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Figure 1.
Mutational Landscape Obtained by cfDNA Testing in Metastatic Prostate Cancer Patients
Mutational Landscape Obtained by cfDNA Testing in Metastatic Prostate Cancer Patients

Each column represents 1 patient with 1 or more alterations reported in at least 1 platform. Only alterations in genes purportedly covered by both commercial gene panels were considered. Exome coverage for each gene in the sequencing panel differs between platforms. Congruence among tests was assessed on confirmation of exome coverage with the counterpart platform for each alteration in the study. cfDNA indicates cell-free DNA; G, results using Guardant360 (Guardant Health, Inc); P, results using PlasmaSELECT (Personal Genome Diagnostics, Inc), PSA, prostate-specific antigen.

Figure 2.
Congruence Analysis of cfDNA-Targeted Next-Generation Sequencing in 2 Independent Commercial Platforms
Congruence Analysis of cfDNA-Targeted Next-Generation Sequencing in 2 Independent Commercial Platforms

Patients negative for cell-free DNA (cfDNA) alterations in both tests were classified as complete congruence for 0 alterations (9/40 [22.5%]). For congruence analysis, patients who had 1 or more alterations reported, but none was covered by both tests, were excluded and classified as not evaluable for patient-level congruence (6/40 [15%]). The proportion of patients with complete congruence for 1 or more alterations, partial, and no congruence was 3 of 40 (7.5%), 6 of 40 (15%), and 16 of 40 (40%), respectively, among the 2 platforms.

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Wan  JCM, Massie  C, Garcia-Corbacho  J,  et al.  Liquid biopsies come of age: towards implementation of circulating tumour DNA.  Nat Rev Cancer. 2017;17(4):223-238.PubMedGoogle ScholarCrossref
2.
Webb  S.  The cancer bloodhounds.  Nat Biotechnol. 2016;34(11):1090-1094.PubMedGoogle ScholarCrossref
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Schwaederle  M, Husain  H, Fanta  PT,  et al.  Use of liquid biopsies in clinical oncology: pilot experience in 168 patients.  Clin Cancer Res. 2016;22(22):5497-5505.PubMedGoogle ScholarCrossref
4.
Lanman  RB, Mortimer  SA, Zill  OA,  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.PubMedGoogle ScholarCrossref
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Leary  RJ, Sausen  M, Kinde  I,  et al.  Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.  Sci Transl Med. 2012;4(162):162ra154.PubMedGoogle ScholarCrossref
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Tannock  IF, Hickman  JA.  Limits to personalized cancer medicine.  N Engl J Med. 2016;375(13):1289-1294.PubMedGoogle ScholarCrossref
Research Letter
June 2018

Patient-Paired Sample Congruence Between 2 Commercial Liquid Biopsy Tests

Author Affiliations
  • 1The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
JAMA Oncol. 2018;4(6):868-870. doi:10.1001/jamaoncol.2017.4027

There is much interest in the potential of using cell-free DNA (cfDNA) to follow tumor evolution and response to therapy over time.1,2 Recently, targeted next-generation sequencing (NGS) of cfDNA has become the first multiplexed form of liquid biopsy to be commercially available in the clinical setting.2,3 The goal of this study was to determine the reliability and potential utility of this technology in the clinical treatment of patients with metastatic prostate cancer, investigating the congruence of reported mutations in 2 independent platforms.

Methods

From January 2017 to July 2017 samples from 40 patients with metastatic prostate cancer were collected at the same time serially via a single blood draw and shipped overnight to 2 different Clinical Laboratory Improvement Amendments (CLIA)-licensed, College of American Pathologists-accredited laboratories for cfDNA next-generation sequencing following the instructions of each vendor.

Guardant360 (Guardant Health, Inc) panel includes 73 genes with complete exon sequencing for 19 cancer genes, critical exons in 54 genes and amplifications (18 genes), fusions (6 genes), and indels (23 genes) with high clinical sensitivity rates (85% in stage III/IV solid tumors) and ultrahigh specificity (>99.9%).2,4

PlasmaSELECT (Personal Genome Diagnostics, Inc) consists of a 64-gene panel with a reported sensitivity for single-base mutations and indels of 99.4% and a per base specificity greater than 99.9%.2,5 Analytic sensitivity for indels and point mutations is reported to be down to 0.1% mutant allele fraction in Guardant360 and 0.5% in PlasmaSELECT.2,4,5

Prostate-specific antigen (PSA) baseline serum levels were determined within 30 days of the genetic test for 90% of patients, mean time from PSA blood work to the cfDNA test was 16 days (range, 0-115 days). Written informed consent was obtained in accordance with Johns Hopkins University School of Medicine institutional review board (IRB) guidelines, and this study received IRB approval.

