Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid

Journal of Molecular Diagnostics

Volumn 19, Issue 4, 2017, Pages 514-524

  Mehrotra, Meenakshi ^a   Singh, Rajesh R ^a   Chen, Wei ^a   Huang, Richard S P ^a,b   Almohammedsalim, Alaa A ^a   Barkoh, Bedia A ^a   Simien, Crystal M ^a   Hernandez, Marcos ^a   Behrens, Carmen ^a   Patel, Keyur P ^a   Routbort, Mark J ^a   Broaddus, Russell R ^a   Medeiros, L Jeffrey ^a   Wistuba, Ignacio I ^a   Kopetz, Scott ^a   Luthra, Rajyalakshmi ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTINEOPLASTIC AGENT; CIRCULATING CELL FREE DNA; DISCOIDIN DOMAIN RECEPTOR 2; DNA; DNA METHYLTRANSFERASE 3A; EDETIC ACID; FOXL2 PROTEIN; K RAS PROTEIN; MAP2K1 PROTEIN; PEPTIDES AND PROTEINS; PROTEIN MSH6; SMAD4 PROTEIN; TRANSCRIPTION FACTOR EZH2; TSC1 PROTEIN; TUMOR MARKER; UNCLASSIFIED DRUG; CELL FREE NUCLEIC ACID;

ADENOCARCINOMA; ADULT; ADVANCED CANCER; AGED; APPENDIX CARCINOMA; ARTICLE; ASTROCYTOMA; BIOINFORMATICS; BLOOD COLLECTION TUBE; BLOOD LEVEL; BLOOD SAMPLING; BRAIN TUMOR; BREAST ADENOCARCINOMA; CANCER CHEMOTHERAPY; CANCER PATIENT; CANCER RADIOTHERAPY; CANCER SURGERY; CLINICAL ARTICLE; CLINICAL LABORATORY; COHORT ANALYSIS; COLLOID CARCINOMA; COLON ADENOCARCINOMA; CONTROLLED STUDY; ENDOMETRIUM CARCINOMA; ESOPHAGEAL ADENOCARCINOMA; FEMALE; GENE FREQUENCY; GENETIC ANALYZER; GENOTYPE; HEMATOLOGICAL PARAMETERS; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; LIMIT OF DETECTION; LIMIT OF QUANTITATION; LIVER ADENOCARCINOMA; LIVER CELL CARCINOMA; LUNG ADENOCARCINOMA; MALE; MUTATIONAL ANALYSIS; NEUROBLASTOMA; NEXT GENERATION SEQUENCING; OVARY CARCINOMA; PARATHYROID CARCINOMA; PLASMA SEPARATION TIME; PROSTATE ADENOCARCINOMA; PROTEIN BLOOD LEVEL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SOMATIC MUTATION; TIME; TONGUE CARCINOMA; BLOOD; DNA MUTATIONAL ANALYSIS; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MIDDLE AGED; MUTATION; NEOPLASM; PROCEDURES; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; BIOMARKERS, TUMOR; CELL-FREE NUCLEIC ACIDS; COHORT STUDIES; DNA MUTATIONAL ANALYSIS; FEMALE; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MUTATION; NEOPLASMS;

EID: 85021258769     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2017.03.003     Document Type: Article

References (37)

