Clinical Trials

To investigate the evolutionary genomic landscape, explore the genetic tumor heterogeneity and microenvironment of multiple primary lung cancer (MPLC) by using tissue genetic analysis and circulating tumor DNA detection, in order to provide robust evidence for the diagnosis, treatment, and surveillance of MPLC.

Resistance to anti-tuberculosis drugs is a continually growing problem. Multidrug-resistant tuberculosis (MDRTB) is resistance to at least rifampicin and isoniazid, and extensively drug-resistant TB is additional resistance to a fluoroquinolone and a second injectable line drug. Methods currently employed in testing for resistance are inadequate and a contributing factor to the 40-50% MDR-TB treatment success rate. Current drug susceptibility testing methods are slow for most drugs, taking weeks. Rapid molecular methods such as the line probe assays, e.g. Hain GenoType MDRTBplus and sl, provide resistant calls to only a limited number of drugs, and are often less useful in smear negative patients. Molecular technologies such as sequencing can provide a comprehensive readout of drug resistance and are able to detect resistant populations at very low levels (≤1%), thus enabling individualized therapy. This can be done directly from sputum. Targeted sequencing amplifies regions of genomic DNA associated with resistance prior to sequencing. Rapid analytic software is used to process the raw sequence data, identify resistance causing mutations and provide a readout of clinically relevant information. However, the feasibility, and more importantly the impact, of this approach has not been evaluated in a clinical trial to establish proof of concept. Aim 1: To conduct a randomised controlled trial to determine the impact of sputum-based targeted sequencing in detecting resistance to second-line TB drugs compared to the current programmatic standard of care (Hain MDRTBplus/sl and adjunct phenotypic drug susceptibility testing) when used to inform of treatment for MDR-TB. Aim 2: To compare currently available drug resistant sequencing pipelines for diagnostic accuracy, sensitivity, specificity and predictive value as compared to culture based phenotypic drug susceptibility testing. Aim 3: To compare the feasibility, accuracy, turn-aroundtime, and cost implications of the above-mentioned diagnostic approaches.

The proposal is to conduct a prospective, multi-cohort study aiming to decipher molecular profiles/biological characteristics of advanced cancer patients during the course of their disease with longitudinal and sequential analyses of tumor and liquid biopsies. This approach will allow i) to develop a model in order to predict tumor response / resistance in real life conditions and to better understand adaptive mechanisms and ii) to potentially propose therapeutic options to enrolled patients following the review of the biological/molecular data generated during this study and during a Molecular Tumor Board in case of disease progression. This study will include 12 cohorts according to tumor type and standard treatment received (See Inclusion criteria I1). Patient will be enrolled before the initiation of standard anti-cancer treatment.

Acetaminophen (APAP) is the most commonly used NSAIDS in clinic, and it is also a common cause of drug-induced liver injury (DILI). In 2012, the proportion of DILI caused by APAP in the United States was 51%, while in Asia, it was only 7.10%. Previously, a small cohort study in the United States screened for some of the susceptibility genes for DILI due to APAP by the Genome wide association study (GWAS) method. However, the genetic susceptibility loci based on the US cohort were not applicable to the Chinese population. Therefore, we make a study design include Chinese population who ingested APAP and divided them into case group and control group according to the occurrence of DILI. We hope to be able to find the root of differences at the genetic level and explore new pathogenic mechanisms.

The main aim of this project is to establish an innovative model of a comprehensive precision oncology platform to help individualizing drug therapy for patients with advanced cancers at The Chinese University of Hong Kong. The other objectives include to optimize the genomic matching and access of patients with unique cancer subtypes to the relevant clinical trials of novel therapies, and to construct a personalized drug screening platform for individuals using novel cancer models established from patient-derived cancer cells and tissues. Other objectives include to investigate the utility and feasibility of genomic sequencing using circulating tumor DNA(ctDNA), and to establish a biobank of tumor tissues derived from patients with unique cancer subtypes.

Precision Acupuncture in the Treatment of Peripheral Neuropathy After Taxane Chemotherapy in Breast Cancer

This study aims to study the correlation between biomarkers of myocardial fibrosis (extracellular volume fraction calculated by cardiac magnetic resonance imaging (MRI) (T1-mapping) and levels of molecular biomarkers of fibrosis) and adverse events in a population of patients with repaired tetralogy of Fallot.

Given that the Emergency Department (ED) has become the entry way for large populations of patients into the health care system, a strategy of sampling MRSA isolates in ED populations and merging this information with patient-level data may present a window to hypothesize and investigate CA-MRSA transmission within the community and its impact on hospital-acquired infections.

