Nicholas A. Vulpescu
A5014714898- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Molecular Biology Techniques and Applications
- Genetic Associations and Epidemiology
- Liver Disease Diagnosis and Treatment
- Hepatocellular Carcinoma Treatment and Prognosis
- Genomics and Chromatin Dynamics
- Ovarian cancer diagnosis and treatment
- RNA Research and Splicing
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- Bone Metabolism and Diseases
- Pancreatic and Hepatic Oncology Research
- Cancer Cells and Metastasis
- Cholangiocarcinoma and Gallbladder Cancer Studies
- MicroRNA in disease regulation
- Colorectal Cancer Treatments and Studies
- Epigenetics and DNA Methylation
- Cancer Immunotherapy and Biomarkers
Sidney Kimmel Comprehensive Cancer Center
2022-2025
Johns Hopkins University
2022-2025
University of Baltimore
2024-2025
Johns Hopkins Medicine
2025
Johns Hopkins Hospital
2024
Sidney Kimmel Cancer Center
2024
Institute for Systems Biology
2020-2022
New York University
2020-2021
NYU Langone Health
2018-2019
Abstract Liver cancer is a major cause of mortality worldwide. Screening individuals at high risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved survival, but current screening methods are inadequate. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome analyses to evaluate 724 from the United States, European Union, or Hong Kong hepatocellular carcinoma (HCC) who were average high-risk HCC. Using machine learning model that incorporated...
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics an outbreak. Viral genome sequencing has emerged as powerful approach link seemingly unrelated cases, large-scale surveillance can inform on critical epidemiological parameters. Here, we report analysis 864 SARS-CoV-2 sequences from cases in New York City metropolitan area during COVID-19 outbreak spring 2020. The majority had no recent travel history or known exposure, genetically linked were...
Abstract Ovarian cancer is a leading cause of death for women worldwide, in part due to ineffective screening methods. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker [cancer antigen 125 (CA-125) human epididymis 4 (HE4)] analyses evaluate 591 with ovarian cancer, benign adnexal masses, or without lesions. Using machine learning model the combined features, detected specificity >99% sensitivities 72%, 69%, 87%, 100% stages I IV,...
Abstract Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics an outbreak. Viral genome sequencing has emerged as powerful approach link seemingly unrelated cases, large-scale surveillance can inform on critical epidemiological parameters. Here, we report analysis 864 SARS-CoV-2 sequences from cases in New York City metropolitan area during COVID-19 outbreak Spring 2020. The majority had no recent travel history or known exposure, genetically...
<p>Supplementary Figure S1. Evaluation of screening model DELFI-Pro scores and comorbidities in individuals without cancer. Supplementary S2. score evaluation available clinical characteristics patients with S3. Stability analysis across fold repeats collection source. S4. Detection ovarian cancer subtypes using model. S5. ROC analyses asymptomatic the or diagnostic models Discovery Cohort. S6. Performance ichorCNA median cfDNA fragment lengths Cohorts. S7. at high specificity. S8....
<div>Abstract<p>Ovarian cancer is a leading cause of death for women worldwide, in part due to ineffective screening methods. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome and protein biomarker [cancer antigen 125 (CA-125) human epididymis 4 (HE4)] analyses evaluate 591 with ovarian cancer, benign adnexal masses, or without lesions. Using machine learning model the combined features, detected specificity >99% sensitivities 72%, 69%, 87%, 100% stages I...
Abstract Introduction: The stepwise progression of colorectal cancer (CRC) from healthy epithelium, to premalignant adenoma, is accompanied by genome-wide epigenetic reprogramming which may be reflected in circulating cell-free DNA (cfDNA). However, current analyses these processes have been hampered the complex mixture cells associated with colonic epithelial tissue, as well absence suitable adenoma model systems. Cultured organoids, comprised pure cells, could enable insights into changes...
Introduction: 80% of adults in the US have metabolic risk factors for Liver Cirrhosis (LCr), but LCr diagnosis is challenging. Elastography and blood-based fibrosis indices limited performance, biopsies are invasive. The lifetime hepatocellular carcinoma (HCC) individuals with ∼30%, yet &lt;20% undergo any HCC surveillance. We previously demonstrated that genome-wide cell-free DNA (cfDNA) fragmentomes can detect blood. Here, we expand these approaches to pre-neoplasia, detection...
Abstract Diagnostic delays in patients with brain cancer are common and can impact patient outcome. Development of a blood-based assay for detection cancers could accelerate diagnosis. In this study, we analyzed genome-wide cell-free (cfDNA) fragmentomes, including fragmentation profiles repeat landscapes, from the plasma individuals (n=148) or without (n=357) cancer. Machine learning analyses cfDNA fragmentome features detected across all grade gliomas (AUC=0.90, 95% CI: 0.87-0.93) these...
