Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits

Scientific Reports

Volumn 7, Issue 1, 2017, Pages

  Alcaide, Miguel ^a   Yu, Stephen ^a   Davidson, Jordan ^a   Albuquerque, Marco ^a   Bushell, Kevin ^a   Fornika, Daniel ^a   Arthur, Sarah ^a   Grande, Bruno M ^a   McNamara, Suzan ^b   Tertre, Mathilde Couetoux Du ^b   Batist, Gerald ^b   Huntsman, David G ^c,d   Cavallone, Luca ^e   Aguilar, Adriana ^e   Basik, Mark ^e   Johnson, Nathalie A ^e   Deyell, Rebecca J ^f   Rassekh, S Rod ^f   Morin, Ryan D ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c BRITISH COLUMBIA CANCER AGENCY   (Canada)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^e MCGILL UNIVERSITY   (Canada)

^f BC CHILDREN S HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULATING TUMOR DNA; DNA; TUMOR MARKER;

BLOOD; CHEMISTRY; CONSENSUS SEQUENCE; DNA BARCODING; GENETIC SCREENING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; NEOPLASM; PERSONALIZED MEDICINE; PROCEDURES;

BIOMARKERS, TUMOR; CIRCULATING TUMOR DNA; CONSENSUS SEQUENCE; DNA BARCODING, TAXONOMIC; DNA, NEOPLASM; GENETIC TESTING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; PRECISION MEDICINE;

EID: 85028940130     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-10269-2     Document Type: Article

References (40)

