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At least 19 recordsLinked to original sources
PubMed2026

Large-scale simulation of coverage and error rate tradeoffs for cancer detection in cell-free DNA whole-genome sequencing.

MOTIVATION: Cell-free DNA (cfDNA) whole-genome sequencing (WGS) is a promising approach for detecting cancer recurrence. It enables cancer detection by identifying all tumor-derived cfDNA (ctDNA) molecules carrying somatic single nucleotide variants (sSNVs). While ideally, a sequencing platform should be highly accurate for reliable ctDNA detection, in reality, all sequencing platforms introduce sequencing errors that generate false positives indistinguishable from true SNVs. Understanding how sequencing parameters influence ctDNA detection sensitivity at low tumor fractions (TFs) in cfDNA samples is essential for guiding sequencing strategies in clinical contexts. To model cfDNA sequencing for tumor detection, which contains asymmetric noise and multiple interacting parameters, analytical modeling is intractable, motivating large-scale parallelized simulation. RESULTS: We developed a simulation framework to generate in silico cfDNA data across 10 cancer types. In total, 480 million cfDNA samples were simulated from tumor WGS profiles. Overall, the lowest detectable TF differs substantially between cancer types under identical sequencing conditions due to variations in mutational load. For cancers with high mutational load, 3× coverage with low-error techniques reliably detects TFs below 0.1%. In contrast, cancers with low mutational load require at least six-fold higher coverage to achieve comparable detection thresholds. Increasing sequencing quality scores from Q30 to Q55 at 30× coverage further enhances sensitivity, enabling detection of TFs as low as 1 × 10-5. This study provides a comprehensive framework for optimizing sequencing parameters, offering valuable guidance for tailoring future technology development for specific cancer types and clinical applications. AVAILABILITY AND IMPLEMENTATION: The code is publicly available at https://github.com/UMCUGenetics/cfdetect/tree/main.

Whole Genome Sequencing↗
PubMed2025

Circulating microRNA panels for multi-cancer detection and gastric cancer screening: leveraging a network biology approach.

BACKGROUND: Screening tests, particularly liquid biopsy with circulating miRNAs, hold significant potential for non-invasive cancer detection before symptoms manifest. METHODS: This study aimed to identify biomarkers with high sensitivity and specificity for multiple and specific cancer screening. 972 Serum miRNA profiles were compared across thirteen cancer types and healthy individuals using weighted miRNA co-expression network analysis. To prioritize miRNAs, module membership measure and miRNA trait significance were employed. Subsequently, for specific cancer screening, gastric cancer was focused on, using a similar strategy and a further step of preservation analysis. Machine learning techniques were then applied to evaluate two distinct miRNA panels: one for multi-cancer screening and another for gastric cancer classification. RESULTS: The first panel (hsa-miR-8073, hsa-miR-614, hsa-miR-548ah-5p, hsa-miR-1258) achieved 96.1% accuracy, 96% specificity, and 98.6% sensitivity in multi-cancer screening. The second panel (hsa-miR-1228-5p, hsa-miR-1343-3p, hsa-miR-6765-5p, hsa-miR-6787-5p) showed promise in detecting gastric cancer with 87% accuracy, 90% specificity, and 89% sensitivity. CONCLUSIONS: Both panels exhibit potential for patient classification in diagnostic and prognostic applications, highlighting the significance of liquid biopsy in advancing cancer screening methodologies.

Neoplasms↗
PubMed1976

Carboxyl-labeled 11C-1-aminocyclopentanecarboxylic acid, a potential agent for cancer detection.

Carboxyl-labeled 11C-1-aminocyclopentanecarboxylic acid (11C-ACPC) has been prepared in multimillicurie amounts. The conversion of H11CN to 11C-ACPC (t1/2 = 20.4 min) was accomplished by a rapid (20-min) two-step high-temperature modification of the Bücherer-Strecker amino acid synthesis technique, which should be applicable at other accelerator installations. Purification was by ion exchange techniques. Animal studies have indicated that 11C-ACPC is a potential tumor-localizing agent for detecting cancer in humans by nuclear medicine scanning techniques.

Animals↗
PubMed1977

Preliminary report of the lung cancer detection program in New York.

The early lung cancer detection program in New York is described, and preliminary prevalence rate data are reported. Cigarette-smoking men over the age of 45, who are considered at high risk, are encouraged to enroll in the program and, to date, 6,612 have done so. These men receive PA and lateral chest x-rays annually, while a randomly selected sub-population of about half also have sputum cytology every four months. A controlled study of sputum cytology as an adjunct to the chest x-ray is now in progress. There were 15 cases of late lung cancer (pathologic stages II and III) detected at the initial examination, and 11 early cases (pathologic stages O and I). In the population of 3,387 men who had x-rays alone there were three early lung cancers detected; in the population of 3,225 men who had both examinations four early cancers were detected by x-ray and four by cytology. In addition, three cases of larynx cancer were detected by cytology. The early lung cancers detected by x-ray were peripheral and most were bronchiolar or adenocarcinoma; the early cancers detected by cytology were central epidermoid carcinoma of major bronchi. No early carcinomas were detected by both techniques. These findings suggest that a combination of chest x-rays and sputum cytology can be more effective than either one alone in detecting early lung cancer.

