Clinical Trials

The investigators propose to conduct a pilot feasibility study of single agent erlotinib in patients with metastatic EGFR mutant adenocarcinoma of the lung with up to one prior treatment with the sole purpose of characterizing the genomic landscape before erlotinib and at the time of disease progression. The logistics of obtaining adequate quality fresh tissue specimens for sequencing studies before therapy and at the time of disease progression in patients with advanced lung cancer are complex and a thorough understanding of the practical challenges in conducting a study like this is crucial. The current proposal will include exome and transcriptome sequencing from blood collected at baseline along with tumor samples obtained prior to starting erlotinib and at the time of disease progression (a total of two tissue samples and one blood sample per patient). If carried out successfully, the proposed strategy very likely will lead to a larger and adequately powered study to understand fully evolving molecular changes due to clonal selection under treatment pressure. The pace of progress in the field of sequencing technology currently underway is only likely to accelerate in the near future yielding richer and highly content-rich information. Moreover, it is likely that genomic information from DNA sequencing and transcriptome will be supplemented by analyses of translatomes and proteomes. The investigators plan to sequence paired tumor specimens from 20 patients with EGFR mutant adenocarcinoma of the lung before treatment with erlotinib and at the time of disease progression following treatment with erlotinib. As the investigators expect some drop off (due to unexpected clinical events precluding a second biopsy at the time of disease progression, poor specimen quality and early discontinuation of therapy for non-progression), the investigators will enroll 40 patients in this trial to get 20-paired specimens.

Fanconi anemia is a rare autosomal or sex linked recessive genetic disease. The disease is characterized by bone marrow hematopoiesis failure, multiple congenital abnormalities, and susceptibility to neoplastic diseases. The cells of FA patients are extremely sensitive to MMC and DEB. The symptoms and ages of FA patients are different, so by comparing the exome of FA patients and their parents, the mutations that were accumulated in FA patients could be found, and these genes might be sensitive to repairment and be important for hematopoiesis maintainance.

Major impacts of air pollution are lung diseases such as granulomatous diseases and mainly sarcoidosis. Understanding the respective role of inorganic / nanoparticles and genetic background in these chronic diseases is a major challenge for the management of patients and prevention strategies. Granulomas are characterized by giant epithelioid and multinucleated cells, reflecting a severe disturbance in immunological pathways induced both by toxic exposure and genetic predisposition. Previous studies demonstrated that professional environmental context and acute exposures (the World Trade Center disaster) to micro/nanoparticles have a pathogenic impact with a sharp increase in sarcoidosis. Sarcoidosis is a multifactorial disease occurring in a genetically vulnerable context. Many gene variants have been linked to an increased odds-ratio of the disease, such BTNL2, CCDC88B, ANNEXIN A11 involved in regulation of T-cell activation and maturation pathways. We have contributed since 2008 to a national cohort (GSF, 28 centers) of ≈ 800 sarcoidosis patients with familial and sporadic presentation of the disease. This collection has been an exceptional (and worldwide unique) tool for the implementation of an exhaustive clinical database on sarcoidosis, modelling of disease evolution and identification of clinical / genetic criteria differentiating sporadic and familial forms. The main goals of the project are: 1. Completion of the genetic data in order to establish a pattern of gene variants segregating with familial forms of the disease, compared to sporadic one. This will be done by WES (WHOLE EXOME) analysis on the previously collected DNA samples. The informed consent for the patients included the information about the BTNL2 gene, which has been already tested since 2008, and related genes connected to immune pathways, thus allowing a unambiguous information about the research finality of the project. 2. Completion of the clinical data about each patient, in cooperation with the GSF network, management of the database established since 2008. The data collected are those which are commonly detailed in the normal follow-up of the patients. The project do not include any new interventions on the patient (neither radiological or invasive tests). 3. Specific biological studies might be done on the white blood cells of the patients, and might need in such cases a new blood sampling, both in patients and first degree related healthy controls. Theses specific studies will be presented to an ethical committee (CCP) in order to validate the feasibility in term of 'new intervention' on the cohort. The samples collected will be at the same volume of a classical blood sampling (2*7 ml). 4. Any other projects, submitted to the GSF network will needed a specific registration and ethical committee validation.

This study collects and studies tissue and blood samples from patients with prostate or bladder/urothelial cancer that has recurred (come back) at or near the same place as the original (primary) tumor or has spread to other parts of the body. Studying samples of blood and tissue samples from patients with prostate or bladder/urothelial cancer in the laboratory may help doctors learn more about new biomarkers, potential drug targets, and resistance developing in response to treatment. It may also help doctors find better ways to treat the cancer.