1. Crowley, E., Di Nicolantonio, F., Loupakis, F. & Bardelli, A. Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol 10, 472-484 (2013)
2. Karachaliou, N., Mayo-de-las-Casas, C., Molina-Vila, M. A. & Rosell, R. Real-time liquid biopsies become a reality in cancer treatment. Ann. Transl. Med. 3, 36 (2015)
3. Esposito, A., Criscitiello, C., Locatelli, M., Milano, M. & Curigliano, G. Liquid biopsies for solid tumors: Understanding tumor heterogeneity and real time monitoring of early resistance to targeted therapies. Pharmacol. Ther. 157, 120-124 (2016)
4. Lebofsky, R. et al. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Mol. Oncol. 9, 783-790 (2015)
5. Cree, I. A. Liquid biopsy for cancer patients: Principles and practice. Pathogenesis 2, 1-4 (2015)
6. Brock, G., Castellanos-Rizaldos, E., Hu, L., Coticchia, C. & Skog, J. Liquid biopsy for cancer screening, patient stratification and monitoring. Transl. Cancer Res. Vol 4, No 3 (June 2015) Transl. Cancer Res. (Application Genomic Technol. Cancer Res. At http://tcr.amegroups.com/article/view/4546 (2015)
7. Newman, A. M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 20, 548-554 (2014)
8. Assouline, S. E. et al. Phase 2 study of panobinostat with or without rituximab in relapsed diffuse large B-cell lymphoma. Blood 128, 185-194 (2016)
9. Bordi, P., Del R., M., Danesi, R. & Tiseo, M. Circulating DNA in diagnosis and monitoring EGFR gene mutations in advanced non-small cell lung cancer. Transl. Lung Cancer Res. 4, 584-597 (2015)
10. Yamada, T. et al. Utility of KRAS mutation detection using circulating cell-free DNA from patients with colorectal cancer. Cancer Sci. 107, 936-943 (2016)
11. Cheng, F., Su, L. & Qian, C. Circulating tumor DNA: a promising biomarker in the liquid biopsy of cancer. Oncotarget doi: 10.18632/oncotarget.9453 (2016)
12. De Mattos-Arruda, L. et al. Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma. Nat Commun 6 (2015)
13. Bettegowda, C. et al. Detection of circulating tumor DNA in early-and late-stage human malignancies. Sci. Transl. Med. 6, 224ra24 (2014)
14. Siravegna, G. & Bardelli, A. Genotyping cell-free tumor DNA in the blood to detect residual disease and drug resistance. Genome Biol. 15, 449 (2014)
15. Ma, M. et al. 'Liquid biopsy'-ctDNA detection with great potential and challenges. Ann. Transl. Med. 3, 235 (2015)
16. Volik, S., Alcaide, M., Morin, R. D. & Collins, C. C. Cell-free DNA (cfDNA): clinical significance and utility in cancer shaped by emerging technologies. Mol. Cancer Res. doi: 10.1158/1541-7786.MCR-16-0044 (2016)
17. Sanmamed, M. F. et al. Quantitative Cell-Free Circulating BRAFV600E Mutation Analysis by Use of Droplet Digital PCR in the Follow-up of Patients with Melanoma Being Treated with BRAF Inhibitors. Clin. Chem. 61, 297-304 (2015)
18. Watanabe, M. et al. Ultra-Sensitive Detection of the Pretreatment EGFR T790M Mutation in Non-Small Cell Lung Cancer Patients with an EGFR-Activating Mutation Using Droplet Digital PCR. Clin. Cancer Res. 21, 3552-3560 (2015)
19. Gregory, M. T. et al. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res. 44, e22 (2016)
20. Forshew, T. et al. Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA. Sci. Transl. Med. 4, 136ra68-136ra68 (2012)
21. Newman, A. M. et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotech 34, 547-555 (2016)
22. Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. USA 109, 14508-14513 (2012)
23. Kennedy, S. R. et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat. Protoc. 9, 2586-2606 (2014)
24. Alcaide, M. et al. Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma. Clin. Chem., doi: 10.1373/clinchem.2016.255315 (2016)
25. Wang, K. et al. Ultra-precise detection of mutations by droplet-based amplification of circularized DNA. BMC Genomics 17, article 214 (2016)
26. Marx, V. Cancer: hunting rare somatic mutations. Nat Meth 13, 295-299 (2016)
27. Jiang, P. et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc. Natl. Acad. Sci. USA 112, E1317-25 (2015)
28. Mouliere, F. & Rosenfeld, N. Circulating tumor-derived DNA is shorter than somatic DNA in plasma. Proc. Natl. Acad. Sci. USA 112, 3178-3179 (2015)
29. Liang, W. et al. Metastatic EML4-ALK fusion detected by circulating DNA genotyping in an EGFR-mutated NSCLC patient and successful management by adding ALK inhibitors: a case report. BMC Cancer 16, 62 (2015)
30. Olsson, E. et al. Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. EMBO Mol. Med. 7, 1034-1047 (2015)
31. Sacher, A. G. et al. Prospective Validation of Rapid Plasma Genotyping for the Detection of EGFR and KRAS Mutations in Advanced Lung Cancer. JAMA Oncol. 2, 1014-1022 (2016)
32. Morin, R. D. et al. Genetic landscapes of relapsed and refractory diffuse large B cell lymphomas. Clin. Cancer Res., doi: 10.1158/1078-0432.CCR-15-2123 (2015)
33. Hughes, T. P. et al. BCR-ABL1 mutation development during first-line treatment with dasatinib or imatinib for chronic myeloid leukemia in chronic phase. Leukemia 29, 1832-1838 (2015)
34. Taly, V. et al. Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin. Chem. 59, 1722-1731 (2013)
35. Andersen, R. F. & Jakobsen, A. Screening for circulating RAS/RAF mutations by multiplex digital PCR. Clin. Chim. Acta. 458, 138-143 (2016)
36. Zonta, E. et al. Multiplex Detection of Rare Mutations by Picoliter Droplet Based Digital PCR: Sensitivity and Specificity Considerations. PLoS One 11, e0159094 (2016)
37. Jackson, J. B. et al. Multiplex Preamplification of Serum DNA to Facilitate Reliable Detection of Extremely Rare Cancer Mutations in Circulating DNA by Digital PCR. J. Mol. Diagn. 18, 235-243 (2016)
38. Kang, Q., Parkin, B., Giraldez, M. D. & Tewari, M. Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation. Biotechniques 60, 175-185 (2016)
39. Schmitt, M. W. et al. Sequencing small genomic targets with high efficiency and extreme accuracy. Nat. Methods 12, 423-425 (2015)
40. Stoler, N., Arbeithuber, B., Guiblet, W., Makova, K. D. & Nekrutenko, A. Streamlined analysis of duplex sequencing data with Du Novo. Genome Biol. 17, 180 (2016).