Age Factors↗
PubMed2026

Novel serum small extracellular vesicle miRNAs with multi-target RCA-CRISPR sensor for liver cancer detection.

BACKGROUND: Detecting liver cancer (LC) remains a significant challenge in clinical practice. Small extracellular vesicle (sEV) miRNAs show promise as non-invasive biomarkers for LC detection, yet their diagnostic potential remains largely unexplored. This study aimed to identify specific sEV miRNA signatures for LC detection and develop a novel synchronized multi-miRNA detection platform to enhance diagnostic efficiency and sensitivity. METHODS: High-throughput sequencing was conducted across four distinct cohorts: normal controls (NC), hepatitis B virus (HBV) patients, liver cirrhosis patients, and LC patients. This sequencing process identified miRNAs with differential expression, followed by RT-qPCR validation in serum sEV miRNAs from LC patients and NC. An innovative detection method, RCA-CRISPR, was introduced, combining rolling circle amplification (RCA) with CRISPR/Cas12a (RCA-CRISPR) for quick and sensitive miRNAs detection. RESULTS: Sequencing results showed a consistent elevation of hsa-miR-203b-5p, hsa-miR-4661-5p, and hsa-miR-219a-2-3p across all cohorts. RT-qPCR validations confirmed significant upregulation of these miRNAs in serum sEVs from LC patients, and the combined three-miRNA panel exhibited high diagnostic accuracy (p = 0.0003; AUC = 0.81). The RCA-CRISPR method demonstrated a detection limit of 3.12 pM for simultaneous multi-target miRNA detection, highlighting its exceptional sensitivity. CONCLUSIONS: Our study identifies hsa-miR-203b-5p, hsa-miR-4661-5p, and hsa-miR-219a-2-3p as promising sEV miRNA biomarkers for LC detection. The developed RCA-CRISPR sensor provides a robust tool for multi-miRNA analysis, potentially advancing non-invasive LC diagnostics. Future validation in larger, prospectively collected cohorts is essential to establish the clinical utility and performance of this biomarker panel and RCA-CRISPR sensor.

MicroRNAs↗
PubMed2026

Development and preliminary validation of plasma cell-free DNA methylation-based diagnostic prediction model for colorectal cancer detection.

BACKGROUND: Colorectal cancer (CRC) is a common malignancy associated with genetic and epigenetic alterations. Several methylation biomarkers have been investigated for non-invasive CRC detection; however, their reported performance varies across clinical settings, and the detection of early-stage or precancerous disease and discrimination from non-malignant colorectal conditions remain challenging. This exploratory study aimed to identify reproducible CRC-associated plasma cell-free DNA (cfDNA) methylation regions and to develop and preliminarily evaluate diagnostic prediction model for distinguishing CRC from healthy controls and benign samples. METHODS: Public CRC tissue methylation datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify reproducible CRC-associated methylation alterations. Plasma cfDNA methylation was profiled using methyl-CpG-binding-domain enrichment followed by paired-end sequencing in patients with CRC, patients with colorectal polyps, and healthy controls. After quality-control filtering, 30 CRC and healthy-control samples were randomly allocated at the participant level in a 7:3 ratio to a development set comprising 10 patients with CRC and 11 healthy controls and a held-out test set comprising 4 patients with CRC and 5 healthy controls. Hypermethylated regions were selected using least absolute shrinkage and selection operator (LASSO) logistic regression. The 12-region model was evaluated in the held-out test set and subsequently applied to 10 colorectal polyp samples without refitting or recalibration. RESULTS: Tissue methylation analysis identified reproducible CRC-associated alterations across independent datasets. In the plasma development set, 707 differentially methylated regions (DMRs) were identified between CRC and healthy-control samples, including 324 hypermethylated and 383 hypomethylated regions. LASSO regression selected a 12-region hypermethylation signature. In the held-out test set, the model achieved an area under the curve (AUC) of 0.85 [95% confidence interval (CI): 0.579-1.000]. At the development-set-derived threshold, sensitivity was 75.0% (3/4), specificity was 60.0% (3/5), and accuracy was 66.7% (6/9). When the original model was applied to colorectal polyp samples, model scores were significantly higher in both CRC and polyp samples than in healthy controls, while CRC samples showed a tendency toward higher scores than polyp samples. CONCLUSIONS: This exploratory study identified a 12-region plasma cfDNA hypermethylation signature associated with CRC and developed a LASSO-based diagnostic prediction model that showed preliminary discrimination between CRC and healthy controls in a small held-out test set. By integrating tissue methylation evidence with plasma cfDNA profiling, this study expands the repertoire of candidate region-level methylation markers for blood-based CRC detection.