This study evaluates the genomic profiles of breast cancer in a prospective and population-based manner. In the first phase, breast tumors are analyzed by whole transcriptome RNA-sequencing. Gene expression profiles, mutational profiles, and transcript isoform-level data will be analyzed in the context of patient information, clinicopathological variables, and outcome, with the purpose to develop new molecular diagnostic assays for breast cancer. Additional genome-scale RNA, DNA, and protein analyses will be performed in the future.

Autoimmune encephalitis are characterized by the subacute development of memory deficits, altered mental status, and psychiatric symptoms, generally in association with anti-neuronal antibodies. Two main groups of autoimmune encephalitis may be distinguished based on the location of the targeted antigen: 1) Intracellular antigens, in which the antibodies are thought not to be pathogenic, and the disorders are usually strongly associated with cancer, constituting therefore paraneoplastic neurological syndromes; 2) Synaptic proteins and surface receptors, in which the antibodies are pathogenic and the frequency of cancer is variable depending on the antibody and the demographic characteristics of the patient. Encephalitis with antibodies against N-methy-D-aspartate receptor is the most common autoimmune encephalitis, being even more frequent than infectious etiologies. It is characterized by subacute onset of memory deficits, psychiatric symptoms, speech dysfunction, seizures, movement disorders, decreased level of consciousness, dysautonomia and central hypoventilation. Nearly 50% of women with anti-NMDAR encephalitis have an ovarian teratoma, while associated tumors in elderly patients are usually carcinomas. In contrast, most cases in children and young men are non-paraneoplastic. Recently, herpes-simplex encephalitis has been described as another trigger of NMDAR encephalitis. Conversely, for the vast majority of the non-paraneoplastic autoimmune encephalitis, no acquired triggers have been described so far. In addition to acquired susceptibility, genetic predisposition may also be important in the pathogenesis of autoimmune encephalitis. The human leukocyte antigen (HLA) is the genetic factor most frequently associated with autoimmune diseases, and it has been already linked to a few autoimmune encephalitis, such as anti-leucine rich glioma inactivated 1 (LGI1), contactin-associated protein-like 2 (CASPR2), IgLON5, and glutamic acid decarboxylase 65 (GAD65) encephalitis. However, no HLA association has been reported for NMDAR encephalitis, suggesting that in this condition, and likely in others, non-HLA loci might be involved in the pathogenesis as well. Genome-wide association studies (GWAS) are useful tools to identify variants at genomic loci that are associated with complex diseases, and in particular, to detect associations between single-nucleotide polymorphisms (SNPs) and diseases. The aim of the study is to detect genetic variants in NMDAR encephalitis and other autoimmune encephalitis.

Glomerulonephritis (GN) generates an enormous individual and social economic burden. However, the therapeutic options are largely based on clinical and pathological parameters and the individual response to therapy or prognosis is uncertain. Recently, along with advances in molecular analysis and computational bioinformatics, genomic data from human renal biopsies could provide a strong foundation for the future of precision medicine in nephrology. In response to a request for applications by the Ministry of Health and Welfare of Korea for the creation of Clinical Research Registry, multi-center N network has been established for prospective cohort with kidney biopsy samples (KORNERSTONE). Through this Network the investigators hope to understand the fundamental biology of glomerulonephritis and aim to bank long-term observational data and corresponding biological data including genomic data from kidney tissues, and kidney pathologic data which is digitalized This database is archived to a web-based platform to access easily and further enrich for researchers.

In multiple sclerosis (MS), the presence of white matter lesions surrounded by a rim of iron is suggested to signify a more severe disease course. Iron rim lesions can be detected through their appearance on susceptibility-based brain MRI at either 3-Tesla or 7-Tesla strength. We know that the formation of chronic active lesions is not uniform across MS cohorts so identifying risk factors which predispose individuals to the formation of rim lesions may provide a useful biomarker for clinical progression. One candidate set of risk factors include genetic variants which prevent some MS patients from resolving acute inflammation following their initial wave of inflammatory demyelination at lesion onset. Additionally, only small longitudinal clinical cohorts have reported the evolution of iron rim lesions many years after their initial formation, as well as their link to clinical disability or disease progression. NUH hold 7T-MRI scans of over 100 patients who received a research MRI with iron-sensitive sequences between 2008-2012. We will recruit 100 patients that received brain MRI several years ago to provide blood samples. The blood samples along with the previously acquired MRI scan will be sent to Johns Hopkins University in the US where genotyping studies will be performed to explore whether this genetic variation contributes to the accrual of chronic active rim lesions in MS. Patients who consent to provide blood samples will also have the option to consent to receive an additional 7-Tesla MRI scan which will allow us to compare how rim lesions evolve and whether their presence is correlated with disability. 30 MRI scans will initially be performed as funding for this amount is already secured. Following analysis of the pilot phase 1 data and securing additional funds, we will contact more patients who have already consented to receive the additional MRI to receive the scan

