Detecting ultralow-frequency mutations by Duplex Sequencing
Open accessAbstract
Duplex Sequencing (DS) is a next-generation sequencing methodology capable of detecting a single mutation among >1 × 10(7) wild-type nucleotides, thereby enabling the study of heterogeneous populations and very-low-frequency genetic alterations. DS can be applied to any double-stranded DNA sample, but it is ideal for small genomic regions of <1 Mb in size. The method relies on the ligation of sequencing adapters harboring random yet complementary double-stranded nucleotide sequences to the sample DNA of interest. Individually labeled strands are then PCR-amplified, creating sequence 'families' that share a common tag sequence derived from the two original complementary strands. Mutations are scored only if the variant is present in the PCR families arising from both of the two DNA strands. Here we provide a detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow. The protocol typically takes 1-3 d.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Duplex sequencing enables the detection of mutations as low as 1 in 10^8 nucleotides sequenced.
“duplex sequencing enables the detection of mutations as low as 1 in 10 8 nucleotides sequenced (17, 18).”
From Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency (2016) · cites this paper as [18]
The Introduction ('The concept of DS'; page not available) says Duplex Sequencing can detect a single mutation among more than 10^7 sequenced bases. That supports ultralow-frequency detection, but the copy does not establish the specific sensitivity of 1 in 10^8 claimed here. (LLM, conf=0.88)
Experimental — accuracy not yet measuredDuplex sequencing is a highly accurate next-generation sequencing methodology that enables the detection of rare mutagenic effects.
“we used duplex sequencing, a highly accurate next-generation sequencing methodology that enables the detection of rare mutagenic effects (18)”
From Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency (2016) · cites this paper as [18]
Use of duplex sequencing enabled study of the mutagenic consequences of UV damage independent of selective pressures and in far greater detail than previously possible.
“In contrast to previous methods, our use of duplex sequencing (18) enabled us to study the mutagenic consequences of UV damage independent of selective pressures and in far greater detail than previously possible.”
From Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency (2016) · cites this paper as [18]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774 · see citing works
Counting absolute numbers of molecules using unique molecular identifiers
Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., & Taipale, J. (2012) · Nature Methods · doi:10.1038/nmeth.1778 · Cited by 1,010 · see citing works
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma
Bolli, N., Avet-Loiseau, H., Wedge, D. C., Van Loo, P., Alexandrov, L. B., Martincorena, I., Dawson, K. J., Iorio, F., Nik-Zainal, S., Bignell, G. R., et al. (2014) · Nature Communications · doi:10.1038/ncomms3997 · Cited by 875 · see citing works
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684 · see citing works
Optimization of DNA polymerase mutation rates during bacterial evolution
Loh, E., Salk, J. J., & Loeb, L. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912451107 · Cited by 81 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 33
- [1]Glenn TC Field guide to next-generation DNA sequencers Mol. Ecol. Resour 2011 11 759 769 21592312
- [2]Loeb LA Springgate CF Battula N Errors in DNA replication as basis of malignant change Cancer Res 1974 34 2311 2321 4136142
- [4]Navin N Tumour evolution inferred by single-cell sequencing Nature 2011 472 90 94 21399628 PMC4504184
- [6]Lawrence MS Mutational heterogeneity in cancer and the for new cancer-associated genes Nature 2013 499 214 218 23770567 PMC3919509
- [7]Kreso A Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer Science 2013 339 543 548 23239622 PMC9747244
- [8]Johnson BE Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma Science 2014 343 189 193 24336570 PMC3998672
- [9]Schmitt MW Prindle MJ Loeb LA Implications of genetic heterogeneity in cancer Ann. NY Acad. Sci 2012 1267 110 116 22954224 PMC3674777
- [10]Liu Z Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans Mol. Biol. Evol 2005 22 659 672 15548752
- [11]Srivatsan A High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies PLoS Genet 2008 4 e1000139 18670626 PMC2474695
- [12]Holt KE High-throughput sequencing provides insights into genome variation and evolution in Salmonella typhi Nat. Genet 2008 40 987 993 18660809 PMC2652037
- [14]Budowle B van Daal A Extracting evidence from forensic DNA analyses: future molecular biology directions Biotechniques 2009 46 339 340 342 350 19480629
- [16]Knapp M Hofreiter M Next-generation sequencing of ancient DNA: requirements, strategies and perspectives Genes 2010 1 227 243 24710043 PMC3954087
- [17]Carlson CA Decoding cell lineage from acquired mutations using arbitrary deep sequencing Nat. Methods 2012 9 78 80 22120468 PMC3248619
- [18]Besaratinia A A high-throughput next-generation sequencing-based method for detecting the mutational fingerprint of carcinogens Nucleic Acids Res 2012 40 e116 22735701 PMC3424585
- [19]Schmitt MW Detection of ultra-rare mutations by next-generation sequencing Proc Natl. Acad. Sci. USA 2012 109 14508 14513 22853953 PMC3437896
