Clinical Trials

Continual surveillance of both community-acquired and nosocomial bloodstream infections for specific target organisms. Analysis of comorbidities, complications, bacterial resistance patterns, bacterial genomics (e. g. via WGS and MLST typing) for the determinants of clinical outcomes. The clinical outcomes are investigated both in the short-term (up until discharge) and the long-term (six months after index blood culture by standardized questionnaire). A predictive point-of-care score is to be developed based on these data to define high-risk patient populations requiring more intensive diagnostic and/or treatment regimens.

Background: Gastric cancers are cancers of the stomach. Hereditary ones are passed from parent to child. Researchers want to gather data about hereditary gastric cancers. They want to learn about changes these cause in the body and about the genes involved. Objective: -To gather data about hereditary gastric cancer. Eligibility: - People at least 2 years old with personal or family history with a hereditary gastric cancer. - People at least 2 years old with gene changes that lead to such cancer or a lesion that may be hereditary. Design: - Participants will be screened in a separate protocol. - Participants will have: - Physical exam - Medical history - Blood tests - Scans - Photos of skin lesions and other findings - Gynecology consultation for women - Cheek swab (some participants) - For some participants, their relatives will be asked to join the study. - Some participants will be asked to allow the study to get stored tissue samples for relatives who have died. - Some samples will be sent to outside labs. All personal data will be protected. Samples will be destroyed when the study ends. - Participants will get the results of genetic testing. - Participants who cannot come to the NIH clinic may just give a cheek swab and have genetic testing done. - Some participants will be contacted for more testing.

In this study, DNA sequencing, computational biology modeling, and ex vivo drug sensitivity assays will be utilized to define clinically relevant gene mutations and identify potential therapeutics for patients with acute myeloid leukemia (AML).

This is a multi-center, observational study designed to explore the regulatory mechanism of palbociclib correlative pathways in therapeutic process of breast cancer, employing next generation sequencing (NGS) on DNA and RNA. This study also monitor the clonal evolution of genes by tracing the ctDNA.

Chronic Obstructive Pulmonary Disease (COPD) is characterized by a chronic airflow limitation associated with an abnormal inflammatory response of the airways to inhaled noxious particles or gases. It is the third leading cause of death worldwide, accounting for approximately 3 million deaths each year and the prevalence is predicted to increase even further during the coming decade (WHO 2015). In the last two decades, there has been a disappointing lack of fundamental breakthroughs in the understanding of the pathophysiology of COPD and there is currently no pharmacological treatment available that halts its relentless progression. A clear alternative for describing COPD does not exist either, while the identification of subgroups of COPD patients based on clinical, genomic and epigenomic factors would be useful. A clinically relevant phenotype with high potential of having a genetic cause is severe early-onset COPD (SEO-COPD), defined by severe airflow obstruction (FEV1 ≤ 40% predicted) at a relatively young age (≤53 years) [1]. In the UMCG, we have a continuous flow of severe COPD patients who are referred to our hospital for bronchoscopic lung volume reduction treatment or lung transplantation. Approximately 40-50% of these patients fulfil the criteria for SEO-COPD. As part of a previously approved study ("Phenotyping in COPD", METc 2014/102), these patients are routinely characterized when they are willing to participate in this study and gave their written informed consent. Characterization is performed using lung function (i.e. spirometry, body box), clinical (i.e. questionnaires, physical examination, measurement of waist-hip ratio), radiologic (HRCT-scan) and systemic parameters (venous blood collection). Moreover, the following additional samples are being extracted: bronchial biopsies, bronchial brushes and nasal brushes. There are two objectives this study adds. The primary objective is to identify the genetic and epigenetic mechanisms underlying SEO-COPD by using the bronchial brushes and biopsies that are already extracted from the SEO-COPD patients. The secondary objective is to add two control groups (i.e. mild-moderate COPD group and healthy non-COPD control group) matched for age and smoking habits (all COPD patients referred for BLVRT or lung transplantation are ex-smokers). Hopefully, this will eventually explore COPD susceptibility and its genetic cause, resulting in a more tailored treatment of this COPD subset.

