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• Multi-institutional collaboration to characterize 5hmC in prostate cancer, both tumor biopsies and cfDNA.

  This study used pull-down sequencing to measure 5-hydroxymethylcytosine (5hmC) levels in tissue biopsy specimens from patients with localized and metastatic castration-resistant (mCRPC) prostate cancer. For a subset of the cohort, the same technique was used to sequence cell-free DNA (cfDNA) isolated from patient plasma. To assess 5hmC levels in cfDNA from a larger number of specimens, plasma samples from another mCRPC cohort were also assayed with this method. The larger cohort of cfDNA samples was further anlayzed with a targeted sequencing gene panel.

  Study EGAS00001004942

• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  In many areas of oncology, we lack sensitive tools to track low burden disease. While cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low disease burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and post-operative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance, and empowering treatment optimization in low-disease burden oncology care

  Study EGAS00001004406

• WGS & RNAseq of paired tumor-normal patients presenting a BRCA2 alteration

  Raw data FASTQ files of RNAseq (Stranded mRNA prep Ligation-Illumina on NovaSeq 6000, 100bp paired-end) & WGS (PCR Free Roche KAPA Hyper Prep Library on Illumina Novaseq 6000, 150bp paired-end) for 40 samples corresponding to the matched tumor/normal of 10 patients. Raw data FASTQ files of WGS (PCR Free Roche KAPA Hyper Prep Library on Illumina Novaseq 6000, 150bp paired-end) of the tumor of two additional patients.

  Dataset EGAD50000000871

• Targeted gene expression analysis on FFPE specimen from NSCLC patients

  This study measured the expression of a panel of over 300 cancer immunotherapy-relavant genes in tumors after neoadjuvant chemoimmunotherapy. It was performed on RNA from FFPE tumor tissue. Differential gene expression analysis was performed between patients achieving or not achieving an event-free survival of 12 months.

  Study EGAS50000001140

• VCRC Imaging Protocol for Magnetic Resonance and Positron Emission Tomography in Large-Vessel Vasculitis (Takayasu's Arteritis): Development as Clinical Trial Outcome Measures Vasculitis Clinical Research Consortium

  Takayasu's arteritis is a rare disease that affects the blood vessels. Takayasu's arteritis can cause swelling of large and medium-sized blood vessels. The blood vessels that are commonly affected are the branches of the aorta (the main blood vessel that leaves the heart). The purpose of this study is to help doctors learn more about this disease by using x-ray like tests to see if they are helpful in taking care of patients with Takayasu's arteritis. This is an imaging study that compares x-ray-like tests that would not be a part of your regular care (PET/CT) with x-ray-like tests that are a part of your regular care (MRI). At two visits, three months apart, patients will have a PET/CT scan performed at the same time as their MRI scan; some patients will also have a third PET/CT scan. A total of 36 people with Takayasu's arteritis at several hospitals will take part in this study. Doctors will use images from the different time points, along with information from exams and symptoms, to learn more about the disease.

  Study phs001715

• Cancer cell and tumor microenvironment biomarkers associated with disease-free survival with adjuvant nivolumab in the phase 3 CheckMate 274 trial

  In the CheckMate 274 trial, adjuvant nivolumab versus placebo demonstrated an improvement in the primary endpoint of disease-free survival (DFS) in patients with high-risk muscle-invasive urothelial carcinoma after radical resection. An extensive analysis of tumor biomarkers, including their associations with DFS, was performed. Analysis of genome-wide differential gene expression and known gene signatures found that immune-related genes and pathways, in particular an IFNγ signature, were predictive of DFS in nivolumab-treated patients. Predictive and prognostic associations, respectively, were found for tumor-infiltrating CD4 and CD8 T cells. Analysis of a composite predictive model suggested that CD4 gene expression and tumor cell PD-L1 expression had the greatest contributions to predicting outcomes in nivolumab-treated patients. These results reinforce recent studies establishing the importance of biomarkers of adaptive immunity, and in particular CD4 T cells, in influencing response to PD-1/PD-L1 blockade and establish the potential predictive rather than solely prognostic nature of such findings.

  Study EGAS50000000560

• Copy number variations and fragmentation features in cell-free DNA predict response in advanced non-small cell lung cancer patients under anti-PD-(L)1 therapy

  Anti-PD-(L)1 therapy is routinely used in metastatic NSCLC. However, response rates vary and biomarkers predicting treatment efficacy are lacking. Liquid biopsies allow monitoring of residual disease during therapy. Residual circulating tumor DNA (ctDNA) after therapy represents a predictive marker for adverse outcome. Here, we assessed copy number variations (CNVs) in serial plasma samples of NSCLC patients receiving PD-(L)1 blockade. We profiled CNV and fragmentation features in 118 plasma samples of advanced NSCLC patients by low-coverage whole genome sequencing taken at baseline, after four therapy cycles and at disease progression. CNVs and fragment features (i.e., fragment length, end motifs, position) were significantly altered in patients compared to healthy donors. Furthermore, fragment length changes at baseline and residual CNVs after four therapy cycles correlated with short progression-free survival. Our results highlight the suitability of plasma-based CNV and fragment analysis for disease monitoring and as a predictive marker for response duration in NSCLC patients under anti-PD-(L)1 therapy.

  Study EGAS50000000441

• Paired FastQ files from deep targeted DNA sequencing

  This dataset comprises paired-end and time-matched FastQ files from 356 cell-free DNA samples and 356 white blood cell DNA samples, derived from 299 patients with metastatic renal cell carcinoma or urothelial carcinoma. A baseline sample was available for all patients. Sequencing was performed using Illumina technology.

  Dataset EGAD50000001267

• A mathematical model of cell-free DNA fragment size reveals cancer-specific fragmentomic patterns

  This study aim to test a mathematical model of cfDNA length distribution across multiple biodiy flulids. It try to investigate biological mechanisms of cfDNA fragmentation and release.

  Study EGAS50000001560

• Longitudinal copy number variation analysis from plasma DNA of head and neck cancer patients under re-radiotherapy

  Recurrent locally advanced head and neck cancer (HNC) patients, receiving re-radiotherapy (re-RT), are presented with short progression-free (PFS) and overall survival. Hence, biomarkers predicting therapy failure are urgently needed. We analyzed copy number variations (CNVs) in blood plasma of HNC patients collected before, during and after re-RT. Detectable CNVs after five and ten fractions of re-irradiation as well as at the end of re-RT were associated with short PFS. Furthermore, we found that CNV kinetics in longitudinally collected plasma reflected therapy response and could detect disease progression in advance of radiographic tumor assessments.

  Study EGAS50000000163