripher Nerv Syst. 2013;18(2):181-4. doi:10.1111/jns5.12028.
43. Britten RJ, Rowen L, Williams J, Cameron RA. Majority of divergence between closely related DNA samples is due to indels. Proc Acad Nat Sci Phila. 2003;100(8):4661-5.
44. Denver DR, Morris K, Lynch M, Thomas WK. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature. 2004;430(7000):679-82.
45. Fortes GG, Speller CF, Hofreiter M, King TE. Phenotypes from ancient DNA: approaches, insights and prospects. Bioessays. 2013;35(8):690-5. doi:10.1002/bies.201300036.
46. Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011;475(7357):493-6.
47. Schiffels S, Durbin R. Inferring human population size and saparation history form multiple genome sequences. Nature Genetics. 2014;46(8):919-25.
48. Mardis ER. Next-generation sequencing platforms. Annu Rev Analytical Chem. 2013;6:287-303.
49. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science. 2009;325(5938):318-21.
50. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Gen. 2013;93:1-13.
51. Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics. 2013;29(13):1682-4.
52. Schubert M, Ermini L, Sarkissian CD, Jónsson H, Ginolhac A, Schaefer R, et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protocols. 2014;9(5):1056-82.
53. Fletcher W, Yang Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 2009;26(8):1879-88.
54. Hasegawa M, Kishino H, Yano TA. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22(2):160-74.
55. Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28(4):593-4.
56. Zhang J, Chiodini R, Badr A, Zhang G. The impact of next-generation sequencing on genomics. J Gen Genom. 2011;38(3):95-109.
57. Knapp M, Hofreiter M. Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes. 2010;1:227-43.
58. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, et al. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol. 2010;20(3):231-6.
59. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754-60.
60. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
61. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.
62. Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011;478(7370):506-10.
63. Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, et al. Improving the performance of true single molecule sequencing for ancient DNA. BMC Genom. 2012;13:177.
64. Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, et al. An aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011;334(6052):94-8.
65. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010;468(7327):1053-60.
66. Bray N, Pachter L. MAVID multiple alignment server. Nucleic Acids Res. 2003;31(13):3525-6.