Prospective, open labelled, monocentric trial to evaluation of the circulating tumor DNA rate in the blood, before and after curative resection of hepatic metastasis of uveal melanoma (HMUM) and during post-surgery follow-up

Essential hypertension is a complex trait which results from interaction between environmental factors and genetic factors. The aim of this study is to investigate the effects of interaction between environmental factors and genetic factors on long-term blood pressure (BP) based on two established cohorts including "the cohort of Hanzhong adolescent hypertension study" and "the cohort of Mei county adult salt-sensitive hypertension study". Firstly, the Hanzhong cohort-based follow-up study is designed to observe the track of BP during the whole life time, and to explore the effects of many risk factors (such as salt-sensitivity, obesity et al) on long-term BP and the occurrence of hypertension, and also to analyze the relationship of different polymorphisms of sodium and potassium metabolism-related gene with BP changes and target organ damages. In addition, by using DNA samples collected from subjects of "Mei county adult salt-sensitive hypertension study"in which all participants had completed a chronic salt loading and potassium intervention trial, we attempt to examine the single nucleotide polymorphisms (SNPs) of sodium and potassium metabolism-related genes, as well as the relationship between these SNPs and BP responses to dietary sodium/potassium intervention, long-term BP change, the risk of hypertension and target organ damages were analyzed. This study would enable us to further explore the etiology of essential hypertension as well as to identify new genetic markers for predicting early hypertension and target organ damage.

Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterized by loss of motor neurons in the anterior horn of the spinal cord and leading to muscle atrophy. SMA has an autosomal recessive inheritance and affects 1 in 6000 infants with a carrier frequency of 1 in 40. In most cases, it is caused by homozygous gene deletion or gene conversion of the SMN1 gene (0+0 genotype) on 5q11-q13. This genomic region has been duplicated and inverted during evolution. Thus the SMN1 gene has a very homologous copy, called SMN2. Genetic counseling aim at detecting carriers with only one copy of the SMN1 gene (0+1 genotype). SMA carrier testing relies on total copy number quantification of the SMN1 copies by quantitative PCR methods. Nevertheless, cis-duplication of the SMN1 gene on one allele and deletion on the second allele (2+0 genotype) can lead to a misinterpretation as molecular methods show 2 copies of the SMN1 gene and cannot detect the carrier status. The aim of the study is the characterization of a biomarker specific of the cis-duplication of the SMN1 gene in order to allow the detection of this 2+0 genotype which constitutes a trap for genetic counseling. We will use molecular combing to identify a genomic morse code (GMC) composed of a combination of probes specific of a structural motif on the cis-duplication chromosome. The characterization of this GMC is based on the comparison of two sample groups: - The test group, with a maximum of 137 individuals carrying 3 copies of the SMN1 gene (suggesting a cis-duplication on one allele) - The control-1 group, with a maximum of 137 individuals carrying 2 copies of the SMN1 gene A pilot study performed on 24 samples in the two groups is needed to define the exact sample number necessary for statistical analysis of the study. When the GMC will be characterized, its specificity will be evaluated by testing two sample groups: - The test group, with 37 individuals carrying 3 copies of the SMN1 gene - The control-2 group, with 37 individuals carrying 3 copies of the SMN2 gene Molecular combing needs long DNA fibers and usual methods for DNA extraction are not appropriate. This project requires new blood samples for specific DNA extraction. If this project is successful, during a second project, this GMC will be converted into a simple and cheap PCR-based method. We will then evaluate the sensitivity of this method on our sample collection, notably on individuals with the 2+0 genotype defined by familial genotyping.

The purpose of this study has evolved and expanded since its inception. Originally the intent was to establish the functional, molecular and genetic profile of fibroblasts from Fibromuscular Dysplasia (FMD) patients as compared to carefully matched control subjects. While this remains among the objectives, the study has been expanded to undertake a fully powered cross-tissue systems genetics analysis of FMD, and now also the related arteriopathies spontaneous coronary artery dissection (SCAD) and cervical artery dissection (CvAD). The overall objective is to disclose the core biologic mechanisms of these disorders.

This research trial studies genomic analysis in tissue and blood samples from young patients with lung cancer. Identifying specific gene mutations (changes in deoxyribonucleic acid [DNA]) may help doctors tailor treatment to target the specific mutations and help plan effective treatment.

The purpose of this study is to determine, by means of DNA and protein analysis, the relationship between DNA and protein profiles and a number of endpoints, which are important for the patient such as overall survival and side effects.

Prospective study to obtain fresh tumor biopsies and three blood samples from patients with a confirmed histological or cytological diagnosis of well-differentiated neuroendocrine tumors (NETs) or well-differentiated pancreatic neuroendocrine tumors (PanNETs) for molecular profiling.

This is a phase 2 study whose main purpose is to evaluate gene changes and immune biomarkers in patients with solid tumors during treatment with pembrolizumab and in relation to response to treatment. Pembrolizumab is a monoclonal antibody that is designed to block a protein called programmed cell death 1 ligand 1 (PD-L1) which will allow the body's immune system to kill the cancer cells.

Making the diagnosis underlying a painful, swollen joint currently involves aspiration followed by numerous microbiological and biochemical laboratory tests. This can be costly, time consuming and in the case of an acutely swollen joint, lead to a lengthy inpatient admission. There is an unmet need to provide a quick, easy, reliable dipstick like test to analyse joint fluid in the community, clinic, or emergency department setting. The investigators aim to use well established metabonomic techniques to: 1. Analyse fluid from patients with swollen joints 2. Identify potential biomarkers of inflammatory, infective and osteoarthritic causes of joint swelling 3. Correlate this with lubrication and wear properties of the fluid The long term goal is to develop time saving, cost effective, non-invasive diagnostic tests to improve management of a swollen joint. The biomedical research centre at Imperial provides a unique and unparalleled clinical and scientific environment to conduct this research. The Imperial College division of Computational and Systems Medicine has an international reputation in metabonomics and this, together with the high volume of patients with swollen joints treated at Imperial National Health Service Trust (c1000/yr) ensures that the study can take place in an environment conductive to success.

