Clinical Trials

Pancreatic ductal adenocarcinoma (PDAC) has a suboptimal response to standard therapies that modestly impact survival due to its ability to evade host immune surveillance. Emerging evidence has shown that the co-inhibitory receptors, such as programmed death 1 (PD-1), play a critical role in cancer immune-editing. Programmed death-ligand 1 (PD-L1) is an immune checkpoint that is often activated in cancer and plays a pivotal role in the initiation and progression of cancer. The advent of immunotherapy, with checkpoint inhibitors, which block PD-L1 interaction between tumor cells and activated T cells, has significantly altered the treatment algorithm for several solid tumors. However, the clinicopathologic significance and prognostic value of PD-L1 in PDAC remains controversial. The main technical ground may be that PDAC PD-L1 expression quantification is limited to surgical resection specimens and dependent on specific immunohistochemistry (IHC) tests. In addition, PD-L1 expression has not been extensively assessed before surgery in treatment-naive PDAC patients, due to the current IHC test requirement for a histologic rather than a cytologic evaluation. However, a recent study showed that EUS-fine needle biopsy (FNB) can successfully determine primary pancreas malignancy PD-L1 status. One recently identified subtype within the genomic landscape of PDAC is the mismatch repair-deficient (dMMR) tumor. Evaluation of dMMR status is particularly important following the FDA approval of the PD-1 inhibitor, pembrolizumab, for the treatment of unresectable or metastatic, microsatellite instability-high (MSI-H) or dMMR PDAC that have progressed following prior treatment, and have no satisfactory alternative treatment options. The objectives of the project will include the assessment of tumor PD-L1/dMMR expression in patients with PDAC using EUS-FNB samples and the prospective correlation of MMR status and PD-L1 expression with overall survival and progression-free survival of PDAC patients.

Colorectal cancer is a common malignant tumor of the digestive tract. It is still a challenging task to detect colorectal cancer at an early stage. Studies have found that DNA methylation has a relationship with the occurrence and development of tumors. Singlera Genomics Inc. has invented the proprietary methyl-Titan sequencing technology and developed a detection method for colorectal cancer and advanced adenoma (Adenoma/Colorectal cancer Early detection, ACE) using the cancer-specific methylation markers. ACE is a blood-based non-invasive diagnostic technique. It has high compliance rate compared with colonoscopy, and sampling is more convenient than stool testing. It also has much higher sensitivity compared to existing blood testing methods. The current study plans to use ACE method to analyze ctDNA in the blood for the cancer-specific DNA methylation markers to aid in the differential diagnosis of patients with colorectal cancer or adenoma. This technique will greatly reduce the discomfort in the diagnosis of suspected patients and improve the diagnosis of high-risk population of colorectal cancer. The goals of this study are: 1) to establish a detection system based on plasma ctDNA methylation sequencing technology for the auxiliary diagnosis of colorectal cancer and adenoma, 2) to assess the diagnostic value of plasma ctDNA methylation signature for colorectal cancer and adenoma, and 3) to assess the association of plasma ctDNA methylation signals with colonoscopy results and pathological results of surgical specimens. A total of 1300 patients (700 cases positive and 600 cases negative) aging between 45 and 80 years old will be enrolled. Colonoscopy will be performed to determine whether patients are positive or negative. Positive patients who need surgical resection will be further classified according to their surgical histopathological results. For negative patients, the type of lesion will be clarified. The plasma samples of all subjects will be analyzed for cancer-specific ctDNA methylation profiles. Based on the results of plasma ctDNA methylation test, the risks of colorectal cancer of the enrolled subjects are scored. Combined with the grouping information, the clinical application value of the cancer-specific methylation profile for early cancer diagnosis will be assessed.

