Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Kou, Ruqin ^a   Lam, Ham ^a   Duan, Hairong ^a   Ye, Li ^a   Jongkam, Narisra ^a   Chen, Weizhi ^a   Zhang, Shifang ^a   Li, Shihong ^a  

^a GENEWIZ INC   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GUANINE; NUCLEOTIDE; THYMINE; DNA DIRECTED DNA POLYMERASE; FGFR3 PROTEIN, HUMAN; FIBROBLAST GROWTH FACTOR RECEPTOR 3;

ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; EXON; FGFR3 GENE; GENE; GENE DELETION; GENE MUTATION; GENETIC PROCEDURES; HRAS GENE; ILLUMINA SEQUENCING; LOW FREQUENCY MUTATION; MEASUREMENT ACCURACY; NEXT GENERATION SEQUENCING; NUCLEIC ACID BASE SUBSTITUTION; PIK3CA GENE; POLYMERASE CHAIN REACTION; RELIABILITY; SAMPLING BIAS; SANGER SEQUENCING; SEQUENCE ANALYSIS; SEQUENCING ERROR RATE; UNIQUE MOLECULAR IDENTIFIER; CHROMOSOME 4; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; DNA TEMPLATE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; MOLECULAR GENETICS; MUTATION RATE; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY;

BASE SEQUENCE; CHROMOSOMES, HUMAN, PAIR 4; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; DNA-DIRECTED DNA POLYMERASE; EXONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION RATE; NUCLEOTIDES; POLYMERASE CHAIN REACTION; RECEPTOR, FIBROBLAST GROWTH FACTOR, TYPE 3; REPRODUCIBILITY OF RESULTS; SEQUENCE DELETION; TEMPLATES, GENETIC;

EID: 84954565671     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0146638     Document Type: Article

References (22)

1. Bejar R, Stevenson KE, Caughey B, Lindsley RC, Brenton GM, Stojanov P, et al. Somatic Mutations Predict Poor Outcome in Patients With Myelodysplastic Syndrome After Hematopoietic Stem-Cell Transplantation. JCO, 2014; 32(25), 2691-2698
2. Bronte G, Rizzo S, La Paglia L, Adamo V, Siragusa S, Ficorella C, et al. Driver mutations and differential sensitivity to targeted therapies: a new approach to the treatment of lung adenocarcinoma. Cancer Treat Rev. 2010; 36Suppl 3: S21-29 doi: 10.1016/S0305-7372(10)70016-5 PMID: 21129606
3. Kompier LC, Lurkin I, van der Aa MN, van Rhijn BW, van der Kwast TH, Zwarthoff EC. FGFR3, HRAS, KRAS, NRAS and PIK3CA mutations in bladder cancer and their potential as biomarkers for surveillance and therapy. PLoS ONE 2010, 5, e13821 doi: 10.1371/journal.pone.0013821 PMID: 21072204
4. Menzo S, Vincenti D, Solmone M, Prosperi M, Bruselles A, Abbate I, et al. Low-Abundance Drug Resistance Mutations: Extending the HIV Paradigm to Hepatitis B Virus. J Infect Dis. 2009, 200 (11):1798-1799 doi: 10.1086/647991 PMID: 19905934
5. Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, et al. Low-abundance drugresistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009, 199:693-701 doi: 10.1086/596736 PMID: 19210162
6. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet. 2010; 11(1):31-46 doi: 10.1038/nrg2626 PMID: 19997069
7. Meldrum C, Doyle MA, Tothill RW. Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective, Clin Biochem Rev. 2011 Nov; 32(4): 177-195 PMID: 22147957
8. Zagordi O, Klein R, Daumer M, Beerenwinkel N. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res 2010, 38:7400-7409 doi: 10.1093/nar/gkq655 PMID: 20671025
9. Tindall KR, Kunkel TA. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 1988, 27:6008-6013 PMID: 2847780
10. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci USA 2011, 108(23):9530-9535 doi: 10.1073/pnas.1105422108 PMID: 21586637
11. Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, et al. Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Nucleic Acids Res 2014, 42:e98 doi: 10.1093/nar/gku355 PMID: 24810852
12. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci USA 2011, 108:20166-20171 doi: 10.1073/pnas.1110064108 PMID: 22135472
13. Fu GK, Hu J, Wang PH, Fodor SP. Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc Natl Acad Sci USA 2011, 108(22):9026-9031 doi: 10.1073/pnas.1017621108 PMID: 21562209
14. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, et al. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007, 35:e91 PMID: 17576693
15. Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 2012, 9:72-74
16. Shiroguchi K, Jia TZ, Sims PA, Xie XS. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci USA 2012, 109 (4):1347-1352 doi: 10.1073/pnas.1118018109 PMID: 22232676
17. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, and Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA 2013, 109: 14508-14513
18. Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci USA 2013, 110: 13463-13468 doi: 10.1073/pnas.1312146110 PMID: 23898164
19. Islam S, Zeisel A, Joost S, Manno GL, Zajac P, Kasper M, et al. Quantitative single cell RNA-seq with unique molecular identifiers. Nature Methods 2014, 11(2), 163-166 doi: 10.1038/nmeth.2772 PMID: 24363023
20. Kunkel TA. The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J Biol Chem 1985, 260:5787-5796 PMID: 3988773
21. Shafikhani S, Siegel RA, Ferrari E, Schellenberger V. Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. Biotechniques 1997, 23(2):304-10 PMID: 9266088
22. Brodin J, Hedskog C, Heddini A, Benard E, Neher RA, Mild M, et al. Challenges with using primer IDs to improve accuracy of next generation sequencing. PLoS ONE 2015, 10(3):e0119123. doi: 10.1371/journal.pone.0119123 eCollection 2015. PMID: 25741706