Results

The genetic alterations determined by cfDNA testing and baseline PSA serum levels in our cohort of patients with metastatic prostate cancer are summarized in Figure 1. Participants were classified as complete congruence, 0 alterations if neither platform detected any alteration, (9/40 [22.5%]) (Figure 2).

For the study of congruence among tests, only genetic alterations in genes purportedly covered by both platforms were considered (42 genes), thus patients with 1 or more alterations demonstrated by at least 1 platform (31/40 [77.5%]) whose all cfDNA alterations were covered by only 1 of the tests were excluded (6/40 [15%]). Out of the 42 genes in the overlapping panel, a total of 25 genes had reported alterations in our cohort (60%); TP53 (n = 10), ATM (n = 6), ALK, BRCA1, and BRCA2 (n = 5) were the most common.

Exome coverage for every gene in each sequencing panel differs between platforms. Congruence among tests was assessed on confirmation of exome coverage in the counterpart platform for each alteration reported, excluding those alterations reported whose chromosomic location was not covered by the other platform.

There were 25 of 40 (62.5%) patients with alterations in the overlapping genes with confirmed coverage. Three (7.5%) of 40 patients had complete congruence with 1 or more alterations, 6 (15%) of 40 had partial congruence, and 16 (40%) of 40 had no congruence. The remaining 15 patients either did not have any reported alteration (complete congruence with 0 alterations, 9/40 [22.5%]) or were not evaluable for patient-level congruence (6/40 [15%]).

Discussion

Despite the limited sample size, our data show very low congruence for same patient-paired samples in 2 CLIA-certified commercially available tests with self-reported high accuracy, specificity, and sensitivity to specifically detect and quantify tumor-specific alterations. These data cannot determine which test is more accurate but suggest that reported gene alterations will not be the same across different platforms, raising the specter that patients could potentially receive different treatments depending on the cfDNA platform. Insufficient genetic profiling congruence could jeopardize the clinical benefit of personalized medicine.1,6

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Article Information

Corresponding Author: Gonzalo Torga, MD, Marburg 113 – Urology Department, Johns Hopkins Hospital, 600 N Wolfe St, Baltimore, MD 21287 (gtorga@jhmi.edu).

Accepted for Publication: September 14, 2017.

Published Online: December 14, 2017. doi:10.1001/jamaoncol.2017.4027

Author Contributions: Drs Torga and Pienta had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

Study concept and design: All authors.

Acquisition, analysis, or interpretation of data: All authors.

Drafting of the manuscript: All authors.

Critical revision of the manuscript for important intellectual content: All authors.

Statistical analysis: Torga.

Obtained funding: Pienta.

Administrative, technical, or material support: Pienta.

Study supervision: Pienta.

Conflict of Interest Disclosures: None reported.

References
1.
Wan  JCM, Massie  C, Garcia-Corbacho  J,  et al.  Liquid biopsies come of age: towards implementation of circulating tumour DNA.  Nat Rev Cancer. 2017;17(4):223-238.PubMedGoogle ScholarCrossref
2.
Webb  S.  The cancer bloodhounds.  Nat Biotechnol. 2016;34(11):1090-1094.PubMedGoogle ScholarCrossref
3.
Schwaederle  M, Husain  H, Fanta  PT,  et al.  Use of liquid biopsies in clinical oncology: pilot experience in 168 patients.  Clin Cancer Res. 2016;22(22):5497-5505.PubMedGoogle ScholarCrossref
4.
Lanman  RB, Mortimer  SA, Zill  OA,  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.PubMedGoogle ScholarCrossref
5.
Leary  RJ, Sausen  M, Kinde  I,  et al.  Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.  Sci Transl Med. 2012;4(162):162ra154.PubMedGoogle ScholarCrossref
6.
Tannock  IF, Hickman  JA.  Limits to personalized cancer medicine.  N Engl J Med. 2016;375(13):1289-1294.PubMedGoogle ScholarCrossref
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