{"doi":"10.1002/ctm2.1778","title":"Single‐molecule epiallelic profiling of DNA derived from routinely collected Pap specimens for noninvasive detection of ovarian cancer","abstract":"Recent advances in molecular analyses of ovarian cancer have revealed a wealth of promising tumour-specific biomarkers, including protein, DNA mutations and methylation; however, reliably detecting such alterations at satisfactorily high sensitivity and specificity through low-cost methods remains challenging, especially in early-stage diseases. Here we present PapDREAM, a new approach that enables detection of rare, ovarian-cancer-specific aberrations of DNA methylation from routinely-collected cervical Pap specimens. The PapDREAM approach employs a microfluidic platform that performs highly parallelized digital high-resolution melt to analyze locus-specific DNA methylation patterns on a molecule-by-molecule basis at or near single CpG-site resolution at a fraction (< 1/10th) of the cost of next-generation sequencing techniques. We demonstrate the feasibility of the platform by assessing intermolecular heterogeneity of DNA methylation in a panel of methylation biomarker loci using DNA derived from Pap specimens obtained from a cohort of 43 women, including 18 cases with ovarian cancer and 25 cancer-free controls. PapDREAM leverages systematic multidimensional bioinformatic analyses of locus-specific methylation heterogeneity to improve upon Pap-specimen-based detection of ovarian cancer, demonstrating a clinical sensitivity of 50% at 99% specificity in detecting ovarian cancer cases with an area under the receiver operator curve of 0.90. We then establish a logistic regression model that could be used to identify high-risk patients for subsequent clinical follow-up and monitoring. The results of this study support the utility of PapDREAM as a simple, low-cost screening method with the potential to integrate with existing clinical workflows for early detection of ovarian cancer. KEY POINTS: We present a microfluidic platform for detection and analysis of rare, heterogeneously methylated DNA within Pap specimens towards detection of ovarian cancer. The platform achieves high sensitivity (fractions <0.00005%) at a suitably low cost (∼$25) for routine screening applications. Furthermore, it provides molecule-by-molecule quantitative analysis to facilitate further study on the effect of heterogeneous methylation on cancer development.","journal":"Clinical and Translational Medicine","year":2024,"id":466068,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9604,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":689103,"name":"Yang Zhao","orcid":"0000-0002-8216-6420","position":1,"is_corresponding":false},{"id":487261,"name":"Leslie Cope","orcid":"0000-0002-4098-3289","position":2,"is_corresponding":false},{"id":226994,"name":"Chih‐Ming Ho","orcid":"0000-0001-7369-5446","position":3,"is_corresponding":false},{"id":62908,"name":"Amanda N. Fader","orcid":"0000-0003-3036-0421","position":4,"is_corresponding":false},{"id":292558,"name":"Rebecca L. Stone","orcid":"0000-0003-3590-5152","position":5,"is_corresponding":false},{"id":1298305,"name":"James S. Ferris","orcid":null,"position":6,"is_corresponding":false},{"id":402039,"name":"Anna Beavis","orcid":"0000-0001-8372-2241","position":7,"is_corresponding":false},{"id":655309,"name":"Kimberly Levinson","orcid":"0000-0002-6457-9635","position":8,"is_corresponding":false},{"id":402040,"name":"Stephanie L. Wethington","orcid":"0000-0003-1069-6112","position":9,"is_corresponding":false},{"id":39771,"name":"Tian‐Li Wang","orcid":"0000-0002-7082-449X","position":10,"is_corresponding":false},{"id":285620,"name":"Thomas R. Pisanic","orcid":"0000-0001-5796-0836","position":12,"is_corresponding":false},{"id":60420,"name":"Ie−Ming Shih","orcid":"0000-0002-1084-2071","position":13,"is_corresponding":false},{"id":246688,"name":"Tza‐Huei Wang","orcid":"0000-0002-3540-9354","position":14,"is_corresponding":false},{"id":363487,"name":"Christine M. O’Keefe","orcid":"0000-0002-7166-6972","position":0,"is_corresponding":true}],"reference_count":46,"raw_metadata":null,"created_at":"2026-07-19T02:04:54.606394Z","pmid":"39083293","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":[]}