1. Diaz, L.A. Jr., Bardelli, A., Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol 32 (2014), 579–586.
2. Cai, X., Janku, F., Zhan, Q., Fan, J.B., Accessing genetic information with liquid biopsies. Trends Genet 31 (2015), 564–575.
3. Esposito, A., Bardelli, A., Criscitiello, C., Colombo, N., Gelao, L., Fumagalli, L., Minchella, I., Locatelli, M., Goldhirsch, A., Curigliano, G., Monitoring tumor-derived cell-free DNA in patients with solid tumors: clinical perspectives and research opportunities. Cancer Treat Rev 40 (2014), 648–655.
4. Gormally, E., Caboux, E., Vineis, P., Hainaut, P., Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance. Mutat Res 635 (2007), 105–117.
5. Ulz, P., Auer, M., Heitzer, E., Detection of circulating tumor DNA in the blood of cancer patients: an important tool in cancer chemoprevention. Methods Mol Biol 1379 (2016), 45–68.
6. Bettegowda, C., Sausen, M., Leary, R.J., Kinde, I., Wang, Y., Agrawal, N., et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med, 6, 2014, 224ra24.
7. Frenel, J.S., Carreira, S., Goodall, J., Roda, D., Perez-Lopez, R., Tunariu, N., Riisnaes, R., Miranda, S., Figueiredo, I., Nava-Rodrigues, D., Smith, A., Leux, C., Garcia-Murillas, I., Ferraldeschi, R., Lorente, D., Mateo, J., Ong, M., Yap, T.A., Banerji, U., Gasi Tandefelt, D., Turner, N., Attard, G., de Bono, J.S., Serial next-generation sequencing of circulating cell-free DNA evaluating tumor clone response to molecularly targeted drug administration. Clin Cancer Res 21 (2015), 4586–4596.
8. El Messaoudi, S., Mouliere, F., Du Manoir, S., Bascoul-Mollevi, C., Gillet, B., Nouaille, M., Fiess, C., Crapez, E., Bibeau, F., Theillet, C.G., Mazard, T., Pezet, D., Mathonnet, M., Ychou, M., Thierry, A.R., Circulating DNA as a strong multi-marker prognostic tool for metastatic colorectal cancer patient management care. Clin Cancer Res 22 (2016), 3067–3077.
9. Toro, P.V., Erlanger, B., Beaver, J.A., Cochran, R.L., VanDenBerg, D.A., Yakim, E., Cravero, K., Chu, D., Zabransky, D.J., Wong, H.Y., Croessmann, S., Parsons, H., Hurley, P.J., Lauring, J., Park, B.H., Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA. Clin Biochem 48 (2015), 993–998.
10. El Messaoudi, S., Rolet, F., Mouliere, F., Thierry, A.R., Circulating cell free DNA: preanalytical considerations. Clin Chim Acta 424 (2013), 222–230.
11. Fawzy, A., Sweify, K.M., El-Fayoumy, H.M., Nofal, N., Quantitative analysis of plasma cell-free DNA and its DNA integrity in patients with metastatic prostate cancer using ALU sequence. J Egypt Natl Canc Inst 28 (2016), 235–242.
12. Thorvaldsdottir, H., Robinson, J.T., Mesirov, J.P., Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14 (2013), 178–192.
13. Singh, R.R., Patel, K.P., Routbort, M.J., Reddy, N.G., Barkoh, B.A., Handal, B., Kanagal-Shamanna, R., Greaves, W.O., Medeiros, L.J., Aldape, K.D., Luthra, R., Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes. J Mol Diagn 15 (2013), 607–622.
14. Ye, K., Schulz, M.H., Long, Q., Apweiler, R., Ning, Z., Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25 (2009), 2865–2871.
15. Wilm, A., Aw, P.P., Bertrand, D., Yeo, G.H., Ong, S.H., Wong, C.H., Khor, C.C., Petric, R., Hibberd, M.L., Nagarajan, N., LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 40 (2012), 11189–11201.
16. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., DePristo, M.A., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20 (2010), 1297–1303.
17. Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
18. Pinzani, P., Salvianti, F., Zaccara, S., Massi, D., De Giorgi, V., Pazzagli, M., Orlando, C., Circulating cell-free DNA in plasma of melanoma patients: qualitative and quantitative considerations. Clin Chim Acta 412 (2011), 2141–2145.
19. Riva, F., Dronov, O.I., Khomenko, D.I., Huguet, F., Louvet, C., Mariani, P., Stern, M.H., Lantz, O., Proudhon, C., Pierga, J.Y., Bidard, F.C., Clinical applications of circulating tumor DNA and circulating tumor cells in pancreatic cancer. Mol Oncol 10 (2016), 481–493.
20. Rothwell, D.G., Smith, N., Morris, D., Leong, H.S., Li, Y., Hollebecque, A., Ayub, M., Carter, L., Antonello, J., Franklin, L., Miller, C., Blackhall, F., Dive, C., Brady, G., Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample. Mol Oncol 10 (2015), 566–574.
21. Yoruker, E.E., Holdenrieder, S., Gezer, U., Blood-based biomarkers for diagnosis, prognosis and treatment of colorectal cancer. Clin Chim Acta 455 (2016), 26–32.
22. Zill, O.A., Greene, C., Sebisanovic, D., Siew, L.M., Leng, J., Vu, M., Hendifar, A.E., Wang, Z., Atreya, C.E., Kelley, R.K., Van Loon, K., Ko, A.H., Tempero, M.A., Bivona, T.G., Munster, P.N., Talasaz, A., Collisson, E.A., Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas. Cancer Discov 5 (2015), 1040–1048.