Colorectal cancer (CRC)↗
PubMed2025

Discovery and performance of DNA methylation panels for cancer detection and classification in blood.

Examining DNA in a liquid biopsy for non-invasive cancer detection relies on identifying dilute signal in a high background. This study aims to identify DNA methylation biomarkers for multi-cancer detection. Utilizing large tissue datasets, we apply novel search algorithms to discover confined biomarker panels capable of distinguishing tumor from normal and determining the tissue of origin. We explore the applicability to blood-based testing using targeted methylation sequencing followed by machine learning classification. We present an 8-marker panel, which successfully predicts tumors across 14 types with a 91% average sensitivity, maintaining a low false positive rate (< 0.04%). Additionally, a panel of 39 CpG sites exhibits accuracies ranging from 69% to 98% for identifying tissue of origin. When tested on 114 patient plasma samples (colon, liver, pancreatic, prostate, and stomach cancer), the 8-marker panel obtains an AUC of 0.78 with a 78% sensitivity among 32 early-stage patients (stage I-II), and 60% overall. Using the 39-marker panel in a multi-class classification model selecting only the best match, 54% of tumor samples were on average correctly assigned to the tissue of origin, and up to 80% when allowing more inclusive criteria. Using a limited set of biomarkers, our work contributes to advancing non-invasive cancer diagnostics.

DNA methylation↗
PubMed1978

Mass screening for early breast cancer detection.

In 1969 the Center for Social Diseases of Florence started a screening program for early breast cancer detection. The female population over 40 years of age of a group of outlying towns of the District was invited. From January 1969 till March 1977, 21,725 women have been examined in the program. Mammography was the diagnostic procedure of choice, followed by physical examination if necessary. Negative cases were controlled with biennial mammography. This paper summarizes and evaluates the results of this screening program. At first mammography, 67 cancers were detected, 37% of which were clinically unapparent, 62.3% staged T1A, and 52% N--. The average stage at diagnosis is certainly better than the average stage of cancers diagnosed in unscreened women, thus a better prognosis is expected. Actuarial survival rate of detected cancers was 94 +/- 3.7% at 5 years. False negative and false positive cases are reported. The possibility of hazards in the use of repeated mammography in mass screening is discussed. According to reported data the value of this screening program in terms of secondary prevention (early diagnosis) is confirmed.

Adult↗
PubMed1977

Cancer detection in working women: a report on 7450 subjects.

A cancer detection programme for women was devised in 1964 by the writer, who attended an increasing number of work centres, mostly on an annual basis. During 12 years 7450 women were examined, some of them more than once. There were 237 abnormal Papanicolaou smears (in 112 of which the histological diagnosis was carcinoma or moderate to severe dysplasia), and 18 carcinomas of the breast. Education about cancer, teaching of breast self-examination and general counseling were also carried out. The high detection rate of cancer emphasizes the need for such services to be taken to the women at risk, and suggests that annual Papanicolaou smears are still the ideal.

Adolescent↗
PubMed2026

Non-invasive strategy for gastric cancer detection: Integration of cell-free DNA fragmentomics and protein biomarkers.

Gastric cancer (GC) ranks as the fifth most common cancer worldwide, however, accurate and non-invasive diagnostic modalities for GC remain limited. Cell-free DNA (cfDNA) fragmentomics has emerged as a promising tool for cancer cell detection. Here we develop a gastric cancer detection model, named GaFraD model. The GaFraD model uses four cfDNA fragmentomics features, including fragment size ratio (FSR), copy number variation (CNV), 9-bp end motif (Motif), and fragment size at transcription start sites (TF). This model achieves an area under the receiver-operating characteristic curve (AUC) of 0.970 (95% CI: 0.944 - 0.990), a sensitivity of 95.0% and a specificity of 80.9%. By combining the GaFraD model and conventional protein biomarkers CA19-9 and PG-I/PG-II, the CONFIRM model was generated. The CONFIRM model attained an AUC of 0.986 (95% CI: 0.966 - 1.000), a sensitivity of 95.0% and a specificity of 95.6% in detecting GC. Moreover, the CONFIRM model achieved remarkable performance (AUC&#x202f;=&#x202f;0.983, sensitivity 95.6%, specificity 94.2%) in distinguishing patients with early-stage GC from controls. Our work showed the high discriminatory power in distinguishing GC patients from controls, indicating the clinical potential of using cfDNA fragmentomics combined with protein biomarkers for non-invasive GC detection. The results of the study provide a new avenue for early, accurate, and non-invasive clinical diagnosis of GC.

