publication . Article . Other literature type . 2018

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

Hellwig, Sabine; Nix, David A.; Gligorich, Keith M.; O’Shea, John M.; Thomas, Alun; Fuertes, Carrie L.; Bhetariya, Preetida J.; Marth, Gabor T.; Bronner, Mary P.; Underhill, Hunter R.;
Open Access English
  • Published: 01 Jul 2018 Journal: PLoS ONE, volume 13, issue 7 (issn: 1932-6203, eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application of cell-free DNA in clinical oncology. In this study, isolation of short cell-free DNA fragments is shown to enrich for tumor variants and improve correction of PCR- and sequencing-associated errors. Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA) were isolated from patients with melanoma, pancreatic ductal adenocarcinoma, and colorectal adenocarcinoma...
Subjects
free text keywords: Molecular biology, Computational Biology, Research Article, Diagnostic medicine, Biomolecular isolation, Sequence Alignment, Genetic Loci, Oncology, Artificial Gene Amplification and Extension, Genetics, Molecular biology techniques, Carcinomas, Genome Analysis, Cancer detection and diagnosis, Genomics, Cancers and Neoplasms, Sequence Analysis, Database and Informatics Methods, Polymerase Chain Reaction, Alleles, DNA sequencing, Sequencing techniques, Biology and life sciences, Next-Generation Sequencing, Biomarkers, Research and analysis methods, Medicine, Adenocarcinomas, Q, R, Melanomas, Science, Bioinformatics, Biochemistry, Medicine and health sciences, Transcriptome Analysis, DNA isolation, Circulating tumor DNA
Funded by
NIH| University of Utah Center for Clinical and Translational Science-UL1
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1RR025764-02S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Protocol Review and Monitoring System
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA042014-23S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| University of Utah Center for Clinical and Translational Science-UL1
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1TR000105-05S1
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| University of Utah Center for Clinical and Translational Science
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5UL1TR001067-05
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
34 references, page 1 of 3

1 Donaldson J, Park BH. Circulating Tumor DNA: Measurement and Clinical Utility. Annu Rev Med. 2017 Epub 2017/08/29. 10.1146/annurev-med-041316-085721 .28846488 [PubMed] [DOI]

2 Lui YY, Chik KW, Chiu RW, Ho CY, Lam CW, Lo YM. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem. 2002;48(3):421–7. Epub 2002/02/28. .11861434 [PubMed]

3 Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, et al Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun. 2015;6:8760 Epub 2015/11/05. 10.1038/ncomms9760 .26530965 [OpenAIRE] [PubMed] [DOI]

4 Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, et al Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA. PLoS One. 2015;10(10):e0140712 Epub 2015/10/17. 10.1371/journal.pone.0140712 .26474073 [OpenAIRE] [PubMed] [DOI]

5 Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra24 Epub 2014/02/21. 10.1126/scitranslmed.3007094 .24553385 [OpenAIRE] [PubMed] [DOI]

6 McGranahan N, Swanton C. Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell. 2017;168(4):613–28. Epub 2017/02/12. 10.1016/j.cell.2017.01.018 .28187284 [OpenAIRE] [PubMed] [DOI]

7 Jiang P, Lo YM. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet. 2016;32(6):360–71. Epub 2016/05/01. 10.1016/j.tig.2016.03.009 .27129983 [PubMed] [DOI]

8 Nagata S. Apoptotic DNA fragmentation. Exp Cell Res. 2000;256(1):12–8. Epub 2000/03/31. 10.1006/excr.2000.4834 .10739646 [PubMed] [DOI]

9 Underhill HR, Kitzman JO, Hellwig S, Welker NC, Daza R, Baker DN, et al Fragment Length of Circulating Tumor DNA. PLoS Genet. 2016;12(7):e1006162 Epub 2016/07/20. 10.1371/journal.pgen.1006162 .27428049 [OpenAIRE] [PubMed] [DOI]

10 Tie J, Wang Y, Tomasetti C, Li L, Springer S, Kinde I, et al Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer. Sci Transl Med. 2016;8(346):346ra92 Epub 2016/07/08. 10.1126/scitranslmed.aaf6219 .27384348 [OpenAIRE] [PubMed] [DOI]

11 Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, et al Direct detection of early-stage cancers using circulating tumor DNA. Sci Transl Med. 2017;9(403). Epub 2017/08/18. 10.1126/scitranslmed.aan2415 .28814544 [OpenAIRE] [PubMed] [DOI]

12 Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, et al Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med. 2010;2(20):20ra14 Epub 2010/04/08. 10.1126/scitranslmed.3000702 .20371490 [OpenAIRE] [PubMed] [DOI]

13 Manley LJ, Ma D, Levine SS. Monitoring Error Rates In Illumina Sequencing. J Biomol Tech. 2016;27(4):125–8. Epub 2016/09/28. 10.7171/jbt.16-2704-002 .27672352 [OpenAIRE] [PubMed] [DOI]

14 Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109(36):14508–13. Epub 2012/08/03. 10.1073/pnas.1208715109 .22853953 [OpenAIRE] [PubMed] [DOI]

15 Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, et al Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS One. 2016;11(1):e0146638 Epub 2016/01/12. 10.1371/journal.pone.0146638 .26752634 [OpenAIRE] [PubMed] [DOI]