23. Sato, K.A., Hachiya, T., Iwaya, T., Kume, K., Matsuo, T., Kawasaki, K., Abiko, Y., Akasaka, R., Matsumoto, T., Otsuka, K., Nishizuka, S.S., Individualized mutation detection in circulating tumor DNA for monitoring colorectal tumor burden using a cancer-associated gene sequencing panel. PLoS One, 11, 2016, e0146275.
24. Uchida, J., Kato, K., Kukita, Y., Kumagai, T., Nishino, K., Daga, H., Nagatomo, I., Inoue, T., Kimura, M., Oba, S., Ito, Y., Takeda, K., Imamura, F., Diagnostic accuracy of noninvasive genotyping of EGFR in lung cancer patients by deep sequencing of plasma cell-free DNA. Clin Chem 61 (2015), 1191–1196.
25. Luo, H., Li, H., Hu, Z., Wu, H., Liu, C., Li, Y., Zhang, X., Lin, P., Hou, Q., Ding, G., Wang, Y., Li, S., Wei, D., Qiu, F., Li, Y., Wu, S., Noninvasive diagnosis and monitoring of mutations by deep sequencing of circulating tumor DNA in esophageal squamous cell carcinoma. Biochem Biophys Res Commun 471 (2016), 596–602.
26. Jovelet, C., Ileana, E., Le Deley, M.C., Motte, N., Rosellini, S., Romero, A., Lefebvre, C., Pedrero, M., Pata-Merci, N., Droin, N., Deloger, M., Massard, C., Hollebecque, A., Ferte, C., Boichard, A., Postel-Vinay, S., Ngo-Camus, M., De Baere, T., Vielh, P., Scoazec, J.Y., Vassal, G., Eggermont, A.M., Andre, F., Soria, J.C., Lacroix, L., Circulating cell-free tumor DNA (cfDNA) analysis of 50-genes by next-generation sequencing (NGS) in the prospective MOSCATO trial. Clin Cancer Res 22 (2016), 2960–2968.
27. Ulivi, P., Silvestrini, R., Role of quantitative and qualitative characteristics of free circulating DNA in the management of patients with non-small cell lung cancer. Cell Oncol (Dordr) 36 (2013), 439–448.
28. Pu, W.Y., Zhang, R., Xiao, L., Wu, Y.Y., Gong, W., Lv, X.D., Zhong, F.Y., Zhuang, Z.X., Bai, X.M., Li, K., Xing, C.G., Prediction of cancer progression in a group of 73 gastric cancer patients by circulating cell-free DNA. BMC Cancer 16 (2016), 943–948.
29. Lanman, R.B., Mortimer, S.A., Zill, O.A., Sebisanovic, D., Lopez, R., Blau, S., Collisson, E.A., Divers, S.G., Hoon, D.S.B., Kopetz, E.S., Lee, J., Nikolinakos, P.G., Baca, A.M., Kermani, B.G., Eltoukhy, H., Talasaz, A., Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PLoS One, 10, 2015, e0140712.
30. Kim, S.T., Lee, W.S., Lanman, R.B., Mortimer, S., Zill, O.A., Kim, K.M., Jang, K.T., Kim, S.H., Park, S.H., Park, J.O., Park, Y.S., Lim, H.Y., Eltoukhy, H., Kang, W.K., Lee, W.Y., Kim, H.C., Park, K., Lee, J., Talasaz, A., Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients. Oncotarget 6 (2015), 40360–40369.
31. Seki, Y., Fujiwara, Y., Kohno, T., Takai, E., Sunami, K., Goto, Y., Horinouchi, H., Kanda, S., Nokihara, H., Watanabe, S., Ichikawa, H., Yamamoto, N., Kuwano, K., Ohe, Y., Picoliter-droplet digital polymerase chain reaction-based analysis of cell-free plasma DNA to assess EGFR mutations in lung adenocarcinoma that confer resistance to tyrosine-kinase inhibitors. Oncologist 21 (2016), 156–164.
32. Thierry, A.R., Mouliere, F., El Messaoudi, S., Mollevi, C., Lopez-Crapez, E., Rolet, F., Gillet, B., Gongora, C., Dechelotte, P., Robert, B., Del Rio, M., Lamy, P.J., Bibeau, F., Nouaille, M., Loriot, V., Jarrousse, A.S., Molina, F., Mathonnet, M., Pezet, D., Ychou, M., Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med 20 (2014), 430–435.
33. Morelli, M.P., Overman, M.J., Dasari, A., Kazmi, S.M., Mazard, T., Vilar, E., Morris, V.K., Lee, M.S., Herron, D., Eng, C., Morris, J., Kee, B.K., Janku, F., Deaton, F.L., Garrett, C., Maru, D., Diehl, F., Angenendt, P., Kopetz, S., Characterizing the patterns of clonal selection in circulating tumor DNA from patients with colorectal cancer refractory to anti-EGFR treatment. Ann Oncol 26 (2015), 731–736.
34. Yoo, C., Ryu, M.H., Na, Y.S., Ryoo, B.Y., Park, S.R., Kang, Y.K., Analysis of serum protein biomarkers, circulating tumor DNA, and dovitinib activity in patients with tyrosine kinase inhibitor-refractory gastrointestinal stromal tumors. Ann Oncol 25 (2014), 2272–2277.
35. Murtaza, M., Dawson, S.J., Tsui, D.W., Gale, D., Forshew, T., Piskorz, A.M., Parkinson, C., Chin, S.F., Kingsbury, Z., Wong, A.S., Marass, F., Humphray, S., Hadfield, J., Bentley, D., Chin, T.M., Brenton, J.D., Caldas, C., Rosenfeld, N., Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497 (2013), 108–112.
36. Newman, A.M., Bratman, S.V., To, J., Wynne, J.F., Eclov, N.C., Modlin, L.A., Liu, C.L., Neal, J.W., Wakelee, H.A., Merritt, R.E., Shrager, J.B., Loo, B.W. Jr., Alizadeh, A.A., Diehn, M., An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 20 (2014), 548–554.
37. Forshew, T., Murtaza, M., Parkinson, C., Gale, D., Tsui, D.W., Kaper, F., Dawson, S.J., Piskorz, A.M., Jimenez-Linan, M., Bentley, D., Hadfield, J., May, A.P., Caldas, C., Brenton, J.D., Rosenfeld, N., Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med, 4, 2012, 136ra68.