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Ultra-Sensitive TP53 Sequencing for Cancer Detection Reveals Progressive Clonal Selection in Normal Tissue over a Century of Human Lifespan.

Salk JJ, Loubet-Senear K, Maritschnegg E, Valentine CC, Williams LN, Higgins JE, Horvat R, Vanderstichele A, Nachmanson D, Baker KT, Emond MJ, Loter E, Tretiakova M, Soussi T, Loeb LA, Zeillinger R, Speiser P, Risques RA.

Cell Rep. 2019 Jul 2;28(1):132-144.e3. doi: 10.1016/j.celrep.2019.05.109.


Single-Molecule Sequencing Reveals Patterns of Preexisting Drug Resistance That Suggest Treatment Strategies in Philadelphia-Positive Leukemias.

Schmitt MW, Pritchard JR, Leighow SM, Aminov BI, Beppu L, Kim DS, Hodgson JG, Rivera VM, Loeb LA, Radich JP.

Clin Cancer Res. 2018 Nov 1;24(21):5321-5334. doi: 10.1158/1078-0432.CCR-18-0167. Epub 2018 Jul 24.


Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.

Salk JJ, Schmitt MW, Loeb LA.

Nat Rev Genet. 2018 May;19(5):269-285. doi: 10.1038/nrg.2017.117. Epub 2018 Mar 26. Review.


Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

Reid-Bayliss KS, Loeb LA.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9415-9420. doi: 10.1073/pnas.1709166114. Epub 2017 Aug 10. Erratum in: Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):E9754.


Evolutionary dynamics and significance of multiple subclonal mutations in cancer.

Beckman RA, Loeb LA.

DNA Repair (Amst). 2017 Aug;56:7-15. doi: 10.1016/j.dnarep.2017.06.002. Epub 2017 Jun 9. Review.


Mutational spectra of aflatoxin B1 in vivo establish biomarkers of exposure for human hepatocellular carcinoma.

Chawanthayatham S, Valentine CC 3rd, Fedeles BI, Fox EJ, Loeb LA, Levine SS, Slocum SL, Wogan GN, Croy RG, Essigmann JM.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E3101-E3109. doi: 10.1073/pnas.1700759114. Epub 2017 Mar 28.


Homozygosity for the WRN Helicase-Inactivating Variant, R834C, does not confer a Werner syndrome clinical phenotype.

Kamath-Loeb AS, Zavala-van Rankin DG, Flores-Morales J, Emond MJ, Sidorova JM, Carnevale A, Cárdenas-Cortés MD, Norwood TH, Monnat RJ, Loeb LA, Mercado-Celis GE.

Sci Rep. 2017 Mar 9;7:44081. doi: 10.1038/srep44081.


Richmond T. Prehn: In Memoriam (1922-2016).

Loeb LA.

Cancer Res. 2017 Feb 1;77(3):593-594. doi: 10.1158/0008-5472.CAN-16-3328. No abstract available.


Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency.

Reid-Bayliss KS, Arron ST, Loeb LA, Bezrookove V, Cleaver JE.

Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10151-6. doi: 10.1073/pnas.1610020113. Epub 2016 Aug 19.


Human Cancers Express a Mutator Phenotype: Hypothesis, Origin, and Consequences.

Loeb LA.

Cancer Res. 2016 Apr 15;76(8):2057-9. doi: 10.1158/0008-5472.CAN-16-0794.


Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells.

Ahn EH, Lee SH, Kim JY, Chang CC, Loeb LA.

Cancer Res. 2016 Aug 1;76(15):4569-78. doi: 10.1158/0008-5472.CAN-15-3462. Epub 2016 May 17.


Ultra-deep sequencing detects ovarian cancer cells in peritoneal fluid and reveals somatic TP53 mutations in noncancerous tissues.

Krimmel JD, Schmitt MW, Harrell MI, Agnew KJ, Kennedy SR, Emond MJ, Loeb LA, Swisher EM, Risques RA.

Proc Natl Acad Sci U S A. 2016 May 24;113(21):6005-10. doi: 10.1073/pnas.1601311113. Epub 2016 May 5.


Exploring the implications of distinct mutational signatures and mutation rates in aging and cancer.

Fox EJ, Salk JJ, Loeb LA.

Genome Med. 2016 Mar 17;8(1):30. doi: 10.1186/s13073-016-0286-z.


The influence of subclonal resistance mutations on targeted cancer therapy.

Schmitt MW, Loeb LA, Salk JJ.

Nat Rev Clin Oncol. 2016 Jun;13(6):335-47. doi: 10.1038/nrclinonc.2015.175. Epub 2015 Oct 20. Review.


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.