Aspirin Exacerbated Respiratory Disease (AERD) is a relatively homogeneous disease characterized by adult-onset severe asthma, development of non-cancerous growths in the nasal canal (i.e. nasal polyps) and aspirin allergy. The cause of AERD is unknown, although likely results from environmental insults in combination with genetic susceptibility. AERD disease homogeneity increases the possibility of discovering narrowly-defined genetic contributors, and makes it an ideal population to study the genetic and epigenetic changes that cause asthma. Researchers recently discovered that gene expression of epithelial growth and repair (EGR) genes are substantially decreased in bronchial airway epithelial cells of severe asthmatics compared to less severe asthmatics and healthy controls. This new finding indicates that epithelial integrity and related processes may be of primary importance to the development of severe asthma, and potentially the severe asthma subtype, AERD. This finding was later supported in a subsequent lab model, which showed that blocking a central epithelial repair and differentiation gene, human epidermal growth factor receptor 2 (ERBB2), decreased healing time of bronchial epithelial cells after injury. Thus, the objective of the proposed study is to determine whether EGR gene are also down-regulated in AERD, a homogeneous severe asthma subtype. As an extension, the researchers will also determine whether genetic mutations and/or epigenetic changes relate to and potentially explain this down-regulation of EGR genes. Specifically, the researchers plan to obtain gene expression of freshly brushed nasal airway epithelial cells of 140 AERD patients, 70 non-aspirin sensitive asthma patients, and 35 healthy controls, noting that nasal epithelial gene expression has recently been shown to mirror lung epithelial changes in asthmatic airways. Swabbing the nasal canal for epithelial cells allows to evaluate airway epithelial cell gene expression non-invasively. Our experimental design contrasts AERD gene expression profiles against healthy controls, and determines whether EGR genes are depressed in AERD relative to health controls. As a corollary, the researchers look to discover an AERD-specific gene expression profile which may one-day aid in diagnosis and expand current knowledge of disease mechanisms. As an extension, the researchers will correlate gene expression changes, specifically any finding of down-regulated EGR genes, with methylation changes (i.e. epigenetic changes) and genetic mutations.

The method to analyze the microsatellite instability (MSI) status by next-generation sequencing (NGS) has been established to assess the deficiency of DNA mismatch repair (MMR) system. The aim of our study is to evaluate the feasibility and reliability of this NGS method by testing the circulating tumor DNA (ctDNA) in blood sample of advanced colorectal cancer patients. If the result is positive, the MSI status could be easily learned without the acquisition of tissue samples.

A prospective study to evaluate consistency of different NGS-panel. Cell free DNA is purified from each malignant hydrothorax from NSCLC .Different NGS-panels are applied to perform in vitro diagnosis to detect Single Nucleotide Variants(SNV) and to calculate TMB value in these DNA samples.Consistency of enrolled NGS-panels are then evaluated by statistical analysis.

Ovarian cancer is the most fatal gynecologic cancer; in the US alone an estimated 22,000 women will be diagnosed in 2019, with over 13,000 dying of the disease. Approximately half of epithelial ovarian cancers (EOC) exhibit defective DNA repair through alterations in the homologous recombination (HR) pathway, with 14% accounted for by germline mutations in BRCA genes (mBRCA); this goes up to about one in five (20%) women when one includes tumor-associated (somatic) mBRCA.The approach to women with mBRCA-associated ovarian cancer has heralded precision treatment in our field with the availability of PARP inhibitors. Now indicated as treatment for women with documented mBRCA (genomic or somatic), it also has shown significant benefits for women with recurrent EOC who respond to platinum-based therapy when administered as maintenance treatment.

This is a research study to evaluate the clinical utility of the Enhanced Preservation Media with Integrated Extraction (EPM-IX)

The purpose of this study is to elucidate the role of acute dietary intake in male populations, and its impact on spermatozoa quality, integrity, content and epigenetic programming.

The C2i-WGS-MRD Test (hereinafter referred to as C2i-Test), a personalized molecular circulating tumor DNA (ctDNA) test, is an in vitro qualitative test that uses next generation sequencing (NGS) based whole-genome sequencing (WGS) data for detecting molecular residual disease (MRD) in patients diagnosed with muscle-invasive bladder cancer (MIBC) and histopathologically classified as stage II-IIIA. The C2i-Test is a single site assay performed in the C2i Genomics' CLIA-certified laboratory. This is a prospective non-interventional study to collect definitive evidence of the safety and effectiveness of C2i-Test for the intended use, in a statistically justified number of subjects.

So far, MRD assessment by liquid biopsy (ctDNA) has not been used to predict postoperative treatment efficacy and recurrence risk of GIST patients because of special disease characteristics and technological limitations. Therefore, we conducted this prospective multi-center, single-arm observational study to collect 45 operable patients with locally advanced, suspected high-risk GIST. NGS genetic testing platform is used to detect tumour tissues and peripheral ctDNA will also be dectected. we try to explore the correlation between PFS/OS and MRD in high-risk GIST patients by analyzing the relationship between dynamic changes in ctDNA mutation spectrum and postoperative adjuvant therapy efficacy, and to evaluate MRD-based genomic characteristics to guide further treatment.