Intellectual disability (ID) is a clinically and genetically heterogeneous condition that often results in a diagnostic odyssey. The deployment of high throughput sequencing (HTS) and in particular exome sequencing (WES) has made it possible to identify many genes responsible for ID. However, the WES does not identify the cause of ID in about two-thirds of patients, due to, for example, the uneven depth and coverage of all exons, or the location of variants in non-exonic areas. It has thus been shown that genome sequencing (WGS), which is still rarely used because it is more complex and costly, would be more efficient, with an expected diagnostic rate of around 60%. In response to the massive contribution of HTS in the diagnosis of patients suffering from rare diseases, France has launched the France Plan Médecine Genomique 2025 (PFMG2025) to deploy HTS platforms, which will be able to carry out WGS, WES and RNA sequencing (RNA-seq), and pilot studies to define the modalities for prescribing these examinations. Two cost-effectiveness evaluations of these technologies, in comparison with the current strategy for diagnosis of ID, are currently underway or planned in the short term in France: 1) PRME DISSEQ, comparing the large DI459 panel versus WES, 2) the DEFIDIAG pilot study of the PFMG2025 comparing WGS, in trio versus solo, versus current strategy. However, there are no studies examining the place of the RNA-seq in the ID diagnostic decision tree. However, some pathogenic variations are likely to have an effect on transcription. WES/WGS can detect them but are not able to affirm their pathogenicity because it focuses on genomic DNA. Only the RNA-seq makes it possible to study the transcription of candidate genes on a large scale, providing an additional level of evidence on both known genes in human pathology (OMIM) and candidate genes. The RNA-seq would increase the diagnostic rate from 10% to 35% in addition to the WGS in negative patients with first-line approaches (including WES) and thus optimize management by reducing diagnostic delays as part of a personalized care pathway.

This is single-center, prospective, non-randomized study

Background: - Genes are the instructions our body uses to function. Researchers can look for changes, or variants, in the genes. The goal of this study is to find new gene changes that lead to lipid disorders. Older research methods looked at one or a few genes at a time. Genomic sequencing looks at most of the genes at once. Genomic sequencing may find the cause researchers haven t been able to find from past methods. Objectives: - To better understand genetic causes of lipid disorders through genomic sequencing. Eligibility: - People age 2 and older with unusual lipid disorders, and their relatives. Design: - Participants will be screened with a physical exam and medical history. They will have blood taken. They may give a saliva sample. - Based on the screening test, researchers will chose 3-5 family members to perform the genomic sequencing. The sequencing will be done on a sample of DNA collected during the blood draw and saliva sample. - Participants may be invited to take part in other protocols that may involve imaging of their heart or blood vessels. They do not have to participate. If they do, they will sign a separate consent for those tests. - If a participant s family member cannot travel to the NIH, the NIH documents and consent will be reviewed during a teleconference. A blood or sputum kit will be mailed to them.

Rare systemic auto inflammatory diseases are a group of diseases that can be inherited and have non specific symptoms (fevers, rashes, joint pain, etc.). These diseases can be divided into two groups: - Diseases for which genetic mutations have been identified - The so-called genetically undetermined diseases for which no genetic mutation has been identified and for which the diagnosis is based on the elimination of other causes of disease At present, the causes and mechanisms of these diseases are poorly understood and their diagnosis is difficult, often leading to misdiagnosis. The usual care integrates anti-inflammatory treatments (aspirin, colchicine, cortisone, biotherapies, etc.) and support for patients and their families by health professionals (doctors, nurses, physiotherapists, etc.). To date, a patient with one of these diseases can receive up to 5 inappropriate or ineffective treatments before the right diagnosis is made and the right therapy is put in place. The objective of this study is to develop rapid and effective diagnostic methods for these diseases by the identification of biological markers present in blood, urine or stool of patient in order to develop a rapid and efficient diagnostic method.

This phase II trial studies how well ponatinib hydrochloride works in treating patients with cancer that has spread to other parts of the body (metastatic), has failed previous treatment (refractory), and has one of several alterations, or mutations, in its deoxyribonucleic acid (DNA) sequence. Ponatinib hydrochloride may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth. It is not yet known whether a patient's genetic alterations may affect how well ponatinib hydrochloride works.