- [20]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 9530 9535 21586637 PMC3111315
- [21]Hiatt JB Patwardhan RP Turner EH Lee C Shendure J Parallel, tag-directed assembly of locally derived short sequence reads Nat. Methods 2010 7 119 122 20081835 PMC2848820
- [22]McCloskey ML Stoger R Hansen RS Laird CD Encoding PCR products with batch-stamps and barcodes Biochem. Genet 2007 45 761 767 17955361
- [23]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 22135472 PMC3250168
- [25]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 e81 21490082 PMC3130290
- [26]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 1347 1352 22232676 PMC3268301
- [27]Zong C Lu S Chapman AR Xie XS Genome-wide detection of single-nucleotide and copy-number variations of a single human cell Science 2012 338 1622 1626 23258894 PMC3600412
- [28]Wang J Fan HC Behr B Quake SR Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm Cell 2012 150 402 412 22817899 PMC3525523
- [29]Wang Y Clonal evolution in breast cancer revealed by single-nucleus genome sequencing Nature 2014 512 155 160 25079324 PMC4158312
- [30]Acevedo A Brodsky L Andino R Mutational and fitness landscapes of an RNA virus revealed through population sequencing Nature 2014 505 686 690 24284629 PMC4111796
- [31]Lou DI High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing Proc. Natl. Acad. Sci. USA 2013 110 19872 19877 24243955 PMC3856802
- [32]Diegoli TM Farr M Cromartie C Coble MD Bille TW An optimized protocol for forensic application of the PreCR repair mix to multiplex STR amplification of UV-damaged DNA Forensic Sci. Int. Genet 2012 6 498 503 22001155
- [33]Kennedy SR Salk JJ Schmitt MW Loeb LA Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage PLoS Genet 2013 9 e1003794 24086148 PMC3784509
- [34]Yost SE Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens Nucleic Acids Res 2012 40 e107 22492626 PMC3413110
- [35]Kerick M Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity BMC Med. Genomics 2011 4 68 21958464 PMC3192667
- [36]Spencer DH Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens J. Mol. Diagn 2013 15 623 633 23810758 PMC4912568
- [39]McKenna A The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 2010 20 1297 1303 20644199 PMC2928508
- [40]DePristo MA A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat. Genet 2011 43 491 498 21478889 PMC3083463
Cited by
Sorted by citations
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
“It has been adopted by various sequencing methods such as Duplex-Seq (Kennedy et al., 2014) and iDES (Newman et al., 2016).”
MethodIntegrated digital error suppression for improved detection of circulating tumor DNA
Newman, A. M., Lovejoy, A. F., Klass, D. M., Kurtz, D. M., Chabon, J. J., Scherer, F., Stehr, H., Liu, C. L., Bratman, S. V., Say, C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3520 · Cited by 1,091 · see citing works
“Previous barcoding strategies for double-stranded (i.e., ‘duplex’) error suppression have incorporated randomers (‘N’s) by synthesizing them as single stranded oligonucleotides, and then enzymatically copying them into double-stranded adapters 12,13 .”
InfluentialSensitive tumour detection and classification using plasma cell-free DNA methylomes
Shen, S. Y., Singhania, R., Fehringer, G., Chakravarthy, A., Roehrl, M. H. A., Chadwick, D., Zuzarte, P. C., Borgida, A., Wang, T. T., Li, T., et al. (2018) · Nature · doi:10.1038/s41586-018-0703-0 · Cited by 983 · see citing works
Prediction of acute myeloid leukaemia risk in healthy individuals
Abelson, S., Collord, G., Ng, S. W. K., Weissbrod, O., Mendelson Cohen, N., Niemeyer, E., Barda, N., Zuzarte, P. C., Heisler, L., Sundaravadanam, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0317-6 · Cited by 850 · see citing works
Lung adenocarcinoma promotion by air pollutants
Hill, W., Lim, E. L., Weeden, C. E., Lee, C., Augustine, M., Chen, K., Kuan, F.-C., Marongiu, F., Evans, E. J., Moore, D. A., et al. (2023) · Nature · doi:10.1038/s41586-023-05874-3 · Cited by 808 · see citing works
Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults
Young, A. L., Challen, G. A., Birmann, B. M., & Druley, T. E. (2016) · Nature Communications · doi:10.1038/ncomms12484 · Cited by 692 · see citing works
“Recently, the development of error-corrected sequencing (ECS) using single molecule tagging with unique molecular identifiers has permitted the detection of rare variants below the error rate of NGS 13–18 .”
Fragment Length of Circulating Tumor DNA
Underhill, H. R., Kitzman, J. O., Hellwig, S., Welker, N. C., Daza, R. M., Baker, D. N., Gligorich, K. M., Rostomily, R., Bronner, M. P., & Shendure, J. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006162 · Cited by 675 · see citing works
“Libraries for Illumina high throughput sequencing were prepared using the KAPA biosystems Hyper Prep Kit with 10 ng input cell-free DNA according to the manufacturer’s instructions using truncated duplex molecular barcode adapters [37].”
MethodThe emerging clinical relevance of genomics in cancer medicine
Berger, M. F., & Mardis, E. R. (2018) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-018-0002-6 · Cited by 627 · see citing works
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
Salk, J. J., Schmitt, M. W., & Loeb, L. A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.117 · Cited by 536 · see citing works
“Together, these pieces allow a separate consensus sequence to be produced for each strand for comparison to that of its mate 78 .”
