Clinical Research Directory

Predictive Biomarkers for Precision Management of Pre-cancerous Cervical Neoplasia

The goal of this observational study (retrospective cohort study) is to determine whether DNA methylation status in archived cervical cytology samples can predict regression, persistence, or progression of high-grade cervical dysplasia (HSIL/CIN2-3) in women who have previously undergone clinical management and follow-up. The main questions it aims to answer are: Can methylation status in archived cervical cytology samples predict histologic regression of HSIL (CIN2/3)? Does the addition of clinical factors, screening history, smoking status, and HPV genotype improve the predictive ability of methylation markers for disease regression, persistence, or progression? Researchers will compare: Women whose lesions regressed with women whose lesions persisted or progressed. Methylation-positive and methylation-negative samples to assess whether methylation status is associated with subsequent clinical outcomes. Participants will: Be identified retrospectively from women aged 23 to 70 years who were previously diagnosed with HSIL/CIN2-3 and managed according to routine clinical practice. Have archived cervical cytology samples retrieved from biobanks for DNA methylation analysis. Contribute existing clinical, cytological, histological, and HPV data collected during routine care. Contribute existing follow-up data from medical records, including outcomes such as regression, persistence, progression, and treatment results. No additional interventions, testing, or follow-up visits will be performed as part of the study; all analyses will be based on retrospectively collected biological samples and clinical data.

Cervical Cytology DNA Methylation for Endometrial Cancer Screening

This study intends to conduct the "Real-world Study on Cervical Cytology Methylation Testing for Endometrial Cancer Screening" project through a multi-center real-world research approach. Led by Peking Union Medical College Hospital, at least 10 institutions will participate in the study. The goal is to complete the enrollment of at least 30 million real-world samples. Focusing on the changes in DNA methylation levels in cervical exfoliated cells as the research entry point, this study aims to provide new ideas and theoretical basis for preventing and treating endometrial cancer by targeting the CDO1/CELF4 double gene methylation. The expectation is to achieve the clinical application of a more optimal endometrial cancer screening protocol, improve the current shortcomings of endometrial cancer screening, make endometrial cancer screening more accurate, effectively reduce the incidence of endometrial cancer, and avoid excessive medical treatment.

Predicting Early Tumor Recurrence in Patients With Esophageal Squamous Cell Carcinoma

The prognosis of patients with esophageal squamous cell carcinoma (ESCC) who develop post-operative early tumor recurrence is often relatively poor. Therefore, biomarker that can detect micro metastases before the start of treatment is required. Epigenomic alterations such as DNA methylation have attracted attention as promising biomarkers. The investigators aim to predict early recurrence based on whole genome DNA methylation analysis of esophageal cancer.

Predicting Postoperative Chemotherapy Efficacy in Patients With Esophageal Squamous Cell Carcinoma

Esophageal cancer remains a disease with a poor prognosis. Chemotherapy is an important part of its treatment, but there are cases in which chemotherapy is ineffective. The investigators aim to develop a model to predict the response to chemotherapy by DNA methylation of preoperative biopsy specimens to identify the chemotherapy ineffective group.

Epigenetic Signature for CRC Early Detection

The epiCED is a noninvasive blood-based assay designed for early detection of colorectal cancer (CRC) using circulating cell-free DNA (cfDNA) 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) epigenetic markers. This study leverages retrospective, multi-center cohorts of CRC patients and non-cancer controls to discover and validate a robust cfDNA methylation signature. Small-scale sequencing and machine learning-based modeling will be applied to identify a minimal panel of methylation markers that can accurately discriminate CRC from non-cancer individuals, including early-stage disease. The ultimate goal is to develop a clinically practical, noninvasive screening tool that enables population-level early detection and improves patient outcomes.

Methylated Biomarkers of Smoking as a Selection Tool in Participants for Lung Cancer Screening

The MET-SELS study aims to revolutionize how we identify individuals for lung cancer screening by moving beyond the limitations of self-reported smoking history. Currently, eligibility for low-dose CT (LDCT) scans relies on "pack-years"-a metric often compromised by recall bias, under-reporting, and an inability to account for the biological nuances of smoke inhalation or environmental exposure. Consequently, current criteria miss nearly half of incidental lung cancers. To bridge this gap, the study investigates DNA methylation as a stable, objective "biological footprint" of smoking. Unlike short-term biomarkers like nicotine or CO levels, specific epigenetic changes in genes such as AHRR and F2RL3 persist long after cessation and correlate accurately with cumulative tobacco exposure. Led by Professor Dr. Annemiek Snoeckx and a multidisciplinary team at UZA and the Centre for Medical Genetics, the research will analyze saliva samples from two groups: roughly 900 participants from the ZORALCS screening trial and 150 volunteers. By comparing saliva-derived genomic signatures against both self-reported data and professional interviews, the team aims to validate a panel of methylation markers that can pinpoint high-risk individuals with far greater precision. The ultimate vision for MET-SELS is to implement a population-based "saliva-first" triage system, similar to the FIT test used for colorectal cancer. In this model, high-risk candidates would provide a saliva sample at home; only those with a confirmed epigenetic risk profile would be invited for a LDCT scan, significantly increasing the yield of early-stage lung cancer detection while streamlining healthcare resources.

