Casbon JA, Osborne RJ, Brenner S, Lichtenstein CP. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids res. 2011;39(12):e81.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(1):72–4.
Article
CAS
Google Scholar
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(23):9530–5.
Article
PubMed
PubMed Central
Google Scholar
Diehl F, Schmidt K, Durkee KH, Moore KJ, Goodman SN, Shuber AP, et al. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology. 2008;135(2):489–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
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(42):16266–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burrell RA, Swanton C. The evolution of the unstable cancer genome. Curr Opin Genet dev. 2014;24:61–7.
Article
CAS
PubMed
Google Scholar
Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, et al. Detection of low-level mixed-population drug resistance in mycobacterium tuberculosis using high Fidelity amplicon sequencing. PLoS One. 2015;10(5):e0126626.
Article
PubMed
PubMed Central
Google Scholar
Van Laethem K, Theys K, Vandamme AM. HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Current Opinion in Virology. 2015;14:16–23.
Article
CAS
PubMed
Google Scholar
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science. 2013;341(6141):1237439.
Article
PubMed
PubMed Central
Google Scholar
Barrick JE, Lenski RE. Genome dynamics during experimental evolution. Nat rev Genet. 2013;14(12):827–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carlson CM, Dupuy AJ, Fritz S, Roberg-Perez KJ, Fletcher CF, Largaespada DA. Transposon mutagenesis of the mouse germline. Genetics. 2003;165(1):243–56.
CAS
PubMed
PubMed Central
Google Scholar
Corless CL, Harrell P, Lacouture M, Bainbridge T, Le C, Gatter K, et al. Allele-specific polymerase chain reaction for the imatinib-resistant KIT D816V and D816F mutations in mastocytosis and acute myelogenous leukemia. The Journal of Molecular Diagnostics : JMD. 2006;8(5):604–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peano C, Lesignoli F, Gulli M, Corradini R, Samson MC, Marchelli R, et al. Development of a peptide nucleic acid polymerase chain reaction clamping assay for semiquantitative evaluation of genetically modified organism content in food. Anal Biochem. 2005;344(2):174–82.
Article
CAS
PubMed
Google Scholar
Karkare S, Bhatnagar D. Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Appl Microbiol Biotechnol. 2006;71(5):575–86.
Article
CAS
PubMed
Google Scholar
Tatsumi K, Mitani Y, Watanabe J, Takakura H, Hoshi K, Kawai Y, et al. Rapid screening assay for KRAS mutations by the modified smart amplification process. The Journal of Molecular Diagnostics : JMD. 2008;10(6):520–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Orum H. PCR clamping. Current Issues in Molecular Biology. 2000;2(1):27–30.
CAS
PubMed
Google Scholar
Troedsson C, Lee RF, Walters T, Stokes V, Brinkley K, Naegele V, et al. Detection and discovery of crustacean parasites in blue crabs (Callinectes sapidus) by using 18S rRNA gene-targeted denaturing high-performance liquid chromatography. Appl Environ Microbiol. 2008;74(14):4346–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dominguez PL, Kolodney MS. Wild-type blocking polymerase chain reaction for detection of single nucleotide minority mutations from clinical specimens. Oncogene. 2005;24(45):6830–4.
Article
CAS
PubMed
Google Scholar
Boessenkool S, Epp LS, Haile J, Bellemain E, Edwards M, Coissac E, et al. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Mol Ecol. 2012;21(8):1806–15.
Article
CAS
PubMed
Google Scholar
Turchaninova MA, Britanova OV, Bolotin DA, Shugay M, Putintseva EV, Staroverov DB, et al. Pairing of T-cell receptor chains via emulsion PCR. Eur J Immunol. 2013;43(9):2507–15.
Article
CAS
PubMed
Google Scholar
Munson DJ, Egelston CA, Chiotti KE, Parra ZE, Bruno TC, Moore BL, et al. Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR. Proc Natl Acad Sci U S a. 2016;113(29):8272–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pao W, Miller VA, Politi KA, Riely GJ, Somwar R, Zakowski MF, et al. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS med. 2005;2(3):e73.
Article
PubMed
PubMed Central
Google Scholar
Shugay M, Zaretsky AR, Shagin DA, Shagina IA, Volchenkov IA, Shelenkov AA, et al. MAGERI: computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput Biol. 2017;13(5):e1005480.
Article
PubMed
PubMed Central
Google Scholar
Grun D, Kester L, van Oudenaarden A. Validation of noise models for single-cell transcriptomics. Nat Methods. 2014;11(6):637–40.
Article
PubMed
Google Scholar
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 U S a. 2013;110(33):13463–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J Immunol. 2014;192(6):2689–98.
Article
CAS
PubMed
Google Scholar
Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, Mamedov IZ, Tuganbaev TR, et al. Towards error-free profiling of immune repertoires. Nat Methods. 2014;11(6):653–5.
Article
CAS
PubMed
Google Scholar
He L, Sok D, Azadnia P, Hsueh J, Landais E, Simek M, et al. Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding. Scientific Reports. 2014;4:6778.
Article
CAS
PubMed
PubMed Central
Google Scholar
Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, et al. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J Immunol. 2015;194(12):6155–63.
Article
CAS
PubMed
Google Scholar
Khan TA, Friedensohn S, de Vries AR, Straszewski J, Ruscheweyh HJ, Reddy ST. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. Sci adv. 2016;2(3):e1501371.
Article
PubMed
PubMed Central
Google Scholar
Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, et al. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature. 2015;528(7580):132–6.
CAS
PubMed
PubMed Central
Google Scholar
Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, et al. Dynamics of individual T cell repertoires: from cord blood to centenarians. J Immunol. 2016;196(12):5005–13.
Article
CAS
PubMed
Google Scholar
Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol. 2015;26(8):1715–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gout JF, Thomas WK, Smith Z, Okamoto K, Lynch M. Large-scale detection of in vivo transcription errors. Proc Natl Acad Sci U S a. 2013;110(46):18584–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, et al. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids res. 2014;42(16):e129.
Article
PubMed
PubMed Central
Google Scholar