BackgroundSelf-citationSomatic mutation landscapes at single-molecule resolution
Abascal, F., Harvey, L. M. R., Mitchell, E., Lawson, A. R. J., Lensing, S. V., Ellis, P., Russell, A. J. C., Alcantara, R. E., Baez‐Ortega, A., Wang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03477-4 · Cited by 508 · see citing works
Adaptive mutability of colorectal cancers in response to targeted therapies
Russo, M., Crisafulli, G., Sogari, A., Reilly, N. M., Arena, S., Lamba, S., Bartolini, A., Amodio, V., Magrì, A., Novara, L., et al. (2019) · Science · doi:10.1126/science.aav4474 · Cited by 433 · see citing works
Zill, O. A., Banks, K. C., Fairclough, S. R., Mortimer, S. A., Vowles, J. V., Mokhtari, R., Gandara, D. R., Mack, P. C., Odegaard, J. I., Nagy, R. J., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-3837 · Cited by 391 · see citing works
“This process reduces the variant-detection error rate by several orders of magnitude (16, 17, 13).”
BackgroundThe mutational landscape of human somatic and germline cells
Moore, L., Cagan, A., Coorens, T. H. H., Neville, M. D. C., Sanghvi, R., Sanders, M. A., Oliver, T. R. W., Leongamornlert, D., Ellis, P., Noorani, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03822-7 · Cited by 379 · see citing works
Odegaard, J. I., Vincent, J. J., Mortimer, S., Vowles, J. V., Ulrich, B. C., Banks, K. C., Fairclough, S. R., Zill, O. A., Sikora, M., Mokhtari, R. B., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-3831 · Cited by 437 · see citing works
Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring
Zviran, A., Schulman, R. C., Shah, M., Hill, S. T., Deochand, S., Khamnei, C., Maloney, D., Patel, K., Liao, W., Widman, A. J., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0915-3 · Cited by 375 · see citing works
Techniques of using circulating tumor DNA as a liquid biopsy component in cancer management
Elazezy, M., & Joosse, S. A. (2018) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2018.10.002 · Cited by 372 · see citing works
“These extreme low concentrations make the detection challenging, particularly at the early stages of tumor development [27,73,74].”
BackgroundPentsova, E. I., Shah, R. H., Tang, J., Boire, A. A., You, D., Briggs, S. R., Omuro, A. M. P., Lin, X., Fleisher, M., Grommes, C., et al. (2016) · Journal of Clinical Oncology · doi:10.1200/jco.2016.66.6487 · Cited by 415 · see citing works
Kurtz, D. M., Soo, J., Keh, L. C. T., Alig, S., Chabon, J. J., Sworder, B. J., Schultz, A., Jin, M. C., Scherer, F., Garofalo, A., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00981-w · Cited by 383 · see citing works
Pickrell, A. M., Huang, C.-H., Kennedy, S. R., Ordureau, A., Sideris, D. P., Hoekstra, J. G., Harper, J. W., & Youle, R. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.06.034 · Cited by 327 · see citing works
“After ligation, bead cleaning and PCR amplification were performed as previously described (Kennedy et al., 2014), and the mtDNA was isolated using the Agilent SureSelectXT Target Enrichment System (Agilent) with probes specific for the mouse mitochondrial genome following the manufacturer’s…”
InfluentialSelf-citationMitochondrial DNA variation and cancer
Kopinski, P. K., Singh, L. N., Zhang, S., Lott, M. T., & Wallace, D. C. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00358-w · Cited by 301 · see citing works
Bianchi, A. S., Pietrantonio, F., Lonardi, S., Mussolin, B., Rua, F., Crisafulli, G., Bartolini, A., Fenocchio, E., Amatu, A., Manca, P., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01886-0 · Cited by 282 · see citing works
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Xu, C. (2018) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2018.01.003 · Cited by 242 · see citing works
“In addition, duplex sequencing that tags double-strand DNA and allows the reads from the two strands to be matched has been implemented to further reduce error rates [64,77].”
MethodHoang, M. L., Kinde, I., Tomasetti, C., McMahon, K. W., Rosenquist, T. A., Grollman, A. P., Kinzler, K. W., Vogelstein, B., & Papadopoulos, N. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1607794113 · Cited by 224 · see citing works
“The only other method that approaches this sensitivity and specificity has been described by Loeb and coworkers (12, 31), but their method is applicable only to predefined regions of the genome.”
MethodGenomic Instability in Cancer: Teetering on the Limit of Tolerance
Andor, N., Maley, C. C., & Ji, H. P. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-1553 · Cited by 235 · see citing works
Aging and the rise of somatic cancer-associated mutations in normal tissues
Risques, R. A., & Kennedy, S. R. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007108 · Cited by 212 · see citing works
Self-citationCirculating tumor DNA: current challenges for clinical utility
Dang, D. K., & Park, B. H. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154941 · Cited by 230 · see citing works
Current and Emerging Applications of Droplet Digital PCR in Oncology
Olmedillas-López, S., García-Arranz, M., & García-Olmo, D. (2017) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-017-0278-8 · Cited by 176 · see citing works
Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA
Shen, S. Y., Burgener, J., Bratman, S., & Carvalho, D. D. D. (2019) · Nature Protocols · doi:10.1038/s41596-019-0202-2 · Cited by 172 · see citing works
Krimmel‐Morrison, J. D., Schmitt, M. W., Harrell, M. I., Agnew, K. J., Kennedy, S. R., Emond, M. J., Loeb, L. A., Swisher, E. M., & Risques, R. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601311113 · Cited by 155 · see citing works
“Data processing was performed as previously described (38).”