Abstract Drug development and biological discovery require effective strategies to map existing genetic associations causal genes. To approach this problem, we began by identifying a set of positive control genes for 12 common diseases traits that cause Mendelian form the disease or are target medicine used treatment. We then identified widely-available genomic features enriching GWAS-associated single nucleotide variants (SNVs) these Using features, trained validated Effector Index ( Ei ),...
Abstract Osteoporosis is a common debilitating chronic disease diagnosed primarily using bone mineral density (BMD). We undertook comprehensive assessment of human genetic determinants in 426,824 individuals, identifying total 518 genome-wide significant loci, (301 novel), explaining 20% the variance BMD—as estimated by heel quantitative ultrasound (eBMD). Next, meta-analysis identified 13 fracture loci ~1.2M which were also associated with BMD. then target genes from cell-specific genomic...
Abstract Drug development and biological discovery require effective strategies to map existing genetic associations causal genes. To approach this problem, we selected 12 common diseases quantitative traits for which highly powered genome-wide association studies (GWAS) were available. For each disease or trait, systematically curated positive control gene sets from Mendelian forms of the targets medicines used treatment. We found that these genes enriched in proximity GWAS-associated...
Abstract Introduction: Pancreatic cancer has a poor prognosis especially when identified at advanced stages. Globally in 2020, &gt;450,000 people died from the disease. For those with locally or metastatic cancer, standard of care treatment is chemotherapy. Preliminary studies show that some patients advanced-stage disease respond to immune checkpoint blockade treatment. Determining response therapy using imaging techniques can be challenging. There clinical unmet need for noninvasive...
Abstract Introduction: The stepwise progression of colorectal cancer from healthy epithelium, to premalignant adenoma, is accompanied by genome-wide epigenetic reprogramming. However, current analyses these processes have been hampered complex mixtures cells in normal, adenoma and tissue samples, as well absence suitable model systems. Cultured organoids, comprised pure epithelial cells, could enable insights on the changes leading cancer. Methods: Using 43 patient-derived organoids derived...
Abstract Determining response to therapy for patients with pancreatic cancer can be challenging using imaging alone, and there is an unmet need noninvasive assessment of tumor burden. We developed a method assessing circulating cell-free DNA (cfDNA) tested it 217 plasma samples from 40 metastatic treated immune checkpoint inhibition radiation as part the CheckPAC trial (NCT02866383). Samples were evaluated before after initiation mutation-independent tumor-independent approach...
Abstract This abstract is being presented as a short talk in the scientific program. A full printed Proffered Abstracts section (PR016) of Conference Program/Proceedings. Citation Format: Nicholas A. Vulpescu, Zachariah H. Foda, Pieter H.A. Wisse, Christopher Cherry, Jaime E. Medina, Vilmos Adleff, Remond J.A. Fijneman, Robert B. Scharpf, Gerrit Meijer, Beatriz Carvalho, Victor Velculescu. Dynamic chromatin landscapes colorectal cancer development and cell-free DNA fragmentation [abstract]....
Abstract Hepatocellular carcinoma (HCC) is a leading cause of cancer death world-wide. In the US, liver has increased in incidence and mortality due to growing population from South Central America, which faces higher risk disease part aflatoxin exposure. Recently, we showed that DELFI (DNA evaluation fragments for early interception) approach using genome-wide cell free DNA (cfDNA) fragmentation profiles machine learning can be used detection other cancers. Having previously demonstrated...
Abstract The stepwise progression of colorectal cancer (CRC) from healthy epithelium, to premalignant adenoma, is accompanied by genome-wide epigenetic reprogramming which may be reflected in circulating cell-free DNA (cfDNA). However, current analyses these processes have been hampered complex mixtures cells normal, adenoma and tissue samples, as well absence suitable model systems. Cultured organoids, comprised pure epithelial cells, could enable insights on the changes leading cancer....
<div>Abstract<p>Liver cancer is a major cause of mortality worldwide. Screening individuals at high risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved survival, but current screening methods are inadequate. In this study, we used whole-genome cell-free DNA (cfDNA) fragmentome analyses to evaluate 724 from the United States, European Union, or Hong Kong hepatocellular carcinoma (HCC) who were average high-risk HCC. Using machine learning...
<p>Supplementary Figure S1 shows contributions of individual genomic regions to the final trained DELFI surveillance model. Supplementary S2 scores in individuals without cancer by age and sex. S3 high-risk across racial or ethnic groups. S4 cirrhotic patients relation severity. S5 BMI. S6 Shows Performance alternative models. S7 Correlation between rank ordered DELFI. S8 with HCC were related tumor characteristics. S9 etiology underlying liver disease. S10 score is correlated AFP...