Epigenetic Biomarkers in the Saliva for the Diagnosis of Squamous Cells Carcinoma of the Oral Cavity

Head and neck squamous cell carcinoma (HNSCC) are malignant tumors originating from the epithelial mucosa of the upper aerodigestive tract. The oral cavity is the most frequent location of HNSCC (oral squamous cell carcinoma: OSCC). Tobacco use and alcohol consumption are the greatest risk factors. The Hauts de France region has one of the highest incidence rates of OSCC. The overall survival of patients with OSCC remains low, with a 5-year overall survival rate of around 60%. In addition to the oncological prognosis, OSCCs and their treatment have a significant impact on the quality of life of patients. An early diagnosis of OSCC is recommended, but it remains difficult. It can be for example challenging to diagnose OSCC in a context of oral premalignant lesions. Identifying objective biomarkers of malignancy would be an advantage and would allow better progress in the field of precision medicine and surgery for these tumors. The investigators propose to establish the diagnostic use of an optimized DNA methylation profile detected in the saliva of OSCC patients by comparing these epigenetic marks before and after tumor resection. The investigators will construct a consolidated signature of 4 genes whose DNA is subject to methylation and gene expression is restricted to cancer cells, by crossing TCGA analysis with single-cell analysis (single-cell RNA sequencing). The investigators propose to analyse DNA methylation of the corresponding genes in the saliva of n=30 OSCC patients recruited for primary surgical resection in the Department of Maxillofacial Surgery vs controls. In addition, the investigators will examine the methylation profiles before / after complete excisional surgery of OSCC. This pilot study will aim to validate the analysis of DNA methylation markers in saliva of OSCC, with the aim of improving the diagnostic precision of OSCC and, secondly, to compare these markers before and after treatment by primary surgery.

PaCIFiC-CUP Classifies Cancer of Unknown Primary

This study aims to initially utilize machine learning on pan-cancer DNA methylation data from public databases to construct a DNA methylation classification model (PaCIFiC-CUP, pan-cancer integrated fingerprinting classifier of CUP) for diagnosing various types of cancer, particularly the primary site of cancer of unknown primary. The goal is to achieve diagnosis of cancer pathology type by analyzing the DNA methylation patterns of cancer specimens, thereby guiding subsequent precision treatment for cancer.

Cervical Cytology DNA Methylation for Endometrial Lesion Screening and Follow-up

The goal of this observational study is to evaluate the accuracy of a novel molecular test for screening and monitoring endometrial lesions in women at medium-to-high risk for endometrial cancer. The main questions it aims to answer are: * What is the sensitivity and specificity of the CISENDO test (a DNA methylation test on cervical cytology samples) for detecting histologically confirmed endometrial intraepithelial neoplasia (EIN) or invasive endometrial cancer? * How do DNA methylation levels change during the follow-up of endometrial lesions? Researchers will compare the results of the CISENDO test to the results from the standard diagnostic procedure (hysteroscopy with histology) to see if the molecular test can reliably identify high-risk lesions and track disease progression. Participants will: * Provide a residual liquid-based cervical cytology sample for the CISENDO test. * Undergo a standard diagnostic hysteroscopy examination (with or without biopsy) for comparison. * Some participants will return for follow-up visits at 6 and 12 months for repeat methylation testing and/or hysteroscopy to monitor their condition.

Construction of Molecular Diagnostic Marker Model for Pancreatic Cystic Tumors Based on Pancreatic Cystic Fluid Samples

The goal of this observational study is to test in patients with cystic tumor of pancreas. The main questions it aims to answer are: Screening of molecular diagnostic markers for pancreatic cystic tumors by cfDNA methylation sequencing of pancreatic cystic fluid and proteomic assays to distinguish benign from malignant and mucinous/non-mucinous, correlate with pathological features, and find molecular features associated with the degree of malignancy. Participants will Provide post-operative cyst fluid specimens.

Cervical Cytology DNA Methylation for Cervical Cancer Screening

Cervical cancer represents one of the foremost causes of cancer-related morbidity and mortality among women worldwide. Given the current limitations, such as the low specificity of human papillomavirus (HPV) testing and the relatively low sensitivity of cytological examinations, there is a pressing need for a novel, non-invasive, safe, and precise screening method. This study aims to undertake a multicentre, real-world investigation, incorporating at least 10 sub-centres and enrolling 30,000 participants. Histopathological examination results will serve as the 'gold standard' for evaluating the screening efficacy of human PAX1 and JAM3 gene methylation assays (PAX1m/JAM3m), HPV testing, and cytological examinations. Furthermore, the study seeks to elucidate the relationship between DNA methylation levels and persistent HPV infection, while also assessing the applicability of PAX1m/JAM3m across diverse clinical settings. By focusing on alterations in DNA methylation levels within cervical exfoliated cells as the primary research trajectory, this study aspires to furnish novel insights and theoretical foundations for the prevention and management of cervical cancer, targeting PAX1m/JAM3m. The ultimate objective is to facilitate the clinical implementation of an enhanced cervical cancer screening protocol, thereby addressing the deficiencies of current screening methodologies, achieving greater precision in cervical cancer screening, and effectively reducing the incidence of cervical cancer while mitigating the risks of overdiagnosis and overtreatment.

Methylation, mIcrobiome, NUtritional sTatus, and dEvelopment of Stunted Children

The investigators will conduct a case-control study among under-two children in Lombok Timur, West Nusa Tenggara, Indonesia. The power required to detect changes in epigenetic markers may not be sufficient in the cohort study. Therefore, specific case-control design of stunted vs non-stunted children will provide the required power to detect potential epigenetic markers which will be further investigated through targeted sequencing of the cohort study. A total of 150 stunted children will be recruited and then it will be matched with 150 non-stunted children with the same sex. The assessments for these study subjects will include: 1) The genetic and epigenetic profile of the children, gut microbiota and nutritional status (Physical component), 2) Food security, Water, Sanitation and Hygiene (WASH) and Infant and Young Child Feeding (IYCF) practices (Home-Food component), 3) Children's psychosocial care and cognitive outcome (Cognition component).