MethodSelf-citationSequencing small genomic targets with high efficiency and extreme accuracy
Schmitt, M. W., Fox, E. J., Prindle, M. J., Reid-Bayliss, K. S., True, L. D., Radich, J. P., & Loeb, L. A. (2015) · Nature Methods · doi:10.1038/nmeth.3351 · Cited by 160 · see citing works
Self-citationAccessing Genetic Information with Liquid Biopsies
Cai, X., Jankú, F., Zhan, Q., & Fan, J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.06.001 · Cited by 155 · see citing works
Deciphering cell states and genealogies of human haematopoiesis
Weng, C., Yu, F., Yang, D., Poeschla, M., Liggett, L. A., Jones, M. G., Qiu, X., Wahlster, L., Caulier, A., Hussmann, J. A., et al. (2024) · Nature · doi:10.1038/s41586-024-07066-z · Cited by 150 · see citing works
Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates
Kis, O., Kaedbey, R., Chow, S., Danesh, A., Dowar, M., Li, T., Li, Z., Liu, J., Mansour, M., Masih‐Khan, E., et al. (2017) · Nature Communications · doi:10.1038/ncomms15086 · Cited by 137 · see citing works
Phase 2 study of panobinostat with or without rituximab in relapsed diffuse large B-cell lymphoma.
Assouline, S., Nielsen, T. H., Yu, S. L., Alcaide, M., Chong, L., Macdonald, D., Tosikyan, A., Kukreti, V., Kezouh, A., Petrogiannis-Haliotis, T., et al. (2016) · Blood · doi:10.1182/blood-2016-02-699520 · Cited by 134 · see citing works
“Our strategy includes a consensus approach that assigns reads to their parental DNA molecules to enable error correction and single-molecule counting.(25) The ctDNA level is represented as the fraction of DNA molecules bearing tumor-specific somatic mutations in the plasma-derived DNA (variant allele fraction [VAF]).”
MethodTissue-specific 5-hydroxymethylcytosine landscape of the human genome
He, B., Zhang, C., Zhang, X., Fan, Y., Zeng, H., Liu, J., Meng, H., Bai, D., Peng, J., Zhang, Q., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24425-w · Cited by 134 · see citing works
Ståhlberg, A., Krzyzanowski, P. M., Egyud, M., Filges, S., Stein, L. D., & Godfrey, T. E. (2017) · Nature Protocols · doi:10.1038/nprot.2017.006 · Cited by 132 · see citing works
Ellis, P., Moore, L., Sanders, M., Butler, T., Brunner, S. F., Lee-Six, H., Osborne, R. J., Farr, B., Coorens, T., Lawson, A., et al. (2020) · Nature Protocols · doi:10.1038/s41596-020-00437-6 · Cited by 127 · see citing works
Chawanthayatham, S., Valentine, C., Fedeles, B., Fox, E., Loeb, L., Levine, S., Slocum, S. L., Wogan, G., Croy, R. G., & Essigmann, J. (2017) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1700759114 · Cited by 122
“Sequencing adapters (Table S1) weremade bymodification of amethod described previously (24, 46).”
MethodSelf-citationImpact of risk factors on early cancer evolution
Weeden, C. E., Hill, W., Lim, E. L., Gronroos, E. C., & Swanton, C. (2023) · Cell · doi:10.1016/j.cell.2023.03.013 · Cited by 143 · see citing works
Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia
Tzoneva, G., Dieck, C. L., Oshima, K., Ambesi‐Impiombato, A., Sánchez-Martín, M., Madubata, C. J., Khiabanian, H., Yu, J., Waanders, E., Iacobucci, I., et al. (2018) · Nature · doi:10.1038/nature25186 · Cited by 117 · see citing works
“Duplex Sequencing was carried out by TwinStrand Biosciences (Seattle, WA) under fully blinded conditions using methods previously described 34,35 .”
Rolfo, C. D., Cardona, A. F., Cristofanilli, M., Paz-Ares, L. G., Díaz‐Mochon, J. J., Durán, I., Raez, L. E., Russo, A., Lorente, J. A., Malapelle, U., et al. (2020) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2020.102978 · Cited by 139 · see citing works
Liquid biopsy for therapy monitoring in early-stage non-small cell lung cancer
Nagasaka, M., Uddin, M. H., Hallak, M. N. A., Rahman, S. B., Balasubramanian, S. K., Sukari, A. W., & Azmi, A. S. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01371-1 · Cited by 114 · see citing works
Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing
Valentine, C. C., Young, R. R., Fielden, M. R., Kulkarni, R. M., Williams, L. N., Li, T., Minocherhomji, S., & Salk, J. J. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013724117 · Cited by 113 · see citing works
“DNA was end-polished, A-tailed, and ligated to DS adapters containing semidegenerate unique molecular identifies (TwinStrand Biosciences) via the general method described previously (10, 16).”