This phase I/II trial studies the side effects and best dose of liposomal irinotecan and rucaparib when given together with fluorouracil and leucovorin calcium and to see how well they work in treating patients with pancreatic, colorectal, gastroesophageal, or biliary cancer that has spread to other places in the body (metastatic). Chemotherapy drugs, such as liposomal irinotecan, fluorouracil, and leucovorin calcium, work in different ways to stop the growth of tumor cells, either by killing the cells, by stopping them from dividing, or by stopping them from spreading. PARPs are proteins that help repair DNA mutations. PARP inhibitors, such as rucaparib, can keep PARP from working, so tumor cells can't repair themselves, and they may stop growing. Giving liposomal irinotecan and rucaparib together with fluorouracil and leucovorin calcium may work better in treating patients with pancreatic, colorectal, gastroesophageal, or biliary cancer.

This phase II/III trial compares the effect of the combination treatment with olaparib and temozolomide to trabectedin or pazopanib (two of the most common chemotherapy drugs used as usual approach) in patients with uterine leiomyosarcoma that may have spread from where it first started to nearby tissue, lymph nodes, or distant parts of the body (advanced) after initial chemotherapy has stopped working. The usual approach is defined as care most people get for advanced uterine leiomyosarcoma. Olaparib is a PARP inhibitor. PARP is a protein that helps repair damaged deoxyribonucleic acid (DNA). Blocking PARP may prevent tumor cells from repairing their damaged DNA, causing them to die. PARP inhibitors are a type of targeted therapy. Temozolomide is in a class of medications called alkylating agents. It works by slowing or stopping the growth of tumor cells in the body. The combination of olaparib and temozolomide may work better than the usual treatment in shrinking or stabilizing advanced uterine leiomyosarcoma after initial chemotherapy has stopped working.

The overarching objective of this study is to use novel precision medicine strategies based on inherited and acquired leukemia-specific genomic features and targeted treatment approaches to improve the cure rate and quality of life of children with acute lymphoblastic leukemia (ALL) and acute lymphoblastic lymphoma (LLy). Primary Therapeutic Objectives: - To improve the event-free survival of provisional standard- or high-risk patients with genetically or immunologically targetable lesions or minimal residual disease (MRD) ≥ 5% at Day 15 or Day 22 or ≥1% at the end of Remission Induction, by the addition of molecular and immunotherapeutic approaches including tyrosine kinase inhibitors or chimeric antigen receptor (CAR) T cell / blinatumomab for refractory B-acute lymphoblastic leukemia (B-ALL) or B-lymphoblastic lymphoma (B-LLy), and the proteasome inhibitor bortezomib for those lacking targetable lesions. - To improve overall treatment outcome of T acute lymphoblastic leukemia (T-ALL) and T-lymphoblastic lymphoma (T-LLy) by optimizing pegaspargase and cyclophosphamide treatment and by the addition of new agents in patients with targetable genomic abnormalities (e.g., activated tyrosine kinases or JAK/STAT mutations) or by the addition of bortezomib for those who have a poor early response to treatment but no targetable lesions, and by administering nelarabine to T-ALL and T-LLy patients with leukemia/lymphoma cells in cerebrospinal fluid at diagnosis or MRD ≥0.01% at the end of induction. - To determine in a randomized study design whether the incidence and/or severity of acute vincristine-induced peripheral neuropathy can be reduced by decreasing the dosage of vincristine in patients with the high-risk CEP72 TT genotype or by shortening the duration of vincristine therapy in standard/high-risk patients with the CEP72 CC or CT genotype. Secondary Therapeutic Objectives: - To estimate the event-free survival and overall survival of children with ALL and to assess the non-inferiority of TOTXVII compared to the historical control given by TOTXVI. - To estimate the event-free survival and overall survival of children with LLy when ALL diagnostic and treatment approaches are used. - To evaluate the efficacy of blinatumomab in B-ALL patients with end of induction MRD ≥0.01% to <1% and those (regardless of MRD level or TOTXVII risk category) with the genetic subtypes of BCR-ABL1, ABL-class fusion, JAK-STAT activating mutation, hypodiploid, iAMP21, ETV6-RUNX1-like, MEF2D, TCF3-HLF, or BCL2/MYC or with Down syndrome, by comparing event-free survival to historical control from TOTXVI. - To determine the tolerability of combination therapy with ruxolitinib and Early Intensification therapy in patients with activation of JAK-STAT signaling that can be inhibited by ruxolitinib and Day 15 or Day 22 MRD ≥5%, Day 42 MRD ≥1%, or LLy patients without complete response at the End of Induction and all patients with early T cell precursor leukemia. Biological Objectives: - To use data from clinical genomic sequencing of diagnosis, germline/remission and MRD samples to guide therapy, including incorporation of targeted agents and institution of genetic counseling and cancer surveillance. - To evaluate and implement deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequencing-based methods to monitor levels of MRD in bone marrow, blood, and cerebrospinal fluid. - To assess clonal diversity and evolution of pre-leukemic and leukemic populations using DNA variant detection and single-cell genomic analyses in a non-clinical, research setting. - To identify germline or somatic genomic variants associated with drug resistance of ALL cells to conventional and newer targeted anti-leukemic agents in a non-clinical, research setting. - To compare drug sensitivity of ALL cells from diagnosis to relapse in vitro and in vivo and determine if acquired resistance to specific agents is related to specific somatic genome variants that are not detected or found in only a minor clone at initial diagnosis. Supportive Care Objectives - To conduct serial neurocognitive monitoring of patients to investigate the neurocognitive trajectory, mechanisms, and risk factors. - To evaluate the impact of low-magnitude high frequency mechanical stimulation on bone mineral density and markers of bone turnover. There are several Exploratory Objectives.