Background: - Breast cancer is the most common malignancy in women, occurring in over 230,000 women annually in the United States. - The vast majority of breast cancers originate in the single layer of epithelial cells that line the ductal/lobular system of the breast milk ducts. The premalignant changes which occur in the transformed epithelium are not well understood, however several cytologic or histologic changes have been identified which are associated with an increased risk for breast cancer, including ductal or lobular hyperplasia, hyperplasia with atypia, and lobular or ductal carcinoma in situ. - The identification of cytological or histological abnormalities in breast epithelial cells is an important component of risk assessment. Objective: Primary objectives are: - To determine the incidence and nature of cytologic changes in ductal epithelial cells from the high-risk breast, in specimens collected by breast ductal lavage, and to determine if these cytologic findings are different from those of female normal volunteers not at increased risk for breast cancer. - To characterize by breast duct endoscopy, high risk breast ductal epithelium and architecture, and correlate these findings with the cytologic findings referenced in above bullet. - To determine what is the global gene expression pattern of high risk breast epithelial cells from the high risk breast, and does this differ from that of breast epithelial cells from female normal volunteersnot at increased risk for breast cancer. The gene expression profile will be determined by cDNA microarray and validated by RT-PCR. Eligibility: Eligibility for high risk individuals will include: - Women with a unilateral invasive or noninvasive (DCIS) breast cancer of epithelial origin. - Women without breast cancer, but with a Gail Index greater than 1.67 percent, or a cumulative lifetime risk greater than or equal to double the age- and race-matched general population risk. - Women known to be BRCA1/2 or other hereditary genes mutation carriers. - Women with cytologic or histologic evidence of ductal hyperplasia, atypical ductal hyperplasia, or lobular carcinoma in situ. - Women may be either premenopausal or postmenopausal. Postmenopausal is defined by the absence of menstrual periods for at least 12 months. - Postmenopausal women who have previously undergone a hysterectomy without oophorectomy must have a serum FSH level of > 40 IU/ml, and a serum estradiol level of less than40 pg/ml to document postmenopausal status. Eligibility for normal volunteers will include: - Women who are premenopausal or postmenopausal with a Gail model risk index less than 1.67 percent, and without a cumulative lifetime risk greater than or equal to double the age- and racematched general population risk. - Women who have previously undergone a hysterectomy without oophorectomy must have a serum FSH level of >40 IU/ml, and a serum estradiol level of less than 40 pg/ml to document postmenopausal status. - Both breasts must be free of any suspicious areas by physical examination and, for women over 30 years of age by mammogram. There must be no history of atypical hyperplasia, invasive or in situ carcinoma. Both groups must have acceptable white blood cell and platelet counts. Design: Breast ductal epithelial cells will be collected by breast ductal lavage from (a) the breast in women at increased risk for breast cancer, and (b) the breast of female normal volunteers who are not at increased risk for breast cancer. Ductal epithelial cell specimens will be analyzed cytologically for the presence of hyperplasia, atypia, or in situ changes. Breast duct endoscopy will be performed in breast cancer patients and in normal volunteers with cytologic atypia on ductal lavage to determine ductal architectural changes associated with increased risk for breast cancer, and to provide correlation with cytologic atypia. The gene expression profile of normal and high-risk ductal epithelial cells will be studied by cDNA-microarray to determine changes in gene expression associated with increased risk for breast cancer. Additional molecular profiling experiments which will be performed as lavage cells are available include DNA whole exome sequencing, Comparative Genomic Hybridization (CGH), proteomic tissue lysate arrays, and identification of mammary stem cells. A total of 104 high-risk subjects and 110 normal volunteers will be studied, divided approximately evenly between premenopausal and postmenopausal women....

This study focuses on advanced lung and head and neck SCC tumours, with adjacent normal lung tissues. Biopsies will be performed in National University Health System, Singapore (NUHS) as part of participants' standard care. Patient blood was also required for extraction of cell free DNA (cfDNA) and genomic DNA (gDNA). Patients' medical records will also be reviewed for the purpose of this study.