Self-citationWu, Z.-Q., Waneka, G., Broz, A. K., King, C. R., & Sloan, D. B. (2020) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1101/2020.02.13.947598 · Cited by 103
Hoekstra, J. G., Hipp, M. J., Montine, T. J., & Kennedy, S. R. (2016) · Annals of Neurology · doi:10.1002/ana.24709 · Cited by 105 · see citing works
“mtDNA Duplex Sequencing and Data Analysis Duplex tag-labeled adapter synthesis and DNA shearing were performed as previously described.(7,10) Briefly, adapters (see Fig”
MethodSelf-citationAristolochic acid-associated cancers: a public health risk in need of global action
Das, S., Thakur, S., Korenjak, M., Sidorenko, V. S., Chung, F. F., & Zavadil, J. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00494-x · Cited by 119 · see citing works
Xu, C., Ranjbar, M. R. N., Wu, Z., Dicarlo, J., & Wang, Y. (2017) · BMC Genomics · doi:10.1186/s12864-016-3425-4 · Cited by 100 · see citing works
“Molecular barcoding has recently been implemented in several NGS target enrichment protocols and researchers have demonstrated its utility in somatic variant detection and RNA quantification [8, 11].”
Xu, C., Gu, X., Padmanabhan, R., Wu, Z., Peng, Q., Dicarlo, J., & Wang, Y. (2018) · bioRxiv · doi:10.1093/bioinformatics/bty790 · Cited by 99 · see citing works
Salk, J. J., Loubet-Senear, K. J., Maritschnegg, E., Valentine, C. C., Williams, L. N., Higgins, J. E., Horvat, R., Vanderstichele, A., Nachmanson, D., Baker, K. T., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.05.109 · Cited by 98 · see citing works
“, 2018), which uses double-stranded molecular barcodes for error correction and decreases the error rate of sequencing from 10 3 to <10 7 (Kennedy et al., 2014; Schmitt et al., 2012).”
BackgroundSelf-citationSelfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes
Maher, G. J., Ralph, H. K., Ding, Z., Koelling, N., Mlcochova, H., Giannoulatou, E., Dhami, P., Paul, D. S., Stricker, S. H., Beck, S., et al. (2018) · Genome Research · doi:10.1101/gr.239186.118 · Cited by 85 · see citing works
“Broad-scale approaches that target both DNA strands and use unique molecular indexes such as Duplex sequencing (Kennedy et al. 2014) or smMIPs (Hiatt et al. 2013) (used here to validate a subset of variants) represent valuable alternatives to direct PCR amplification in future studies to reduce…”
MethodAge-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues
Arbeithuber, B., Hester, J., Cremona, M., Stoler, N., Zaidi, A. A., Higgins, B., Anthony, K., Chiaromonte, F., Diaz, F., & Makova, K. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000745 · Cited by 89 · see citing works
“The amount of mtDNA in a single oocyte (<5 pg) is several orders of magnitude lower than the minimal amount of DNA required for library preparation in a published duplex sequencing protocol (approximately 100 ng) [48].”
BackgroundMethodInfluentialMapping the Evolutionary Potential of RNA Viruses
Dolan, P., Whitfield, Z. J., & Andino, R. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.03.012 · Cited by 91 · see citing works
“…of sitespecific negative selection through the observation of dynamics of low frequency alleles in naturally evolving populations (Acevedo et al., 2014; Jabara et al., 2011; Kennedy et al., 2014; Kosik et al., 2018) and the high-resolution screening of mutant libraries before and after selection.”
BackgroundCost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer
Stackpole, M. L., Zeng, W., Li, S., Liu, C.-C., Zhou, Y., He, S., Yeh, A., Wang, Z., Sun, F., Li, Q., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32995-6 · Cited by 108 · see citing works
“…HC T4 DNA ligase (30 Weiss Unit/ µ l), 5 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al 25 PCR ampli fi cation was done using the NEBNext Multiplex Oligos for Illumina (2.5 µ l of universal and index primer each) and 25 µ l KAPA HiFi…”
MethodInfluentialA critical spotlight on the paradigms of FFPE-DNA sequencing
Steiert, T., Parra, G., Gut, M., Arnold, N., Trotta, J., Tonda, R., Moussy, A., Gerber, Z., Abuja, P., Zatloukal, K., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad519 · Cited by 87 · see citing works
Anderson, K., Auclair, D., Kelloff, G., Sigman, C., Avet-Loiseau, H., Farrell, A., Gormley, N., Kumar, S. K., Landgren, O., Munshi, N., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-2895 · Cited by 86 · see citing works
“To detect MRD will require integration of molecular barcoding techniques to enable error suppression at levels <10 (49, 50) as well as expansion of the targeted genomic regions”
BackgroundLauer, E. M., Mutter, J., & Scherer, F. (2022) · Leukemia · doi:10.1038/s41375-022-01618-w · Cited by 91 · see citing works
Salk, J. J., & Kennedy, S. R. (2019) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22342 · Cited by 89 · see citing works
“Duplex Sequencing was the first method to use double-stranded consensuses to remove both sequencer and early PCR derived errors (Schmitt et al. 2012; Kennedy et al. 2014; Fig.”
MethodSelf-citationCirculating-tumor DNA as an early detection and diagnostic tool
Butler, T. M., Spellman, P. T., & Gray, J. W. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.12.003 · Cited by 88 · see citing works
The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors.
