Characterization of background noise in capture-based targeted sequencing data

Genome Biology

Volumn 18, Issue 1, 2017, Pages

  Park, Gahee ^a,b   Park, Joo Kyung ^c   Shin, Seung Ho ^a,d   Jeon, Hyo Jeong ^a   Kim, Nayoung K D ^a   Kim, Yeon Jeong ^a   Shin, Hyun Tae ^a   Lee, Eunjin ^a   Lee, Kwang Hyuck ^c,d   Son, Dae Soon ^a   Park, Woong Yang ^a,c,d   Park, Donghyun ^a  

^a Samsung Medical Center   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

^c Sungkyunkwan University School of Medicine   (South Korea)

^d Sungkyunkwan University   (South Korea)

Author keywords

Background error; DNA fragmentation; Next generation sequencing; Plasma DNA; Substitution rate; Targeted deep sequencing

Indexed keywords

DNA FRAGMENT; GENOMIC DNA; GUANINE; DNA;

ALLELE; ARTICLE; ARTIFACT REDUCTION; CONTROLLED STUDY; DIGITAL FILTERING; DNA FRAGMENTATION; DNA STRAND BREAKAGE; FALSE POSITIVE RESULT; HUMAN; HYBRID; LEUKOCYTE; NEXT GENERATION SEQUENCING; NUCLEIC ACID BASE SUBSTITUTION; OXIDATION; PANCREAS CANCER; PLASMA; SEQUENCE ANALYSIS; TARGETED DEEP SEQUENCING; ADULT; ARTIFACT; GENETICS; HIGH THROUGHPUT SEQUENCING; PANCREAS TUMOR; REPRODUCIBILITY;

ADULT; ARTIFACTS; DNA; DNA FRAGMENTATION; DNA, NEOPLASM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PANCREATIC NEOPLASMS; REPRODUCIBILITY OF RESULTS;

EID: 85025098177     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1275-2     Document Type: Article

References (59)

1. Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, Gao J, Socci ND, Solit DB, Olshen AB, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016;34:155-63.
2. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333-9.
3. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505:495-501.
4. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27:182-9.
5. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7:111-8.
6. Wong SQ, Li J, Salemi R, Sheppard KE, Do H, Tothill RW, McArthur GA, Dobrovic A. Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. Sci Rep. 2013;3:3494.
7. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366:883-92.
8. Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan MD, Dooling D, Abbott R, et al. Clonal architecture of secondary acute myeloid leukemia. N Engl J Med. 2012;366:1090-8.
9. Diaz Jr LA, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486:537-40.
10. Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, Valtorta E, Schiavo R, Buscarino M, Siravegna G, et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature. 2012;486:532-6.
11. Diaz Jr LA, Bardelli A. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol. 2014;32:579-86.
12. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, Diaz Jr LA, Goodman SN, David KA, Juhl H, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005;102:16368-73.
13. Alix-Panabieres C, Pantel K. Clinical applications of circulating tumor cells and circulating tumor DNA as liquid biopsy. Cancer Discov. 2016;6:479-91.
14. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6:224ra224.
15. Heitzer E, Ulz P, Geigl JB. Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem. 2015;61:112-23.
16. Lo YM, Rainer TH, Chan LY, Hjelm NM, Cocks RA. Plasma DNA as a prognostic marker in trauma patients. Clin Chem. 2000;46:319-23.
17. Rainer TH, Wong KS, Lam W, Lam NY, Graham CA, Lo YM. Comparison of plasma beta-globin DNA and S-100 protein concentrations in acute stroke. Clin Chim Acta. 2007;376:190-6.
18. Lui YY, Woo KS, Wang AY, Yeung CK, Li PK, Chau E, Ruygrok P, Lo YM. Origin of plasma cell-free DNA after solid organ transplantation. Clin Chem. 2003;49:495-6.
19. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008;105:16266-71.
20. Gundry M, Vijg J. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res. 2012;729:1-15.
21. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109:14508-13.
22. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A. 2011;108:9530-5.
23. Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform. 2016;17:154-79.
24. Minoche AE, Dohm JC, Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011;12:R112.
25. Cline J, Braman JC, Hogrefe HH. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 1996;24:3546-51.
26. Kuchta RD, Benkovic P, Benkovic SJ. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry. 1988;27:6716-25.
27. Chen G, Mosier S, Gocke CD, Lin MT, Eshleman JR. Cytosine deamination is a major cause of baseline noise in next-generation sequencing. Mol Diagn Ther. 2014;18:587-93.
28. Do H, Wong SQ, Li J, Dobrovic A. Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin Chem. 2013;59:1376-83.
29. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, et al. Signatures of mutational processes in human cancer. Nature. 2013;500:415-21.
30. Chung J, Son DS, Jeon HJ, Kim KM, Park G, Ryu GH, Park WY, Park D. The minimal amount of starting DNA for Agilent's hybrid capture-based targeted massively parallel sequencing. Sci Rep. 2016;6:26732.
31. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008;36:e105.
32. Qu W, Hashimoto S, Morishita S. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res. 2009;19:1309-15.
33. Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015;43:e37.
34. Wang XV, Blades N, Ding J, Sultana R, Parmigiani G. Estimation of sequencing error rates in short reads. BMC Bioinformatics. 2012;13:185.
35. Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016;34:547-55.
36. Akasaka S, Yamamoto K. Mutagenesis resulting from DNA damage by lipid peroxidation in the supF gene of Escherichia coli. Mutat Res. 1994;315:105-12.
37. McBride TJ, Preston BD, Loeb LA. Mutagenic spectrum resulting from DNA damage by oxygen radicals. Biochemistry. 1991;30:207-13.
38. Neeley WL, Essigmann JM. Mechanisms of formation, genotoxicity, and mutation of guanine oxidation products. Chem Res Toxicol. 2006;19:491-505.
39. Valentine MR, Rodriguez H, Termini J. Mutagenesis by peroxy radical is dominated by transversions at deoxyguanosine: evidence for the lack of involvement of 8-oxo-dG1 and/or abasic site formation. Biochemistry. 1998;37:7030-8.
40. Pitterl F, Chervet JP, Oberacher H. Electrochemical simulation of oxidation processes involving nucleic acids monitored with electrospray ionization-mass spectrometry. Anal Bioanal Chem. 2010;397:1203-15.
41. Kino K, Sugiyama H. UVR-induced G-C to C-G transversions from oxidative DNA damage. Mutat Res. 2005;571:33-42.
42. Shibutani S, Takeshita M, Grollman AP. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature. 1991;349:431-4.
43. Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 2013;41:e67.
44. Kino K, Sugiyama H. Possible cause of G-C-->C-G transversion mutation by guanine oxidation product, imidazolone. Chem Biol. 2001;8:369-78.
45. Chen L, Liu P, Evans Jr TC, Ettwiller LM. DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification. Science. 2017;355:752-6.
46. Swenberg JA, Lu K, Moeller BC, Gao L, Upton PB, Nakamura J, Starr TB. Endogenous versus exogenous DNA adducts: their role in carcinogenesis, epidemiology, and risk assessment. Toxicol Sci. 2011;120 Suppl 1:S130-45.
47. Clark MJ, Chen R, Lam HY, Karczewski KJ, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29:908-14.
48. Butler TM, Johnson-Camacho K, Peto M, Wang NJ, Macey TA, Korkola JE, Koppie TM, Corless CL, Gray JW, Spellman PT. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease. PLoS One. 2015;10:e0136407.
49. Bebenek K, Joyce CM, Fitzgerald MP, Kunkel TA. The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I. J Biol Chem. 1990;265:13878-87.
50. Kim J, Mrksich M. Profiling the selectivity of DNA ligases in an array format with mass spectrometry. Nucleic Acids Res. 2010;38:e2.
51. Poptsova MS, Il'icheva IA, Nechipurenko DY, Panchenko LA, Khodikov MV, Oparina NY, Polozov RV, Nechipurenko YD, Grokhovsky SL. Non-random DNA fragmentation in next-generation sequencing. Sci Rep. 2014;4:4532.
52. Chandrananda D, Thorne NP, Bahlo M. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med Genomics. 2015;8:29.
53. Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164:57-68.
54. Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014;20:548-54.
55. Olivier M, Hollstein M, Hainaut P. TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol. 2010;2:a001008.
56. Norton SE, Lechner JM, Williams T, Fernando MR. A stabilizing reagent prevents cell-free DNA contamination by cellular DNA in plasma during blood sample storage and shipping as determined by digital PCR. Clin Biochem. 2013;46:1561-5.
57. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
58. 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;25:2078-9.
59. 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;20:1297-303.