Congenital heart disease (CHD) is the most common type of birth defect but the cause for the majority of cardiac birth defects remains unknown. Numerous epidemiologic studies have demonstrated evidence that genetic factors likely play a contributory, if not causative, role in CHD. While numerous genes have been identified by us and other investigators using traditional genetic approaches, these genes account for a minority of the non-syndromic CHDs. Therefore, we are now utilizing whole genome sequencing (WGS), with the addition of more traditional genetic techniques such as chromosomal microarray or traditional linkage analysis, to identify genetic causes of familial and isolated CHD. With WGS we are able to sequence all of the genetic material of an individual and apply different data analysis techniques based on whether we are analyzing a multiplex family or a cohort of trios (mother, father and child with CHD) with a specific isolated CHD. Therefore, WGS is a robust method for identification of novel genetic causes of CHD which will have important diagnostic and therapeutic consequences for these children.

Adult acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy associated with poor prognosis, especially after relapse. High-throughput genomic studies have highlighted the importance of molecular alteration in the pathophysiology, clinical evolution and treatment response of AML. In addition, identification of specific gene mutation can be targeted by specific inhibitors, opening the way to personalized treatments. However, only a limited number of gene mutations are druggable or actionable, highlighting the need for additional information to guide treatment choices. Among them, new Drug Screening Tests (DST) allow for the screening of library of hundreds of drugs to ex-vivo patient-derived AML cells. Combination of genomic and pharmacologic approaches might therefore improve prediction of drug effects. There is an urgent need to bring these approaches into the clinic but feasibility trials are necessary before incorporating them into treatments strategies.The proposed study is a prospective multicentre feasibility study of a combined "chemo-genomic" approach in patients with advanced AML.

Foundation Medicine Inc. (FMI) is interested in studying the concordance of genomic alterations between primary and/or metastatic surgical biopsies, and circulating tumor DNA (ctDNA) within different solid tumor types and has been developing an assay in order to do so.

Characterization of the driver mutations in an individual metastatic breast cancer patient is critical for many reasons. Effective targeted therapies require identifying genomic alterations in the tumoral tissue. The scarce efficacy of many currently available targeted drugs may be due to the outbreak of resistant clones with different genotype that already present at the initiation of therapy. It is well known the intra-tumor heterogeneity with genetic and non-genetic factors considered as the origin of the tumor cell-clon composition. The acquisition of multiple mutations (driver and passenger), altogether with the stage of differentiation, according to the cancer stem cell hypothesis, confers to the tumor cells clinically important properties, such as resistance to therapies and seeding abilities. Moreover, there is a current challenge in establishing whether the metastatic cells arise from the most aggressive and dominant clone in the primary tumor or the metastasic tissue diverges with substantial genetic changes very early in the evolution of the disease. Primary and metastatic tumor may have a close clonal relationship or evolve in parallel and acquire different genomic alterations. In the real life, it is plausible that both models coexist with different predominance according to the tumoral tissue and etiology. The study hypothesizes that breast cancer metastases and primary tumors could harbor different genomic profiles related to genomic regions of interest in a clinically relevant proportion of metastatic breast cancer patients. Moreover, the genomic aberrations found in the metastatic breast cancer tissue could also be detected in CTCs and circulating free DNA. If true, CTCs and circulating free DNA would be convenient, non-invasive, easily accessible sources of genomic material for the analysis of mutations and other genomic aberrations.

This comprehensive genomic analysis and biospecimen repository study incorporates Next Generation Sequencing (NGS) of archival tumor tissue from 200 subjects with metastatic urothelial cancer in support of several parallel goals. The immediate goal involves generation of a comprehensive report identifying subject specific genetic mutations and/or alterations based on NGS. Additionally, DNA and RNA extracted from tumor specimens and any remaining blocks/slides from the NGS will be stored for future research. Long-term, the goal of this endeavor is to support collaborative translational research projects in metastatic urothelial cancer by allowing investigators to interrogate abstracted coded clinical data linked to data from any biospecimen studies.

The primary objective is to develop an in vitro model of cancer for laboratory study using liver, biliary and pancreatic cancer tissue. The secondary objective is to study the genetic and cellular biology of cancer of the liver, biliary tract and the pancreas. As well the investigators hope to compare molecular and cellular biology of cancer cells with normal cells as well as potentially test the efficacy of current and future anti-cancer therapies. Samples will be collected from tissue that has been resected as part of the treatment for a patient diagnosed with liver, bile duct or pancreas cancer.

A randomized controlled trial looking at the effects of vaginal estrogen and a nonhormonal alternative on the vaginal and urinary microbiome in women with genitourinary syndrome of menopause.