34 references, page 1 of 3
Abstract
Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application of cell-free DNA in clinical oncology. In this study, isolation of short cell-free DNA fragments is shown to enrich for tumor variants and improve correction of PCR- and sequencing-associated errors. Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA) were isolated from patients with melanoma, pancreatic ductal adenocarcinoma, and colorectal adenocarcinoma...
Subjects
free text keywords: Molecular biology, Computational Biology, Research Article, Diagnostic medicine, Biomolecular isolation, Sequence Alignment, Genetic Loci, Oncology, Artificial Gene Amplification and Extension, Genetics, Molecular biology techniques, Carcinomas, Genome Analysis, Cancer detection and diagnosis, Genomics, Cancers and Neoplasms, Sequence Analysis, Database and Informatics Methods, Polymerase Chain Reaction, Alleles, DNA sequencing, Sequencing techniques, Biology and life sciences, Next-Generation Sequencing, Biomarkers, Research and analysis methods, Medicine, Adenocarcinomas, Q, R, Melanomas, Science, Bioinformatics, Biochemistry, Medicine and health sciences, Transcriptome Analysis, DNA isolation, Circulating tumor DNA
Funded by
NIH| University of Utah Center for Clinical and Translational Science-UL1
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1RR025764-02S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Protocol Review and Monitoring System
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P30CA042014-23S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| University of Utah Center for Clinical and Translational Science-UL1
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1TR000105-05S1
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
,
NIH| University of Utah Center for Clinical and Translational Science
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5UL1TR001067-05
  • Funding stream: NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES
34 references, page 1 of 3

1 Donaldson J, Park BH. Circulating Tumor DNA: Measurement and Clinical Utility. Annu Rev Med. 2017 Epub 2017/08/29. 10.1146/annurev-med-041316-085721 .28846488 [PubMed] [DOI]

2 Lui YY, Chik KW, Chiu RW, Ho CY, Lam CW, Lo YM. Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem. 2002;48(3):421–7. Epub 2002/02/28. .11861434 [PubMed]

3 Murtaza M, Dawson SJ, Pogrebniak K, Rueda OM, Provenzano E, Grant J, et al Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun. 2015;6:8760 Epub 2015/11/05. 10.1038/ncomms9760 .26530965 [OpenAIRE] [PubMed] [DOI]

4 Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, et al Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA. PLoS One. 2015;10(10):e0140712 Epub 2015/10/17. 10.1371/journal.pone.0140712 .26474073 [OpenAIRE] [PubMed] [DOI]

5 Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6(224):224ra24 Epub 2014/02/21. 10.1126/scitranslmed.3007094 .24553385 [OpenAIRE] [PubMed] [DOI]

6 McGranahan N, Swanton C. Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell. 2017;168(4):613–28. Epub 2017/02/12. 10.1016/j.cell.2017.01.018 .28187284 [OpenAIRE] [PubMed] [DOI]

7 Jiang P, Lo YM. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet. 2016;32(6):360–71. Epub 2016/05/01. 10.1016/j.tig.2016.03.009 .27129983 [PubMed] [DOI]

8 Nagata S. Apoptotic DNA fragmentation. Exp Cell Res. 2000;256(1):12–8. Epub 2000/03/31. 10.1006/excr.2000.4834 .10739646 [PubMed] [DOI]

9 Underhill HR, Kitzman JO, Hellwig S, Welker NC, Daza R, Baker DN, et al Fragment Length of Circulating Tumor DNA. PLoS Genet. 2016;12(7):e1006162 Epub 2016/07/20. 10.1371/journal.pgen.1006162 .27428049 [OpenAIRE] [PubMed] [DOI]

10 Tie J, Wang Y, Tomasetti C, Li L, Springer S, Kinde I, et al Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer. Sci Transl Med. 2016;8(346):346ra92 Epub 2016/07/08. 10.1126/scitranslmed.aaf6219 .27384348 [OpenAIRE] [PubMed] [DOI]

11 Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, et al Direct detection of early-stage cancers using circulating tumor DNA. Sci Transl Med. 2017;9(403). Epub 2017/08/18. 10.1126/scitranslmed.aan2415 .28814544 [OpenAIRE] [PubMed] [DOI]

12 Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, et al Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med. 2010;2(20):20ra14 Epub 2010/04/08. 10.1126/scitranslmed.3000702 .20371490 [OpenAIRE] [PubMed] [DOI]

13 Manley LJ, Ma D, Levine SS. Monitoring Error Rates In Illumina Sequencing. J Biomol Tech. 2016;27(4):125–8. Epub 2016/09/28. 10.7171/jbt.16-2704-002 .27672352 [OpenAIRE] [PubMed] [DOI]

14 Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109(36):14508–13. Epub 2012/08/03. 10.1073/pnas.1208715109 .22853953 [OpenAIRE] [PubMed] [DOI]

15 Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, et al Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS One. 2016;11(1):e0146638 Epub 2016/01/12. 10.1371/journal.pone.0146638 .26752634 [OpenAIRE] [PubMed] [DOI]

34 references, page 1 of 3
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publication . Article . Other literature type . 2018

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

Hellwig, Sabine; Nix, David A.; Gligorich, Keith M.; O’Shea, John M.; Thomas, Alun; Fuertes, Carrie L.; Bhetariya, Preetida J.; Marth, Gabor T.; Bronner, Mary P.; Underhill, Hunter R.;