Mattox, A., Yan, H., & Bettegowda, C. (2019) · Neuro-Oncology · doi:10.1093/neuonc/noz156 · Cited by 79 · see citing works
When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review
Rodríguez, J. K., Ávila, J., Rolfo, C. D., Ruíz-Patiño, A., Russo, A., Ricaurte, L., Ordóñez‐Reyes, C., Arrieta, O. G., Zatarain-Barrón, Z. L., Recondo, G., et al. (2021) · Oncology and Therapy · doi:10.1007/s40487-021-00144-6 · Cited by 89 · see citing works
Wright, C. F., Prigmore, E., Rajan, D., Handsaker, J., McRae, J. F., Kaplanis, J., Fitzgerald, T. W., FitzPatrick, D. R., Firth, H. V., & Hurles, M. E. (2019) · Nature Communications · doi:10.1038/s41467-019-11059-2 · Cited by 86 · see citing works
High-throughput sequencing for noninvasive disease detection in hematologic malignancies
Scherer, F., Kurtz, D. M., Diehn, M., & Alizadeh, A. A. (2017) · Blood · doi:10.1182/blood-2017-03-735639 · Cited by 80 · see citing works
“0001% (Figure 2).(16,19,20) Furthermore, HTS-based assays facilitate assessmentof intra- and intertumorheterogeneity, allowing individualized detection of clonal evolution.”
BackgroundPécuchet, N., Rozenholc, Y., Zonta, E., Pietrasz, D., Didelot, A., Combe, P., Gibault, L., Bachet, J., Taly, V., Fabre, E., et al. (2016) · Clinical Chemistry · doi:10.1373/clinchem.2016.258236 · Cited by 87 · see citing works
Patel, M. R., Miriyala, G., Littleton, A. J., Yang, H.-K., Trịnh, K., Young, J. M., Kennedy, S. R., Yamashita, Y. M., Pallanck, L., & Malik, H. S. (2016) · eLife · doi:10.7554/elife.16923 · Cited by 75 · see citing works
Self-citationDetection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands
Cohen, J., Douville, C., Dudley, J., Mog, B., Popoli, M., Ptak, J., Dobbyn, L., Silliman, N., Schaefer, J., Tie, J., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00900-z · Cited by 74 · see citing works
Sanchez-Contreras, M., Sweetwyne, M. T., Tsantilas, K. A., Whitson, J. A., Campbell, M. D., Kohrn, B. F., Kim, H. J., Hipp, M. J., Fredrickson, J., Nguyen, M. M., et al. (2023) · eLife · doi:10.7554/elife.83395 · Cited by 71 · see citing works
Self-citationNoyes, N. R., Weinroth, M. D., Parker, J. K., Dean, C. J., Lakin, S. M., Raymond, R., Rovira, P., Doster, E., Abdo, Z., Martin, J. N., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0361-8 · Cited by 97 · see citing works
“The ResistomeUMI and Metagenome-UMI libraries were created using a protocol that incorporated dual-indexed UMI adapters (see Additional file 13) into sequence libraries [23], with modifications to allow for integration with Agilent SureSelect protocols (see Additional file 1: Supplementary Methods for details).”
Chen, S.-F., Zhou, Y., Chen, Y., Huang, T., Liao, W., Xu, Y., Li, Z., & Gu, J. (2018) · BMC Bioinformatics · doi:10.1186/s12859-019-3280-9 · Cited by 69
Wang, P., Song, Q., Ren, J., Zhang, W., Wang, Y., Zhou, L., Wang, D., Chen, K., Jiang, L., Zhang, B., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abp8704 · Cited by 79 · see citing works
Somatic mutation and selection at population scale
Lawson, A. R. J., Abascal, F., Nicola, P. A., Lensing, S. V., Roberts, A. L., Kalantzis, G., Baez‐Ortega, A., Brzozowska, N., Moustafa, J. S. E.-S., Vaitkute, D., et al. (2025) · Nature · doi:10.1038/s41586-025-09584-w · Cited by 72 · see citing works
cfDNA Sequencing: Technological Approaches and Bioinformatic Issues
Bohers, E., Viailly, P., & Jardin, F. (2021) · Pharmaceuticals · doi:10.3390/ph14060596 · Cited by 67 · see citing works
“Duplex sequencing is an improvement of the Safe-SeqS technique [77,78].”
BackgroundMethodThe present and future of measurable residual disease testing in acute myeloid leukemia
Blachly, J., Walter, R., & Hourigan, C. (2022) · Haematologica · doi:10.3324/haematol.2022.282034 · Cited by 66 · see citing works
Liquid biopsy in pancreatic cancer: the beginning of a new era
Yadav, D. K., Bai, X., Yadav, R. K., Singh, A., Li, G., Ma, T., Chen, W., & Liang, T. (2018) · Oncotarget · doi:10.18632/oncotarget.24809 · Cited by 60 · see citing works
“com PCR (dPCR) [289], droplet digital PCR (ddPCR) [290], BEAMing [291, 292], cancer personalized profiling by deep sequencing (CAPP-Seq) [293], tagged amplicon deep sequencing (TAM-Seq) [276], safe-sequencing (SafeSeq) [294], duplex sequencing [295], integrated digital error suppression (iDES)-enhanced CAPP-Seq [296],…”
MethodDetecting rare mutations and DNA damage with sequencing-based methods
Sloan, D. B., Broz, A. K., Sharbrough, J., & Wu, Z.-Q. (2018) · Trends in Biotechnology · doi:10.1016/j.tibtech.2018.02.009 · Cited by 63 · see citing works
Reinert, T., Petersen, L. M. S., Henriksen, T. V., Larsen, M. Ø., Rasmussen, M. H., Johansen, A. F. B., Øgaard, N., Knudsen, M., Nordentoft, I., Vang, S., et al. (2022) · International Journal of Cancer · doi:10.1002/ijc.33924 · Cited by 62 · see citing works
“some minor adjustments.(23) In brief, libraries were generated using KAPA Hyper Library Preparation Kit (KAPA Biosystems).”