Sequencing small genomic targets with high efficiency and extreme accuracy.

Schmitt MW, Fox EJ, Prindle MJ, Reid-Bayliss KS, True LD, Radich JP, Loeb LA.

Nat Methods. 2015 May;12(5):423-5. doi: 10.1038/nmeth.3351. Epub 2015 Apr 6.


Accuracy of Next Generation Sequencing Platforms.

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

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


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.


Cancer: One cell at a time.

Fox EJ, Loeb LA.

Nature. 2014 Aug 14;512(7513):143-4. doi: 10.1038/nature13650. Epub 2014 Jul 30. No abstract available.


Sphingosine, a modulator of human translesion DNA polymerase activity.

Kamath-Loeb AS, Balakrishna S, Whittington D, Shen JC, Emond MJ, Okabe T, Masutani C, Hanaoka F, Nishimura S, Loeb LA.

J Biol Chem. 2014 Aug 1;289(31):21663-72. doi: 10.1074/jbc.M114.570242. Epub 2014 Jun 13.


A rapid assay for measuring nucleotide excision repair by oligonucleotide retrieval.

Shen JC, Fox EJ, Ahn EH, Loeb LA.

Sci Rep. 2014 May 8;4:4894. doi: 10.1038/srep04894.


Clonal expansions and short telomeres are associated with neoplasia in early-onset, but not late-onset, ulcerative colitis.

Salk JJ, Bansal A, Lai LA, Crispin DA, Ussakli CH, Horwitz MS, Bronner MP, Brentnall TA, Loeb LA, Rabinovitch PS, Risques RA.

Inflamm Bowel Dis. 2013 Nov;19(12):2593-602. doi: 10.1097/MIB.0b013e3182a87640.


Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.

Kennedy SR, Salk JJ, Schmitt MW, Loeb LA.

PLoS Genet. 2013;9(9):e1003794. doi: 10.1371/journal.pgen.1003794. Epub 2013 Sep 26.


APOBEC3B mutagenesis in cancer.

Kuong KJ, Loeb LA.

Nat Genet. 2013 Sep;45(9):964-5. doi: 10.1038/ng.2736.


Altered RECQ Helicase Expression in Sporadic Primary Colorectal Cancers.

Lao VV, Welcsh P, Luo Y, Carter KT, Dzieciatkowski S, Dintzis S, Meza J, Sarvetnick NE, Monnat RJ Jr, Loeb LA, Grady WM.

Transl Oncol. 2013 Aug 1;6(4):458-69. Print 2013 Aug.


An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy.

Weedon MN, Ellard S, Prindle MJ, Caswell R, Lango Allen H, Oram R, Godbole K, Yajnik CS, Sbraccia P, Novelli G, Turnpenny P, McCann E, Goh KJ, Wang Y, Fulford J, McCulloch LJ, Savage DB, O'Rahilly S, Kos K, Loeb LA, Semple RK, Hattersley AT.

Nat Genet. 2013 Aug;45(8):947-50. doi: 10.1038/ng.2670. Epub 2013 Jun 16.


Do mutator mutations fuel tumorigenesis?

Fox EJ, Prindle MJ, Loeb LA.

Cancer Metastasis Rev. 2013 Dec;32(3-4):353-61. doi: 10.1007/s10555-013-9426-8. Review.


A substitution in the fingers domain of DNA polymerase δ reduces fidelity by altering nucleotide discrimination in the catalytic site.

Prindle MJ, Schmitt MW, Parmeggiani F, Loeb LA.

J Biol Chem. 2013 Feb 22;288(8):5572-80. doi: 10.1074/jbc.M112.436410. Epub 2013 Jan 2.


DNA polymerase delta in DNA replication and genome maintenance.

Prindle MJ, Loeb LA.

Environ Mol Mutagen. 2012 Dec;53(9):666-82. doi: 10.1002/em.21745. Epub 2012 Oct 13. Review.


Implications of genetic heterogeneity in cancer.

Schmitt MW, Prindle MJ, Loeb LA.

Ann N Y Acad Sci. 2012 Sep;1267:110-6. doi: 10.1111/j.1749-6632.2012.06590.x.


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.


The Werner syndrome exonuclease facilitates DNA degradation and high fidelity DNA polymerization by human DNA polymerase δ.

Kamath-Loeb AS, Shen JC, Schmitt MW, Loeb LA.

J Biol Chem. 2012 Apr 6;287(15):12480-90. doi: 10.1074/jbc.M111.332577. Epub 2012 Feb 17.


The Werner syndrome protein is distinguished from the Bloom syndrome protein by its capacity to tightly bind diverse DNA structures.

Kamath-Loeb A, Loeb LA, Fry M.

