Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Mar 14:15:200-218.
doi: 10.18632/oncotarget.28565.

Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay

Josette Northcott  1 , Gabor Bartha  1 , Jason Harris  1 , Conan Li  1 , Fabio C P Navarro  1 , Rachel Marty Pyke  1 , Manqing Hong  1 , Qi Zhang  1 , Shuyuan Ma  1 , Tina X Chen  1 , Janet Lai  1 , Nitin Udar  1 , Juan-Sebastian Saldivar  1 , Erin Ayash  1 , Joshua Anderson  1 , Jiang Li  1 , Tiange Cui  1 , Tu Le  1 , Ruthie Chow  1 , Randy Jerel Velasco  1 , Chris Mallo  1 , Rose Santiago  1 , Robert C Bruce  1 , Laurie J Goodman  1 , Yi Chen  1 , Dan Norton  1 , Richard O Chen  1   2 , John M Lyle  1   2
Affiliations

Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay

Josette Northcott et al. Oncotarget. .

Abstract

We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.

Keywords: analytical validation; circulating tumor DNA; molecular residual disease; tumor-informed assay; whole genome sequencing.

PubMed Disclaimer

Conflict of interest statement

CONFLICTS OF INTEREST

All authors have or had a financial relationship as employees of Personalis, Inc.

Figures

Figure 1
Figure 1. The NeXT Personal tumor-informed ctDNA detection process.
Figure 2
Figure 2. Measured ctDNA signal reported on NeXT Personal as a function of known ctDNA concentration.
The solid line is the identity line (y = x).
Figure 3
Figure 3. Measured ctDNA signal versus target ctDNA concentration (PPM), showing the linearity of the NeXT Personal assay.
Figure 4
Figure 4. The plot of measured ctDNA concentration versus expected (target) concentration is shown for the contrived cell line and two clinical samples.
The 95th percentile confidence intervals for the samples are shown as matching colored lines.
Figure 5
Figure 5
(A) Number of raw, unfiltered somatic variants detected by WGS. (B) Number of somatic variant targets per panel.
Figure 6
Figure 6
(A) Age distribution of donor normal samples used in specificity studies. (B) Self-reported demographics of donor normal samples used in specificity studies.
Figure 7
Figure 7. Normalized mean ctDNA signal for 5 cancer samples and 3 contrived samples at various cfDNA input quantities.
Points represent the mean of replicates normalized to the 15 ng input level.
Figure 8
Figure 8. Major analytical performance measurements of the NeXT Personal assay.
See this image and copyright information in PMC

References

    1. Ococks E, Frankell AM, Masque Soler N, Grehan N, Northrop A, Coles H, Redmond AM, Devonshire G, Weaver JMJ, Hughes C, Lehovsky K, Blasko A, Nutzinger B, et al.. Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling. Ann Oncol. 2021; 32:522–32. 10.1016/j.annonc.2020.12.010. - DOI - PubMed
    1. Wan JCM, Mughal TI, Razavi P, Dawson SJ, Moss EL, Govindan R, Tan IB, Yap YS, Robinson WA, Morris CD, Besse B, Bardelli A, Tie J, et al.. Liquid biopsies for residual disease and recurrence. Med. 2021; 2:1292–313. 10.1016/j.medj.2021.11.001. - DOI - PubMed
    1. Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, et al.. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discov. 2017; 7:1394–403. 10.1158/2159-8290.CD-17-0716. - DOI - PMC - PubMed
    1. Larribère L, Martens UM. Advantages and Challenges of Using ctDNA NGS to Assess the Presence of Minimal Residual Disease (MRD) in Solid Tumors. Cancers (Basel). 2021; 13:5698. 10.3390/cancers13225698. - DOI - PMC - PubMed
    1. Coombes RC, Page K, Salari R, Hastings RK, Armstrong A, Ahmed S, Ali S, Cleator S, Kenny L, Stebbing J, Rutherford M, Sethi H, Boydell A, et al.. Personalized Detection of Circulating Tumor DNA Antedates Breast Cancer Metastatic Recurrence. Clin Cancer Res. 2019; 25:4255–63. 10.1158/1078-0432.CCR-18-3663. - DOI - PubMed