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Janku F, Huang HJ, Fujii T, Shelton DN, Madwani K, Fu S, Tsimberidou AM, Piha-Paul SA, Wheler JJ, Zinner RG, Naing A, Hong DS, Karp DD, Cabrilo G, Kopetz ES, Subbiah V, Luthra R, Kee BK, Eng C, Morris VK, Karlin-Neumann GA, Meric-Bernstam F. Multiplex KRASG12/G13 mutation testing of unamplified cell-free DNA from the plasma of patients with advanced cancers using droplet digital polymerase chain reaction. Ann Oncol 2017; 28:642-650. [PMID: 27993791 PMCID: PMC5834133 DOI: 10.1093/annonc/mdw670] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Cell-free DNA (cfDNA) from plasma offers easily obtainable material for KRAS mutation analysis. Novel, multiplex, and accurate diagnostic systems using small amounts of DNA are needed to further the use of plasma cfDNA testing in personalized therapy. Patients and methods Samples of 16 ng of unamplified plasma cfDNA from 121 patients with diverse progressing advanced cancers were tested with a KRASG12/G13 multiplex assay to detect the seven most common mutations in the hotspot of exon 2 using droplet digital polymerase chain reaction (ddPCR). The results were retrospectively compared to mutation analysis of archival primary or metastatic tumor tissue obtained at different points of clinical care. Results Eighty-eight patients (73%) had KRASG12/G13 mutations in archival tumor specimens collected on average 18.5 months before plasma analysis, and 78 patients (64%) had KRASG12/G13 mutations in plasma cfDNA samples. The two methods had initial overall agreement in 103 (85%) patients (kappa, 0.66; ddPCR sensitivity, 84%; ddPCR specificity, 88%). Of the 18 discordant cases, 12 (67%) were resolved by increasing the amount of cfDNA, using mutation-specific probes, or re-testing the tumor tissue, yielding overall agreement in 115 patients (95%; kappa 0.87; ddPCR sensitivity, 96%; ddPCR specificity, 94%). The presence of ≥ 6.2% of KRASG12/G13 cfDNA in the wild-type background was associated with shorter survival (P = 0.001). Conclusion(s) Multiplex detection of KRASG12/G13 mutations in a small amount of unamplified plasma cfDNA using ddPCR has good sensitivity and specificity and good concordance with conventional clinical mutation testing of archival specimens. A higher percentage of mutant KRASG12/G13 in cfDNA corresponded with shorter survival.
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Affiliation(s)
- F. Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - H. J. Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - T. Fujii
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | | | - K. Madwani
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - S. Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - A. M. Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - S. A. Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - J. J. Wheler
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - R. G. Zinner
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - A. Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - D. S. Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - D. D. Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - G. Cabrilo
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - E. S. Kopetz
- Departments of Gastrointestinal Medical Oncology
| | - V. Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
| | - R. Luthra
- Hematopathology, Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B. K. Kee
- Departments of Gastrointestinal Medical Oncology
| | - C. Eng
- Departments of Gastrointestinal Medical Oncology
| | - V. K. Morris
- Departments of Gastrointestinal Medical Oncology
| | | | - F. Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston
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Adjei AA, Mandrekar SJ, Dy GK, Molina JR, Adjei AA, Gandara DR, Ziegler KLA, Stella PJ, Rowland KM, Schild SR, Zinner RG. A phase II second-line study of pemetrexed (pem) in combination with bevacizumab (bev) in patients with advanced non-small cell lung cancer (NSCLC): An NCCTG and SWOG study. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.8080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Peng G, Zinner RG, Wang Y, Treat J, Monberg M, Obasaju CK, Herbst RS, Novello S, Scagliotti GV. Comparison of patient outcomes stratified by histology among pemetrexed (P)-treated patients (pts) with stage IIIB/IV non-small cell lung cancer (NSCLC) in two phase II trials. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.8096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Altundag O, Stewart DJ, Stevens C, Rice DC, Ayers GD, Blumenschein GR, Karp DD, Hong WK, Fossella FV, Zinner RG. The risk of distant metastases in patients with non-small cell lung cancer (NSCLC) with cytologically proven malignant pleural effusion, stage IIIB: A retrospective analysis. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.9568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- O. Altundag
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | - D. J. Stewart
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | - C. Stevens
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | - D. C. Rice
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | - G. D. Ayers
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | | | - D. D. Karp
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | - W. K. Hong
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
| | | | - R. G. Zinner
- Univ of Texas M. D. Anderson Cancer Ctr, Houston, TX
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Zinner RG, Barrett BL, Volgin AY, Gelovani JG, Huang J, Tran HT, Mills GB, Hong WK, Fu Y, Mao L. Higher order relationships and the Medicinal Algorithmic Combinatorial Screen (MACS). J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.3079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- R. G. Zinner
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - B. L. Barrett
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - A. Y. Volgin
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - J. G. Gelovani
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - J. Huang
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - H. T. Tran
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - G. B. Mills
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - W. K. Hong
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - Y. Fu
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
| | - L. Mao
- M.D. Anderson Cancer Ctr, Houston, TX; UT Sch of Public Health Houston, Houston, TX
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Koshy S, Herbst RS, Obasaju CK, Fossella F, Papadimitrakopoulou V, Pisters KMW, Blumenschein G, Peeples BO, Hong WK, Zinner RG. A phase II trial of pemetrexed (P) plus carboplatin (C) in patients (pts) with advanced non-small-cell lung cancer (NSCLC). J Clin Oncol 2004. [DOI: 10.1200/jco.2004.22.90140.7074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- S. Koshy
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - R. S. Herbst
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - C. K. Obasaju
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - F. Fossella
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | | | - K. M. W. Pisters
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - G. Blumenschein
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - B. O. Peeples
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - W. K. Hong
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
| | - R. G. Zinner
- M. D. Anderson Cancer Center, Houston, TX; Eli Lilly Oncology, Indianapolis, IN
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