Cell-free DNA↗
PubMed1977

The pathology of breast cancer detected by mass population screening.

Breast cancer was detected in 156 of 17,526 asymptomatic women, (8.9/1000), aged 45-64 years, screened by mammography, thermography, and physical examination, Twenty-six percent of 149 pathologically reviewed cases metastasized to axillary nodes. Thirty-six percent of tumors were in situ, minimally invasive, or low grade tubular carcinomas, none of which metastasized. Increased rates of detection were shown for intraductal and tubular types. Frankly invasive ductal and lobular carcinomas had a mean diameter of 2.3 cm., 46% of which had axillary lymph node metastases. Seventy-percent of these were to only one to three nodes, however. Multicentricity with intraductal and lobular carcinoma in situ was frequently observed. Metastatic potential was related to tumor size, degree of stromal invasion, lymphatic permeation, and histologic grade. Few histological parameters other than size could be considered favorable. Forty-two percent of tumors were not palpable, the majority being in situ, minimally invasive, and tubular types. Only five nonpalpable invasive carcinomas metastasized. While the initial results of mass screening appear favorable, prolonged follow-up is needed to determine its impact on the population at risk.

Adult↗
PubMed1976

Interim report: mammographic exposures at the breast cancer detection demonstration project screening centers.

In the interests of uniformly high radiological physics standards at ACS-NCI Breast Cancer Detection Demonstration Projects, measurements were made at 29 breast cancer screening clinics. These measurements were made throughout the country with equipment calibrated with standards traceable to National Bureau of Standards. Histograms which indicate the frequency distribution of exposures to the surface of a 6 cm breast for various machine/receptor combinations were prepared.

Breast Neoplasms↗
PubMed1977

[The value of sputum cytodiagnosis as a screening method for lung cancer detection--results of a study (author's transl)].

In the course of a screening program for lung cancer detection which has been going on for several years, 2432 male risk persons, aged 42-67, were examined cytologically in 1974 and 1975. The annual rate of incidence of lung cancer in this population is unknown. We estimate it at 3-4%. From two sputa of each patient we screened one specimen. 24.7% of the sputa were unsatisfactory. In the remaining preparations there were neither tumor cells nor cells suspicious for cancer. This result is discussed in view of the experiences of other authors, that the sensitivity of cytological screening for lung cancer is 33-38%. Recommendations are given for increasing the number of detected cases.

Adult↗
PubMed1978

The primary-care physician and cancer detection: the role of the Pap smear.

This is a retrospective 5 year study of cancer detection in the suburban office of a primary-care physician. There were 127 diagnoses of malignancy confirmed in 5,011 patients, 62 in the reproductive system and 62 in other organ systems. More than 9,000 Pap smears resulted in the final diagnosis of carcinoma of the cervix in only seven patients. 374 curettages yielded 37 cases of endometrial carcinoma. All of these patients had Class I Pap smears preoperatively.

Adult↗
PubMed2025

Enhancing the sensitivity of non-invasive cervical cancer detection using CpG methylation haplotype profiling.

DNA methylation is a critical epigenetic modification that regulates gene expression and plays a significant role in cancer development. This methylation signature can be detected in cancer-derived DNA from non-invasive samples, such as plasma, urine or Pap smears. However, in early-stage cancers-when detection is most critical-the concentration of cancer DNA is often low, limiting the sensitivity of current detection methods. Traditional DNA methylation detection techniques, which rely on methylation ratio-based measurements, may obscure subtle variations in methylation patterns, further reducing detection sensitivity. In this study, we analyzed cervical scraping specimens and examined whether detecting cancer-specific methylation patterns in cervical cancer could be enhanced using a Highly Methylated Haplotype (HMH) approach. This novel approach captures highly methylated haplotypes at single-molecule resolution using next-generation sequencing, providing greater detail than conventional methods. HMHs in specific DNA regions are a hallmark of cancer and stand out in contrast to sporadic methylation commonly observed in non-cancerous tissues. We applied HMH profiling to a gene panel of four biomarkers (CA10, DPP10, FMN2, and HAS1) previously validated in cervical cancer studies. At pre-specified cutoffs (99th percentile of normals), haplotype-based scoring achieved 89.9% sensitivity for invasive cancer at high specificity (~&#x2009;94-98%), outperforming median (78.0%) and single-CpG (71.6%) methods. For clinically relevant endpoints, the combined panel detected 51-52% of CIN2&#x2009;+&#x2009;and 66-67% of CIN3&#x2009;+&#x2009;cases, again exceeding the performance of median- and single-CpG-based scoring methods.These findings demonstrate the potential of HMH to substantially enhance sensitivity in cervical cancer detection, offering a promising approach for non-invasive diagnostics.

Humans↗