{"doi":"10.18632/oncotarget.28719","title":"Analytical validation of a circulating tumor DNA assay using PhasED-Seq technology for detecting residual disease in B-cell malignancies","abstract":null,"journal":"Oncotarget","year":2025,"id":612024,"datarank":0.4398551277900191,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.09446736384091221,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.09446736384091221,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":4,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1575608,"name":"Sandra Close","orcid":null,"position":1,"is_corresponding":false},{"id":252125,"name":"David M. Kurtz","orcid":"0000-0002-6382-4651","position":2,"is_corresponding":false},{"id":1575610,"name":"Richard D. Hockett","orcid":null,"position":3,"is_corresponding":false},{"id":1575611,"name":"Laura Hyland","orcid":null,"position":4,"is_corresponding":false},{"id":1575606,"name":"Nina Klimova","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Analytical validation of a circulating tumor DNA assay using PhasED-Seq technology for detecting residual disease in B-cell malignancies","abstract":"// Nina Klimova 1 , Sandra Close 1 , David M. Kurtz 1 , Richard D. Hockett 1 and Laura Hyland 1 1 Foresight Diagnostics, Boulder, CO 80301, USA Correspondence to: Laura Hyland, email: laura.hyland@foresight-dx.com Keywords: MRD; ctDNA; PhasED-Seq; CLARITY; residual disease Received: January 13, 2025     Accepted: April 28, 2025     Published: May 09, 2025 Copyright: © 2025 Klimova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Background: Circulating tumor DNA (ctDNA) can be used as a tool to detect minimal residual disease (MRD) which can provide important prognostic information in diffuse large B-cell lymphomas (DLBCL). Here, we present an ultra-sensitive MRD assay reliant on Phased Variant Enrichment and Detection Sequencing (PhasED-Seq), which leverages phased variants to detect ctDNA. Methods: Blank plasma samples were used to assess assay specificity and a limiting dilution series with a DLBCL clinical-contrived sample was performed to assess assay sensitivity and precision. DLBCL plasma patient samples with MRD comparator assay results were tested with PhasED-Seq technology to assess assay accuracy. Results: The assay’s false positive rate was 0.24% and the background error rate was 1.95E-08. The limit of detection at 95% detection rate with 120 ng of input DNA was 0.7 parts in 1,000,000 and precision was >96%. Positive percent agreement for the MRD assay was 90.62% (95% CI 74.98%, 98.02%) and negative percent agreement was 77.78% (95% CI 52.73, 93.59) using a single nucleotide variant-based method as reference. Conclusions: The PhasED-Seq-based MRD assay has strong analytical and clinical performance in B-cell malignancies. Improved ctDNA detection methods such as this may improve patient outcomes through detection of residual disease or early relapse.","is_dataset_classified":null,"base_score":2.302585092994046,"endowment":2.302585092994046,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40353795","pmcid":"PMC12068320","openalex_id":"https://openalex.org/W4410251487","authors":[],"funders":[],"total_grants":0,"fwci":4.0919,"citation_percentile":0.94712061,"influential_citations":0,"citation_trend":[{"year":2025,"count":6},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.oncotarget.com/article/28719/pdf/","host_type":"journal"},{"url":"https://www.oncotarget.com/article/28719/pdf/","host_type":"publisher"},{"url":"https://www.oncotarget.com/lookup/doi/10.18632/oncotarget.28719","host_type":"publisher"},{"url":"https://doi.org/10.18632/oncotarget.28719","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40353795","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12068320","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC12068320","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC12068320?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Cancer Genomics and Diagnostics","Lymphoma Diagnosis and Treatment","Lung Cancer Treatments and Mutations"],"mesh_terms":["Circulating Tumor DNA","Humans","Sensitivity and Specificity","Biomarkers, Tumor","Reproducibility of Results","Lymphoma, Large B-Cell, Diffuse","Neoplasm, Residual","High-Throughput Nucleotide Sequencing"],"keywords":["Minimal residual disease","Medicine","Cancer research","Disease","Circulating tumor DNA","Computational biology","Oncology","Cancer","Immunology","Biology","Pathology","Internal medicine","Leukemia","Clarity","ctDNA","Residual Disease","Mrd","Phased-seq"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T01:01:23.359762Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}