Polymerase specific error rates and profiles identified by single molecule sequencing

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 784-785, Issue , 2016, Pages 39-45

  Hestand, Matthew S ^a   Van Houdt, Jeroen ^a   Cristofoli, Francesca ^a   Vermeesch, Joris R ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Heteroduplex; Polymerase fidelity; Single molecule sequencing

Indexed keywords

DNA; DNA POLYMERASE; DOUBLE STRANDED DNA; HETERODUPLEX; DNA DIRECTED DNA POLYMERASE; PURINE; PURINE DERIVATIVE; PYRIMIDINE; PYRIMIDINE DERIVATIVE; TAQ POLYMERASE;

ACCURACY; AMPLICON; ARTICLE; BASE PAIRING; DNA DETERMINATION; GENE MUTATION; MUTATION RATE; MUTATIONAL ANALYSIS; NUCLEIC ACID BASE SUBSTITUTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; DNA SEQUENCE; GENETICS; METABOLISM; MUTATION; PROCEDURES;

BASE PAIRING; DNA-DIRECTED DNA POLYMERASE; MUTATION; NUCLEIC ACID HETERODUPLEXES; POLYMERASE CHAIN REACTION; PURINES; PYRIMIDINES; SEQUENCE ANALYSIS, DNA; TAQ POLYMERASE;

EID: 84955564885     PISSN: 00275107     EISSN: 18792871     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2016.01.003     Document Type: Article

References (36)

1. Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., Kang H.M., Marth G.T., McVean G.A., Altshuler D.M., et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491(7422):56-65.
2. Aboul-ela F., Koh D., Tinoco I., Martin F.H. Base-base mismatches Thermodynamics of double helix formation for dCA3XA3G+dCT3YT3G (X, Y=A,C,G,T). Nucleic Acids Res. 1985, 13(13):4811-4824.
3. Alexandrov L.B., Nik-Zainal S., Wedge D.C., Aparicio S.A., Behjati S., Biankin A.V., Bignell G.R., Bolli N., Borg A., Børresen-Dale A.L., et al. Signatures of mutational processes in human cancer. Nature 2013, 500(7463):415-421.
4. Bebenek K., Pedersen L.C., Kunkel T.A. Replication infidelity via a mismatch with Watson-Crick geometry. Proc. Natl. Acad. Sci. U. S. A. 2011, 108(5):1862-1867.
5. Bedard P.L., Hansen A.R., Ratain M.J., Siu L.L. Tumour heterogeneity in the clinic. Nature 2013, 501(7467):355-364.
6. Biesecker L.G., Spinner N.B. A genomic view of mosaicism and human disease. Nat. Rev. Genet. 2013, 14(5):307-320.
7. Carneiro M.O., Russ C., Ross M.G., Gabriel S.B., Nusbaum C., DePristo M.A. Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 2012, 13:375.
8. Ding L., Ley T.J., Larson D.E., Miller C.A., Koboldt D.C., Welch J.S., Ritchey J.K., Young M.A., Lamprecht T., McLellan M.D., et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012, 481(7382):506-510.
9. Dressman D., Yan H., Traverso G., Kinzler K.W., Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl. Acad. Sci. U. S. A. 2003, 100(15):8817-8822.
10. Eckert K.A., Kunkel T.A. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1991, 1(1):17-24.
11. Erickson R.P. Recent advances in the study of somatic mosaicism and diseases other than cancer. Curr. Opin. Genet. Dev. 2014, 26:73-78.
12. Fischer S.G., Lerman L.S. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. U. S. A. 1983, 80(6):1579-1583.
13. Fuller C.W., Middendorf L.R., Benner S.A., Church G.M., Harris T., Huang X., Jovanovich S.B., Nelson J.R., Schloss J.A., Schwartz D.C., Vezenov D.V. The challenges of sequencing by synthesis. Nat. Biotechnol. 2009, 27(11):1013-1023.
14. Gregory M.T., Bertout J.A., Ericson N.G., Taylor S.D., Mukherjee R., Robins H.S., Drescher C.W., Bielas J.H. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res. 2015, Gkv915.
15. Guo X., Lehner K., O'Connell K., Zhang J., Dave S.S., Jinks-Robertson S. SMRT sequencing for parallel analysis of multiple targets and accurate SNP phasing. G3 (Bethesda) 2015, pii: g3.115.023317.
16. Harris V.H., Smith C.L., Jonathan Cummins W., Hamilton A.L., Adams H., Dickman M., Hornby D.P., Williams D.M. The effect of tautomeric constant on the specificity of nucleotide incorporation during DNA replication: support for the rare tautomer hypothesis of substitution mutagenesis. J. Mol. Biol. 2003, 326(5):1389-1401.
17. Jiao X., Zheng X., Ma L., Kutty G., Gogineni E., Sun Q., Sherman B.T., Hu X., Jones K., Raley C., et al. A benchmark study on error assessment and quality control of CCS reads derived from the PacBio RS. J. Data Mining Genomics Proteomics 2013, 4(3). pii:16008.
18. Kennedy S.R., Schmitt M.W., Fox E.J., Kohrn B.F., Salk J.J., Ahn E.H., Prindle M.J., Kuong K.J., Shen J.C., Risques R.A., Loeb L.A. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat. Protoc. 2014, 9(11):2586-2606.
19. Keohavong P., Thilly W.G. Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. U. S. A. 1989, 86(23):9253-9257.
20. Kinde I., Wu J., Papadopoulos N., Kinzler K.W., Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. U. S. A. 2011, 108(23):9530-9535.
21. Kircher M., Heyn P., Kelso J. Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 2011, 12:382.
22. Kunkel T.A. 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(9):5787-5796.
23. Leinonen R., Akhtar R., Birney E., Bower L., Cerdeno-Tarraga A., Cheng Y., Cleland I., Faruque N., Goodgame N., Gibson R., et al. The European Nucleotide Archive. Nucleic Acids Res. 2011, 39:28-31. (Database issue).
24. 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(16):2078-2079.
25. Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595.
26. Li M., Diehl F., Dressman D., Vogelstein B., Kinzler K.W. BEAMing up for detection and quantification of rare sequence variants. Nat. Methods 2006, 3(2):95-97.
27. Ling L.L., Keohavong P., Dias C., Thilly W.G. Optimization of the polymerase chain reaction with regard to fidelity: modified T7, Taq, and vent DNA polymerases. PCR Methods Appl. 1991, 1(1):63-69.
28. McInerney P., Adams P., Hadi M.Z. Error rate comparison during polymerase chain reaction by DNA polymerase. Mol. Biol. Int. 2014, 2014:287430.
29. Mensah M.A., Hestand M.S., Larmuseau M.H., Isrie M., Vanderheyden N., Declercq M., Souche E.L., Van Houdt J., Stoeva R., Van Esch H., et al. Pseudoautosomal region 1 length polymorphism in the human population. PLoS Genet. 2014, 10(11):e1004578.
30. Nik-Zainal S., Van Loo P., Wedge D.C., Alexandrov L.B., Greenman C.D., Lau K.W., Raine K., Jones D., Marshall J., Ramakrishna M., et al. The life history of 21 breast cancers. Cell 2012, 149(5):994-1007.
31. Puente X.S., Pinyol M., Quesada V., Conde L., Ordonez G.R., Villamor N., Escaramis G., Jares P., Bea S., Gonzalez-Diaz M., et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011, 475(7354):101-105.
32. Robinson J.T., Thorvaldsdottir H., Winckler W., Guttman M., Lander E.S., Getz G., Mesirov J.P. Integrative genomics viewer. Nat. Biotechnol. 2011, 29(1):24-26.
33. Schmitt M.W., Kennedy S.R., Salk J.J., Fox E.J., Hiatt J.B., Loeb L.A. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. U. S. A. 2012, 109(36):14508-14513.
34. Shah S.P., Morin R.D., Khattra J., Prentice L., Pugh T., Burleigh A., Delaney A., Gelmon K., Guliany R., Senz J., et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2010, 461(7265):809-813.
35. Watson J.D., Crick F.H. Genetical implications of the structure of deoxyribonucleic acid. Nature 1953, 171(4361):964-967.
36. De Wolf V., Crepel A., Schuit F., van Lommel L., Ceulemans B., Steyaert J., Seuntjens E., Peeters H., Devriendt K. A complex Xp11. 22 deletion in a patient with syndromic autism: exploration of FAM120C as a positional candidate gene for autism. Am. J. Med. Genet. A 2014, 164A(12):3035-3041.