Analysis of cell free DNA(cfDNA), unlike tissue biopsy, presents a new tool for the monitoring and treatment of cancer. The investigators have developed a differentiated sequencing assay, Digital Sequencing Technology (DST) that enables detection of rare genomic abnormalities with ultra high-specificity and sensitivity. The investigators assay is able to eliminate the error and distortion created by sample-prep and sequencing processes in standard NGS(next-generation sequencing ) workflows and produce near-perfect representations of all rare variants. The investigators have shown that in sequencing a comprehensive cancer panel of 80kbp in 0.1% cancer cell line titration samples, standard Illumina SBS(sequencing by synthesis ) generates many high-quality false positive variant calls in the range of 0.05-5%, while the investigators assay resulted in highly sensitive and completely error-free variant calls across the entire panel. This work indicates the remarkable potential of using the investigators assay in deep analysis of cfDNA, thereby allowing researchers and clinicians to comprehensively and non-invasively monitor the genetic dimension of cancer throughout the body.

BRCA1 or BRCA2 genes, are implicated in 10-15% of ovarian cancer cases, increased to 22% germline BRCA1/2 mutation frequency in patients with high grade serous histology subtype, including those women who have no family history of breast or ovarian cancer. With the rapid advancement of therapeutics targeted this population, this protocol seeks to provide genetic BRCA1/2 screening to all patients with high grade serous ovarian cancer. This information may help in selection of future treatment options and genetic testing for BRCA1/2 may be used to potentially prevent a proportion of cancer for the family members. This study will be an opportunity for patient to improve access at genetic and molecular testing for BRCA1/2 mutation which could impact her future treatment option. Moreover, this study will allow to prospectively assess the proportion of patients with BRCA mutation in ovarian cancer and describe the type of mutations identified in a large population.

Caribbean Hispanics are a population with a disproportionately high prevalence of cardio-metabolic disorders but with a limited expectation of benefits from current pharmacogenetic algorithms derived mainly in subjects of relatively pure ancestry. The investigators focus on warfarin responses to develop urgently-needed DNA-driven prescription guidelines for this population, who have arisen from European, West African and Amerindian genomic origins to produce a highly heterogeneous population. Our project combines admixture analysis and DNA-sequencing with development of more accurate rules for better predictability of warfarin dosing to immediately serve this medically underserved population.

To study the risk prediction of chemotherapy-induced peripheral neuropathy (CIPN) by the clinical bioinformatics and genomic profile.

The aim of this study is to employ genomic detection methodologies to measure the relative amount of tumor nucleic acids in the blood of a cancer patient with diagnosed metastatic disease that is either commencing, currently undergoing or completed cytotoxic chemotherapy treatment. More generally, this approach will allow us to develop a quantitative measure of therapy efficacy via the counting of the relative changes in tumor molecules over the course of treatment.

BOVARY-Pilot is a monocentric prospective transversal pilot study with a total duration of 6 months. The purpose of this study is to determine the feasibility of detecting somatic tumor mutations in the blood of patients with ovarian cancer in order to determine whether a blood test can replace a tissue biopsy to prescribe a personalized treatment. The method will consist of a single blood sample during the patient's visit and prior to the establishment of any newly diagnosed cancer treatment. The concordance of somatic mutations (SNV) found in tissue and in cell-free DNA (cfDNA) extracted from blood will then be compared

5-HT3 antagonists (ondansetron) are highly effective medications for the treatment of nausea and vomiting. However, these medications also associated with potentially severe and life-threatening cardiac adverse drug reactions (ADRs), particularly QT prolongation. Data regarding the cardiac safety and inter-individual variability in cardiac effects of ondansetron when used in vulnerable populations such as children and pregnant women are very limited. The results of this study will enable better-informed therapeutic decision-making regarding the use of ondansetron in children and pregnant women, with the overall goal to improve the safety of these commonly used antiemetic medications. Furthermore, predictive pharmacogenetic markers of severe 5-HT3 antagonist toxicity could be used to identify patients at risk of cardiac toxicity before the drug is administered.

