Development of a clinical-grade ultrasensitive droplet digital PCR test for monitoring of relevant ESR1 variants by liquid biopsy
- 1Biodesix, Inc., 919 W. Dillon Rd, Louisville, CO, 80027, USA
- 2Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
Abstract
Breast cancer is the second most prevalent cancer-type globally. The current standard of care for hormone receptor-positive (HR+), human epidermal growth factor 2-negative (HER2-) advanced breast cancer (ABC) is endocrine therapy (ET) plus cyclin-dependent kinase 4/6 inhibitor (CDK4/6i). Most ABC patients receiving ET + CDK4/6i eventually develop resistance, leading to disease progression. In approximately 20-40% of HR + cases, resistance is driven by acquired activating mutations in the ligand binding domain (LBD) of the estrogen receptor gene (ESR1). The next-generation oral selective estrogen receptor degraders (SERDs) comprise an advanced class of ETs intended for use in ER+/HER2- ABC with ESR1 mutation(s) that has progressed on prior ET. We have developed and validated a New York State Clinical Laboratory Evaluation Program (CLEP)-approved laboratory developed test (LDT) for detection of clinically relevant, and the most prevalent ESR1 LBD mutations in ABC. The LDT uses advanced multiplexing on the QX600 ddPCR system to identify the presence of ESR1 E380Q, V422del, S463P, L536 H/P/R, Y537C/D/N/S, and D538G in plasma. Our test was clinically validated for accuracy and found to be 100% concordant when compared to two NGS reference tests (11/11 eligible ESR1 variants and 18/18 ESR1 WT samples were correctly called). One variant was detected by the ddPCR test at 0.01% VAF that was not present in the reference dataset, likely due to sample input differences between our test and the reference. Analytic specificity was 100%, and the 95% analytic limit of detection (LoD95) was as low as 0.065% VAF. The Limit of Blank (LOB) was 0 - 3.4 copies depending on the assay. These findings support the use of our multiplexed ddPCR test as a rapid, sensitive, and scalable liquid biopsy approach for identifying emerging ESR1 mutations and may inform endocrine therapy selection in the treatment of HR+/HER2− advanced breast cancer.
Related
- ACE2 Polymorphisms rs2285666 and rs147311723 Are Clinically Relevant Variants in SARS-CoV-2 and Mycobacterium tuberculosis Co-infection.
- Clinical deep sequencing to diagnose pathogenic mosaic variants in malformations of cortical development and epilepsy
- Diagnostic Yield of Expanded Multigene Testing in Hereditary Polyposis Syndromes: Functional Characterization of Clinically Relevant Variants
- Textile-Integrated Electrochemical Sensing Approaches for Monitoring Wound-Relevant Biochemical Markers.
- Unplanned Inpatient Admission After Intended Outpatient Total Extraperitoneal Inguinal Hernia Repair: Precautionary Monitoring or Clinically Relevant Morbidity?
BibTeX
@article{jackson2026development,
title = {{Development of a clinical-grade ultrasensitive droplet digital PCR test for monitoring of relevant ESR1 variants by liquid biopsy}},
author = {Leisa P. Jackson and Ethan Barnett and Helen Halpin and Brittany D'Alessio and Emma Longshore and Kristen A. Eller and Kathleen Szuhany and Tatiana Erazo and Gary A. Pestano and Pedram Razavi},
journal = {The Journal of Liquid Biopsy},
year = {2026},
month = oct,
doi = {10.1016/j.jlb.2026.100675},
url = {https://doi.org/10.1016/j.jlb.2026.100675},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Development of a clinical-grade ultrasensitive droplet digital PCR test for monitoring of relevant ESR1 variants by liquid biopsy
AU - Leisa P. Jackson
AU - Ethan Barnett
AU - Helen Halpin
AU - Brittany D'Alessio
AU - Emma Longshore
AU - Kristen A. Eller
AU - Kathleen Szuhany
AU - Tatiana Erazo
AU - Gary A. Pestano
AU - Pedram Razavi
PY - 2026
DA - 2026/10/13
JO - The Journal of Liquid Biopsy
DO - 10.1016/j.jlb.2026.100675
UR - https://doi.org/10.1016/j.jlb.2026.100675
AB - Breast cancer is the second most prevalent cancer-type globally. The current standard of care for hormone receptor-positive (HR+), human epidermal growth factor 2-negative (HER2-) advanced breast cancer (ABC) is endocrine therapy (ET) plus cyclin-dependent kinase 4/6 inhibitor (CDK4/6i). Most ABC patients receiving ET + CDK4/6i eventually develop resistance, leading to disease progression. In approximately 20-40% of HR + cases, resistance is driven by acquired activating mutations in the ligand binding domain (LBD) of the estrogen receptor gene (ESR1). The next-generation oral selective estrogen receptor degraders (SERDs) comprise an advanced class of ETs intended for use in ER+/HER2- ABC with ESR1 mutation(s) that has progressed on prior ET. We have developed and validated a New York State Clinical Laboratory Evaluation Program (CLEP)-approved laboratory developed test (LDT) for detection of clinically relevant, and the most prevalent ESR1 LBD mutations in ABC. The LDT uses advanced multiplexing on the QX600 ddPCR system to identify the presence of ESR1 E380Q, V422del, S463P, L536 H/P/R, Y537C/D/N/S, and D538G in plasma. Our test was clinically validated for accuracy and found to be 100% concordant when compared to two NGS reference tests (11/11 eligible ESR1 variants and 18/18 ESR1 WT samples were correctly called). One variant was detected by the ddPCR test at 0.01% VAF that was not present in the reference dataset, likely due to sample input differences between our test and the reference. Analytic specificity was 100%, and the 95% analytic limit of detection (LoD95) was as low as 0.065% VAF. The Limit of Blank (LOB) was 0 - 3.4 copies depending on the assay. These findings support the use of our multiplexed ddPCR test as a rapid, sensitive, and scalable liquid biopsy approach for identifying emerging ESR1 mutations and may inform endocrine therapy selection in the treatment of HR+/HER2− advanced breast cancer.
SN - 2950-1954
ER -