MethodSobesky, S., Mammadova, L., Cirillo, M., Drees, E. E. E., Mattlener, J., Dörr, H., Altmüller, J., Shi, Z., Bröckelmann, P. J., Weiss, J. M., et al. (2021) · Med · doi:10.1016/j.medj.2021.09.002 · Cited by 78 · see citing works
Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer
Huang, C., Du, M., & Wang, L. (2019) · Cancers · doi:10.3390/cancers11060805 · Cited by 64 · see citing works
Arbeithuber, B., Makova, K. D., & Tiemann‐Boege, I. (2016) · DNA Research · doi:10.1093/dnares/dsw038 · Cited by 55 · see citing works
“One attomole of adapter-ligated DNA was used for the generation of amplified tag families, and the optimal cycle number for amplification was evaluated by real-time PCR, as suggested by Kennedy et al.45 Purifications of DNA between the different steps of library preparation were performed with Agencourt AMPure XP bead…”
MethodInfluentialHigh efficiency error suppression for accurate detection of low-frequency variants
Wang, T.-T., Abelson, S., Zou, J., Li, T.-T., Zhao, Z., Dick, J., Shlush, L., Pugh, T. J., & Bratman, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz474 · Cited by 61 · see citing works
“7––based on previous literature (9)), otherwise an N was assigned.”
BackgroundMethodBronkhorst, A. J., & Holdenrieder, S. (2023) · Medizinische Genetik · doi:10.1515/medgen-2023-2065 · Cited by 47 · see citing works
“It reportedly outperforms existing duplex sequencing methods [126,133,134,139,141–143] with significant input recovery improvements (5-to 75-fold) and achieves over a 100-fold enhancement in error correction compared to standard PCR and ligation-based approaches using strand-agnostic molecular…”
BackgroundMethodWaters, M., Warren, S., Hughes, C., Lewis, P., & Zhang, F.-Y. (2021) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22471 · Cited by 59 · see citing works
“(Kennedy et al., 2014; Valentine et al., 2020).”
Polymerase specific error rates and profiles identified by single molecule sequencing
Hestand, M. S., Houdt, J. V., Cristofoli, F., & Vermeesch, J. R. (2016) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2016.01.003 · Cited by 58 · see citing works
Hellwig, S., Nix, D. A., Gligorich, K. M., O'Shea, J. M., Thomas, A., Fuertes, C. L., Bhetariya, P., Marth, G., Bronner, M., & Underhill, H. (2018) · PLoS ONE · doi:10.1371/journal.pone.0197333 · Cited by 57 · see citing works
“Although duplex molecular barcoding, the assignment of unique molecular identifiers to both strands of DNA, has the greatest theoretical potential to reduce sequencing and PCR errors [25], the associated low ligation efficiency (10±20%) has limited applications seeking to detect very low frequency ctDNA variants due t…”
BackgroundHighly heterogeneous mutation rates in the hepatitis C virus genome
Geller, R., Estada, Ú., Peris, J. B., Andreu, I., Bou, J.-V., Garijo, R., Cuevas, J., Sabariegos, R., Mas, A., & Sanjuán, R. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.45 · Cited by 57
Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients
Christensen, E., Nordentoft, I., Vang, S., Birkenkamp-Demtröder, K., Jensen, J. B., Agerbæk, M., Pedersen, J. S., & Dyrskjøt, L. (2018) · Scientific Reports · doi:10.1038/s41598-018-20282-8 · Cited by 56 · see citing works
Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort
Yang, X., Liu, A., Xu, X., Yang, X., Zeng, Q., Ye, A. Y., Yu, Z., Wang, S., Huang, A. Y., Wu, X., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-15814-7 · Cited by 57 · see citing works
Ng, S. B. H., Chua, C., Ng, M., Gan, A., Poon, P., Teo, M., Fu, C., Leow, W., Lim, K., Chung, A., et al. (2017) · Scientific Reports · doi:10.1038/srep40737 · Cited by 55 · see citing works
Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency
Reid-Bayliss, K. S., Arron, S. T., Loeb, L. A., Bezrookove, V., & Cleaver, J. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1610020113 · Cited by 55 · see citing works
“Therefore, to determine definitively whether CS cells show an elevated frequency of UV-induced mutations, we used duplex sequencing, a highly accurate next-generation sequencing methodology that enables the detection of rare mutagenic effects (18), to study UV-induced mutagenesis in primary cells derived from normal p…”
BackgroundMethodInfluentialSelf-citationClonal selection of hematopoietic stem cells after gene therapy for sickle cell disease
Chapman, M. S., Cull, A. H., Ciuculescu, M. F., Esrick, E. B., Mitchell, E., Jung, H., O’Neill, L., Roberts, K., Fabre, M. A., Williams, N., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02636-6 · Cited by 65 · see citing works
“To examine the acquisition of additional driver mutations in more detail, we performed targeted high-depth duplex sequencing 38,39 on pre-GT and at least two post-GT bulk myeloid cell samples from each patient.”