PLoS One. 2012;7(1):e30189. doi: 10.1371/journal.pone.0030189. Epub 2012 Jan 17.


Somatic mutations in aging, cancer and neurodegeneration.

Kennedy SR, Loeb LA, Herr AJ.

Mech Ageing Dev. 2012 Apr;133(4):118-26. doi: 10.1016/j.mad.2011.10.009. Epub 2011 Nov 3. Review.


XPG and WRN: an unexpected partnership.

Kamath-Loeb AS, Loeb LA.

Cell Cycle. 2011 Sep 15;10(18):3051. Epub 2011 Sep 15. No abstract available.


Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication.

Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, Camps M.

Nucleic Acids Res. 2011 Sep 1;39(16):7020-33. doi: 10.1093/nar/gkr157. Epub 2011 May 26.


Human cancers express mutator phenotypes: origin, consequences and targeting.

Loeb LA.

Nat Rev Cancer. 2011 Jun;11(6):450-7. doi: 10.1038/nrc3063. Epub 2011 May 19. Review.


The biochemistry and fidelity of synthesis by the apicoplast genome replication DNA polymerase Pfprex from the malaria parasite Plasmodium falciparum.

Kennedy SR, Chen CY, Schmitt MW, Bower CN, Loeb LA.

J Mol Biol. 2011 Jul 1;410(1):27-38. doi: 10.1016/j.jmb.2011.04.071. Epub 2011 May 5.


A random mutation capture assay to detect genomic point mutations in mouse tissue.

Wright JH, Modjeski KL, Bielas JH, Preston BD, Fausto N, Loeb LA, Campbell JS.

Nucleic Acids Res. 2011 Jun;39(11):e73. doi: 10.1093/nar/gkr142. Epub 2011 Apr 1.


Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461.

Mullins JI, Heath L, Hughes JP, Kicha J, Styrchak S, Wong KG, Rao U, Hansen A, Harris KS, Laurent JP, Li D, Simpson JH, Essigmann JM, Loeb LA, Parkins J.

PLoS One. 2011 Jan 14;6(1):e15135. doi: 10.1371/journal.pone.0015135.


Mutator phenotype in cancer: origin and consequences.

Loeb LA.

Semin Cancer Biol. 2010 Oct;20(5):279-80. doi: 10.1016/j.semcancer.2010.10.006. Epub 2010 Oct 16. No abstract available.


Lethal mutagenesis: targeting the mutator phenotype in cancer.

Fox EJ, Loeb LA.

Semin Cancer Biol. 2010 Oct;20(5):353-9. doi: 10.1016/j.semcancer.2010.10.005. Epub 2010 Oct 8. Review.


The mutator phenotype in cancer: molecular mechanisms and targeting strategies.

Prindle MJ, Fox EJ, Loeb LA.

Curr Drug Targets. 2010 Oct;11(10):1296-303. Review.


Reply: Is There Any Genetic Instability in Human Cancer?

Fox EJ, Beckman RA, Loeb LA.

DNA Repair (Amst). 2010 Aug 5;9(8):859-860. Epub 2010 Jun 29. No abstract available.


Active site mutations in mammalian DNA polymerase delta alter accuracy and replication fork progression.

Schmitt MW, Venkatesan RN, Pillaire MJ, Hoffmann JS, Sidorova JM, Loeb LA.

J Biol Chem. 2010 Oct 15;285(42):32264-72. doi: 10.1074/jbc.M110.147017. Epub 2010 Jul 13.


Princess takamatsu symposium on DNA repair and human cancers.

Loeb LA, Nishimura S.

Cancer Res. 2010 Jun 1;70(11):4269-73. doi: 10.1158/0008-5472.CAN-10-0320. Epub 2010 May 11.


Mitochondrial mutagenesis induced by tumor-specific radiation bystander effects.

Gorman S, Fox E, O'Donoghue D, Sheahan K, Hyland J, Mulcahy H, Loeb LA, O'Sullivan J.

J Mol Med (Berl). 2010 Jul;88(7):701-8. doi: 10.1007/s00109-010-0616-3. Epub 2010 Mar 28.


Frameshift mutagenesis and microsatellite instability induced by human alkyladenine DNA glycosylase.

Klapacz J, Lingaraju GM, Guo HH, Shah D, Moar-Shoshani A, Loeb LA, Samson LD.

Mol Cell. 2010 Mar 26;37(6):843-53. doi: 10.1016/j.molcel.2010.01.038.


Optimization of DNA polymerase mutation rates during bacterial evolution.

Loh E, Salk JJ, Loeb LA.

Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1154-9. doi: 10.1073/pnas.0912451107. Epub 2009 Dec 28.

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