This will be a prospective, observational, cohort study to determine the impact of integrated diagnostics using quantitative magnetic resonance imaging, whole genome sequencing and digital pathology on intended patient management for liver cancer patients referred for liver resection. Participants with primary or secondary liver cancer will be recruited from Hampshire Hospitals NHS Foundation Trust in Basingstoke or Oxford University Hospitals NHSFoundation Trust in Oxford. The incidence of treatable liver tumours is on the rise globally, driven by obesity, viral hepatitis and metastases from colorectal cancers. Survival rates can be improved with optimised allocation of treatment options including surgical resection, radiofrequency ablation, embolisation, chemotherapy and targeted molecular therapies (including immunotherapy). The key motivation of this study is to help patients access the most suitable treatment combinations, based on integrating clinical, radiological and genomic data. A similar integrated approach, integrating radiology and pathology, has been shown to improve outcomes in breast cancer care. Detailed pathologic analysis of the surgical specimen from breast carcinoma biopsy provides valuable feedback to the radiologist, establishes the completeness of surgical intervention, and generates predictive information for therapeutic decisions. Whole genome sequencing (WGS) has discovered cancer driver mutations and the complex molecular profile of liver cancer. In many metastatic solid tumours, WGS has been used to identify a significant patient population (31%) who present with a biomarker that predicts sensitivity to a drug and lacked any known resistance biomarkers for the same drug. Identifying which patients possess druggable mutations will allow clinicians to make the optimal treatment decisions. The next challenge is integrating WGS into scalable clinical practice

The current study will test the ability and likelihood of successfully implementing individualized combination treatment recommendations for adult patients with surgically-resectable recurrent glioblastoma in a timely fashion. Collected tumor tissue and blood will be examined using a new diagnostic testing called University of California, San Francisco (UCSF) 500 Cancer Gene Panel which is done at the UCSF Clinical Cancer Genomics Laboratory. The UCSF 500 Cancer Gene Panel will help identify genetic changes in the DNA of a patient's cancer, which helps oncologists improve treatment by identifying targeted therapies.

The primary objectives of this study are to obtain clinically meaningful data on the survival, outcomes, prognosis and treatment effect of all the patients with spinal muscular atrophy (SMA) 5q types 1 to 3 (according to international classification), being followed in the Children's Hospital, Zhejiang University School of Medicine since October 2019. The registry will collect retrospectively and prospectively the longitudinal data of the long-term follow-up for children patients, under real life conditions of current medical practice, in order to document the clinical evolution of patients (survival, motor, respiratory, orthopedic and nutritional and so on), the conditions of use of the treatments, the mortality rates of treated and untreated patients, the tolerance of the treatments, adverse events.

Improved standards of care and the regular early use of glucocorticoid treatment have changed the natural history of Duchenne muscular dystrophy (DMD), affecting both survival and time of loss of functional milestones. More recently, there has been increasing evidence of an additional benefit from new therapeutic approaches based on mechanisms targeting specific types of mutation, as Atarulen, authorised in the European Union as Translarna since 31 July 2014 to treat DMD boys with non sense mutations. As there is increasing evidence that specific groups of mutations may have different progression of the disease, it has become mandatory to obtain more detailed long-term information about the patterns of progression related to different genotypes. Natural history of DMD boys carrying deletions has been more studied and less is known about boys carrying small mutations that represent 20% of DMD patients. The aim of this project is to better define the natural history of these patients and to better understand the clinical response to mutation-specific therapies aimed at restoring dystrophin protein production.