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Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study. Nat Med 2019; 25:744-750. [PMID: 31011206 PMCID: PMC6553618 DOI: 10.1038/s41591-019-0407-5] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/22/2019] [Indexed: 12/17/2022]
Abstract
Cancer treatments have evolved from indiscriminate cytotoxic agents to
selective genome- and immune-targeted drugs that have transformed outcomes for
some malignancies.1 Tumor
complexity and heterogeneity suggest that the “precision medicine”
paradigm of cancer therapy requires treatment to be personalized to the
individual patient.2–6 To date, precision oncology
trials have been based upon molecular matching with predetermined
monotherapies.7–14 Several of these trials have
been hindered by very low matching rates, often in the 5–10%
range,15 and low
response rates. Low matching rates may be due to the use of limited gene panels,
restrictive molecular matching algorithms, lack of drug availability or the
deterioration and death of end-stage patients before therapy can be implemented.
We hypothesized that personalized treatment with combination therapies would
improve outcomes in patients with refractory malignancies. As a first test of
this concept, we implemented a cross-institutional, prospective study
(I-PREDICT, NCT02534675) that used tumor DNA sequencing and timely
recommendations for individualized treatment with combination therapies. We
found that administration of customized multi-drug regimens was feasible, with
49% of consented patients receiving personalized treatment. Targeting of a
larger fraction of identified molecular alterations, yielding a higher
“matching score,” was correlated with significantly improved
disease control rates, as well as longer progression-free and overall survival
rates, as compared to when fewer somatic alterations were targeted. Our findings
suggest that the current clinical trial paradigm for precision oncology, which
pairs one driver mutation with one drug, may be optimized by treating
molecularly complex and heterogeneous cancers with combinations of customized
agents.
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Schrock AB, Pavlick D, Klempner SJ, Chung JH, Forcier B, Welsh A, Young L, Leyland-Jones B, Bordoni R, Carvajal RD, Chao J, Kurzrock R, Sicklick JK, Ross JS, Stephens PJ, Devoe C, Braiteh F, Ali SM, Miller VA. Hybrid Capture-Based Genomic Profiling of Circulating Tumor DNA from Patients with Advanced Cancers of the Gastrointestinal Tract or Anus. Clin Cancer Res 2018; 24:1881-1890. [PMID: 29363525 DOI: 10.1158/1078-0432.ccr-17-3103] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/06/2017] [Accepted: 01/17/2018] [Indexed: 12/12/2022]
Abstract
Purpose: Genomic profiling of tumor biopsies from advanced gastrointestinal and anal cancers is increasingly used to inform treatment. In some cases, tissue biopsy can be prohibitive, and we sought to investigate whether analysis of blood-derived circulating tumor DNA (ctDNA) may provide a minimally invasive alternative.Experimental Design: Hybrid capture-based genomic profiling of 62 genes was performed on blood-based ctDNA from 417 patients with gastrointestinal carcinomas to assess the presence of genomic alterations (GA) and compare with matched tissue samples.Results: Evidence of ctDNA was detected in 344 of 417 samples (82%), and of these, ≥1 reportable GA was detected in 89% (306/344) of samples. Frequently altered genes were TP53 (72%), KRAS (35%), PIK3CA (14%), BRAF (8%), and EGFR (7%). In temporally matched ctDNA and tissue samples available from 25 patients, 86% of alterations detected in tissue were also detected in ctDNA, including 95% of short variants, but only 50% of amplifications. Conversely, 63% of alterations detected in ctDNA were also detected in matched tissue. Examples demonstrating clinical utility are presented.Conclusions: Genomic profiling of ctDNA detected potentially clinically relevant GAs in a significant subset of patients with gastrointestinal carcinomas. In these tumor types, most alterations detected in matched tissue were also detected in ctDNA, and with the exception of amplifications, ctDNA sequencing routinely detected additional alterations not found in matched tissue, consistent with tumor heterogeneity. These results suggest feasibility and utility of ctDNA testing in advanced gastrointestinal cancers as a complementary approach to tissue testing, and further investigation is warranted. Clin Cancer Res; 24(8); 1881-90. ©2018 AACR.
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Affiliation(s)
| | - Dean Pavlick
- Foundation Medicine, Inc. Cambridge, Massachusetts
| | | | - Jon H Chung
- Foundation Medicine, Inc. Cambridge, Massachusetts
| | | | | | - Lauren Young
- Foundation Medicine, Inc. Cambridge, Massachusetts
| | | | | | - Richard D Carvajal
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Joseph Chao
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, California
| | - Razelle Kurzrock
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Jason K Sicklick
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Jeffrey S Ross
- Foundation Medicine, Inc. Cambridge, Massachusetts.,Albany Medical College, Albany, New York
| | | | | | - Fadi Braiteh
- Comprehensive Cancer Centers of Nevada, Las Vegas, Nevada
| | - Siraj M Ali
- Foundation Medicine, Inc. Cambridge, Massachusetts
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