Comprehensive identification of somatic nucleotide variants in human brain tissue
Brain Somatic Mosaicism Network, Wang, Y., Bae, T., Thorpe, J., Sherman, M. A., Jones, A., Cho, S., Daily, K., Dou, Y., Ganz, J., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02285-3 · Cited by 49 · see citing works
Nachmanson, D., Lian, S.-Y., Schmidt, E. K., Hipp, M. J., Baker, K. T., Zhang, Y.-Z., Tretiakova, M., Loubet-Senear, K. J., Kohrn, B. F., Salk, J., et al. (2018) · Genome Research · doi:10.1101/gr.235291.118 · Cited by 54 · see citing works
“1C; Kennedy et al. 2014).”
InfluentialSelf-citationMansukhani, S., Barber, L. J., Kleftogiannis, D., Moorcraft, S. Y., Davidson, M., Woolston, A., Proszek, P., Griffiths, B. L., Fenwick, K., Herman, B., et al. (2018) · Clinical Chemistry · doi:10.1373/clinchem.2018.289629 · Cited by 55 · see citing works
“Consensus families 193 contained a median of 8 to 15 supporting reads in samples sequenced with the 194 optimized protocol (online Supplemental Figure 4), which was within the optimal 195 range for barcode error correction [21].”
MethodLeBlanc, D., Meier, M., Lo, F. Y., Schmidt, E. K., Valentine, C., Williams, A., Salk, J., Yauk, C., & Marchetti, F. (2022) · BMC Genomics · doi:10.1186/s12864-022-08752-w · Cited by 53 · see citing works
“Duplex Sequencing (DS) is one such error-corrected NGS (ecNGS) method that is able to resolve spontaneous and chemically-induced mutations at ultra-low frequencies directly from extracted DNA [17, 19].”
BackgroundSelf-citationExtensive subclonal mutational diversity in human colorectal cancer and its significance
Loeb, L. A., Kohrn, B. F., Loubet-Senear, K. J., Dunn, Y. J., Ahn, E. H., O'Sullivan, J. N., Salk, J. J., Bronner, M. P., & Beckman, R. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1910301116 · Cited by 66 · see citing works
“Sequencing library preparation was carried out as previously described with minor modifications (6, 46, 47).”
Self-citationCirculating tumour cells and DNA as liquid biopsies in gastrointestinal cancer
Nordgård, O., Tjensvoll, K., Gilje, B., & Søreide, K. (2018) · British journal of surgery · doi:10.1002/bjs.10782 · Cited by 55 · see citing works
Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies
Lu, I., Muller, C. P., & HeFeng, F. Q. (2020) · Virus Research · doi:10.1016/j.virusres.2020.197963 · Cited by 56 · see citing works
“Characterization of variants of double-strand RNA viruses that only account for a small fraction of pathological viruses could benefit from particular approaches, such as DupSeq, which has been reported to detect ultralow-frequency variants from double-strand DNA samples (Kennedy et al., 2014; Schmitt et al., 2012).”
Filges, S., Yamada, E., Ståhlberg, A., & Godfrey, T. (2019) · Scientific Reports · doi:10.1038/s41598-019-39762-6 · Cited by 51 · see citing works
Sánchez, R., Ayala, R., & Martínez-López, J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20112832 · Cited by 50
“Thol et al. also reported the use of UMI sequences during library preparation and duplex sequencing data analysis for ECS [77].”
MethodPatient monitoring through liquid biopsies using circulating tumor DNA
Ulz, P., Heitzer, E., Geigl, J., & Speicher, M. (2017) · International Journal of Cancer · doi:10.1002/ijc.30759 · Cited by 49 · see citing works
“In addition PCR efficiency is relatively inefficient when limited amounts of input DNA are used—as it is most likely the case for cfDNA—resulting in primer/adapter dimers.(73) To sum up, in order to correctly identify MAF for specific mutations, tremendous technological efforts, for example, digital PCR systems employ…”
BackgroundNext-generation sequencing methodologies to detect low-frequency mutations: “Catch me if you can”
Menon, V., & Brash, D. E. (2023) · Mutation Research - Reviews in Mutation Research · doi:10.1016/j.mrrev.2023.108471 · Cited by 48 · see citing works
- Authors
- 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.
- Affiliations
- University of Washington (US)
- Portland State University (US)
- Corresponding author
- Loeb, Lawrence A
- Venue
- Nature Protocols
- Published
- 2014-10-09
- Volume
- 9
- Issue
- 11
- Pages
- 2586-2606
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC4271547
- OpenAlex
- W2011645981
- Cited by
- 503
- References
- 40
- Citations by year
- 2026: 43 · 2025: 62 · 2024: 60 · 2023: 36 · 2022: 52 · 2021: 48 · 2020: 34 · 2019: 43 · 2018: 46 · 2017: 40 · 2016: 29 · 2015: 8 · 2014: 2
- FWCI
- 10.80
- Type
- journal article
- Language
- en
- Update notices
- erratum (2014-11-20)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute on Aging (T32AG000057, P01AG001751)
- National Cancer Institute (R01CA160674, R01CA102029, P01 CA77852, R33CA181771, P01CA077852)
- National Institute of General Medical Sciences (T32GM007266)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- duplex sequencing, single nucleotide variant detection, sequencing error rate, adapter ligation, library preparation, target enrichment, data analysis pipeline
- MeSH terms
- DNA Mutational Analysis, DNA, Mitochondrial, Humans, Gene Library, Polymerase Chain Reaction, Workflow, High-Throughput Nucleotide Sequencing, Mutation Rate
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
