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Items: 1 to 20 of 81

1.

Detection of ultra-rare mutations by next-generation sequencing.

Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14508-13. doi: 10.1073/pnas.1208715109. Epub 2012 Aug 1.

2.

Sequence error storms and the landscape of mutations in cancer.

Kirsch S, Klein CA.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14289-90. doi: 10.1073/pnas.1212246109. Epub 2012 Aug 21. No abstract available.

3.

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations.

Zhou S, Jones C, Mieczkowski P, Swanstrom R.

J Virol. 2015 Aug;89(16):8540-55. doi: 10.1128/JVI.00522-15. Epub 2015 Jun 3.

4.

Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.

Arbeithuber B, Makova KD, Tiemann-Boege I.

DNA Res. 2016 Dec;23(6):547-559. Epub 2016 Jul 31.

5.

Targeted sequencing of both DNA strands barcoded and captured individually by RNA probes to identify genome-wide ultra-rare mutations.

Wang Q, Wang X, Tang PS, O'leary GM, Zhang M.

Sci Rep. 2017 Jun 13;7(1):3356. doi: 10.1038/s41598-017-03448-8.

6.

Detecting ultralow-frequency mutations by Duplex Sequencing.

Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, Prindle MJ, Kuong KJ, Shen JC, Risques RA, Loeb LA.

Nat Protoc. 2014 Nov;9(11):2586-606. doi: 10.1038/nprot.2014.170. Epub 2014 Oct 9. Erratum in: Nat Protoc. 2014 Dec;9(12):2903.

7.

Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing.

Ahn EH, Hirohata K, Kohrn BF, Fox EJ, Chang CC, Loeb LA.

PLoS One. 2015 Aug 25;10(8):e0136216. doi: 10.1371/journal.pone.0136216. eCollection 2015.

8.

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data.

Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT.

BMC Genomics. 2015 Mar 24;16:229. doi: 10.1186/s12864-015-1456-x.

9.

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.

Lou DI, Hussmann JA, McBee RM, Acevedo A, Andino R, Press WH, Sawyer SL.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19872-7. doi: 10.1073/pnas.1319590110. Epub 2013 Nov 15.

10.

Targeted single molecule mutation detection with massively parallel sequencing.

Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH.

Nucleic Acids Res. 2016 Feb 18;44(3):e22. doi: 10.1093/nar/gkv915. Epub 2015 Sep 17.

11.

Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations.

Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, Zhang S, Li S.

PLoS One. 2016 Jan 11;11(1):e0146638. doi: 10.1371/journal.pone.0146638. eCollection 2016.

12.

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.

13.

[Role of high-throughput sequencing in oncology].

Rodrigues MJ, Gomez-Roca C.

Bull Cancer. 2013 Mar;100(3):295-301. doi: 10.1684/bdc.2013.1717. Review. French.

PMID:
23501647
14.

ADEPT, a dynamic next generation sequencing data error-detection program with trimming.

Feng S, Lo CC, Li PE, Chain PS.

BMC Bioinformatics. 2016 Feb 29;17:109. doi: 10.1186/s12859-016-0967-z.

15.

Accuracy of Next Generation Sequencing Platforms.

Fox EJ, Reid-Bayliss KS, Emond MJ, Loeb LA.

Next Gener Seq Appl. 2014;1. pii: 1000106.

16.

Studying cancer genomics through next-generation DNA sequencing and bioinformatics.

Doyle MA, Li J, Doig K, Fellowes A, Wong SQ.

Methods Mol Biol. 2014;1168:83-98. doi: 10.1007/978-1-4939-0847-9_6. Review.

PMID:
24870132
17.

The role of replicates for error mitigation in next-generation sequencing.

Robasky K, Lewis NE, Church GM.

Nat Rev Genet. 2014 Jan;15(1):56-62. doi: 10.1038/nrg3655. Epub 2013 Dec 10. Review.

18.

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.

Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, Fostel JL, Friedrich DC, Perrin D, Dionne D, Kim S, Gabriel SB, Lander ES, Fisher S, Getz G.

Nucleic Acids Res. 2013 Apr 1;41(6):e67. doi: 10.1093/nar/gks1443. Epub 2013 Jan 8.

19.

Sequencing error correction without a reference genome.

Sleep JA, Schreiber AW, Baumann U.

BMC Bioinformatics. 2013 Dec 18;14:367. doi: 10.1186/1471-2105-14-367.

20.

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

Moens LN, Falk-Sörqvist E, Ljungström V, Mattsson J, Sundström M, La Fleur L, Mathot L, Micke P, Nilsson M, Botling J.

J Mol Diagn. 2015 Nov;17(6):729-39. doi: 10.1016/j.jmoldx.2015.06.009. Epub 2015 Sep 3.

PMID:
26354930

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