The study aims at developing and validating an integrated clinico-molecular model for an accurate survival prognostication in newly diagnosed SMZL. Already existing and coded tumor biological material and health-related personal data will be retrospectively collected. Mutation analysis will be performed by targeted deep next generation sequencing of tumor genomic DNA. Deletion of 7q will be assessed by FISH on nuclei isolated from tumor tissues. Immunoglobulin gene rearrangement and mutation status will be analyzed on tumor genomic DNA by PCR and Sanger sequencing. The methylation status of target genes will be assessed by methylation specific PCR on tumor genomic DNA. The adjusted association between exposure variables and OS will be estimated by Cox regression. This approach will provide the covariates independently associated with OS that will be utilized in the development of a hierarchical molecular model to predict OS. The hierarchical order of relevance in predicting OS among covariates will be established by recursive partitioning analysis. An amalgamation algorithm will be used to merge terminal nodes showing homogenous OS. The discrimination capacity of the model will be assessed by calculating the c-index. Relative survival analysis will be used to provide a measure of the excess mortality experienced by patient's subgroups stratified according to the developed hierarchical molecular models, irrespective of whether the excess mortality is directly or indirectly attributable to the disease. The model developed in the training set will be tested in the validation sets and the model performance (c-index) in the validation set will be compared with that in the training set.

Rationale: Psoriasis (PsO) is a common inflammatory skin disease. Besides the skin, it is recognized that this disease can affect multiple domains such as nails, joints and entheses. About 30% of the patients with PsO will develop symptoms in the musculoskeletal domains. Untreated inflammation in psoriatic arthritis (PsA) can lead to irreversible joint damage and further reduces quality of life. Since musculoskeletal involvement is often preceded by the dermatological symptoms of PsO, patients with pure cutaneous psoriasis (PsC) should be routinely screened for joint involvement. Current screening questionnaires, like the often used Psoriasis Epidemiology Screening Tool (PEST), offer a moderate discrimination between patients with PsA and PsC at best. Our aim is to assert the prevalence of known and previously undiagnosed PsA in a PsC cohort. By comparing the gathered data of the PsA and PsC patients, we hope to improve the screening of PsC patients, and to reduce both undertreatment of locomotor symptoms as well as unnecessary diagnostic investigations. Objective: To ascertain the prevalence of PsA in a tertiary PsO cohort. Secondary objectives will be to ascertain the clinical features of these patients. With these features we want to find clinical, laboratory or genetic markers to predict the presence of PsA in PsO patients. Moreover, we wish to establish the added value of PsA screening for the quality of life (QoL) of PsO patients. Study design: Multicenter cross-sectional study with a single follow-up visit after 1 year. Patients will be screened at baseline for PsA symptoms by a rheumatology resident and referred to a rheumatology clinic if deemed necessary. At baseline, several clinical and sociodemographic parameters will be assessed. We will collect blood samples for diverse biochemical studies and genomic DNA. Patients will be followed for 1 year after active screening for PsA. Quality of life (QoL) and treatment change will be recorded after this period, to assess the effect of screening and referral.

The immediate goal of this study is to collect biological samples (i.e., tissue and/or fluid), clinical information, and laboratory data from disease and non-disease subjects seen at Intermountain Healthcare affiliated facilities. The long-term goal is to annotate tissue and/or fluid biomarker data to clinical information and laboratory data for the purpose of improving health care delivery and prognostic potential.

The purpose of this study is to study the relationship between the bile acids, short chain fatty acids and bacteria within the intestines. The hypothesis is that changes in the bacterial composition of the stool are associated with the differences in bile acids and short chain fatty acids in patients having irritable bowel syndrome compared to healthy individuals.