This study will investigate the utility of integrative sequencing of individuals and families at risk of hereditary cancer syndromes and will uncover novel contributors to tumourigenesis. Integrative sequencing refers to: 1. Whole genome sequencing (WGS) of the germline (inherited) genome 2. Whole exome sequencing (WES) or targeted/panel sequencing of tumour(s) (somatic, tumour-specific mutations) 3. DNA methylation (methylome) analysis of tumour(s) 4. RNA sequencing (transcriptome) of tumour(s) Eligible patients receiving genetic care at Princess Margaret Cancer Centre and the University Health Network may be approached by their genetic counsellor for participation in this study.

This protocol will assess patients with AL amyloidosis who achieve a complete response (CR) or very good partial response (VGPR) to therapy for minimal residual disease (MRD). Three approaches to MRD testing will be used since there is no established method. The investigators will clone and sequence each patient's light chain (LC) gene and design patient-specific primers to evaluate genomic DNA from future marrow specimens. Whole genome sequencing (WGS) will be used to test baseline and follow-up marrow cell DNA, seeking copy number variations in chromosomes 1 and 2 or 22, and structural variations in chromosomes 11 and 14, consistent with the known genetic abnormalities in AL and with clonal LC gene use. Plasma protein analysis by mass spectrometry will also be used to look for fragmentary protein sequences associated with the culprit LC gene of each subject. The feasibility and predictive value of these three approaches in patients achieving CR or VGPR will be evaluated. This protocol will help provide insight into the ways that the disease changes and progresses. MRD testing is likely an important next step in AL management.

The researchers are trying to develop a way to measure the risk of transplant rejection with a blood test.

The study aims include: - Exploring potential predictive molecular profiles to immunotherapy/chemotherapy - Investigating the role of circulating tumor DNA as a dynamic biomarker during immunotherapy/chemotherapy - Identifying possible resistance mechanisms to immunotherapy/chemotherapy Materials and methods: Approximately 150 patients diagnosed with metastatic NSCLC assigned for immunotherapy or chemotherapy will be candidates for inclusion during a 1-2 years period. A comprehensive molecular profiling will be made from the diagnostic biopsy. Before every treatment-cycle a blood sample will be taken to quantify ctDNA. At time of progressive disease during/after first line treatment, patients will be asked to participate in a new biopsy and a comprehensive molecular profiling will be performed. The tissue and blood samples collected will be stored in a biobank. Clinical data will be collected to perform a comprehensive database. Analysis: Potentially predictive molecular profiles for immunotherapy/chemotherapy will be found by comparison of treatment outcome for patients with specific molecular characteristics. Through quantification of ctDNA during treatment and upon progression, the role of ctDNA as a dynamic biomarker will be further strengthened. Differences in molecular profiles pre- and post-treatment may reveal resistance mechanisms to treatment. Molecular profiling on progression can be valuable in second-line treatment guidance.

The general aim of the project is the identification of dynamic molecular markers that can help the early and real time prediction of sustained benefit or no benefit from ibrutinib treatment in CLL harboring TP53 mutations. Specific aims of the project include: 1) Assess whether clearance of TP53 mutated clones translates into a predictive biomarker of long term benefit from ibrutinib treatment in CLL. 2) Assess whether plasma cell free DNA represents a sensitive tool that can early and dynamically inform on the development of ibrutinib resistant mutations in CLL.

The purpose of this study is to validate the impact of ALDH2 Glu504Lys polymorphism on aortic dissection.

New strategies are needed to early detect myocardial involvement in these diseases. Histological studies showed that diffuse fibrosis and cardiomyocyte hypertrophy precede the LV remodelling (dilatation) observed by cardiac imaging. Quantification of LV diffuse myocardial fibrosis using magnetic resonance imaging (MRI) could reach this goal. Recently, contrast enhanced cardiac MRI has been used to measure the extracellular volume fraction (ECV) of the myocardium, and it has been able to detect diffuse myocardial fibrosis. In diseases in which increased collagen deposition enlarges the extra-cellular space, the ECV can act as a fibrosis index. ECV is correlated with the amount of fibrosis measured by histology. Left ventricular overloads induced by regurgitant VHD result in cardiomyocyte hypertrophy and diffuse fibrosis. Other methods can be used to estimate the degree of myocardial fibrosis such as the serum level of galectine-3 or ST2. Moreover, although the pathophysiological mechanisms leading to the occurrence of myocardial fibrosis differ in patients with various cardiac diseases, the cellular effectors of fibrotic remodelling are common and involve similar signalling pathways. At the cellular level, key progression of ventricular hypertrophy is associated with increased cardiomyocytes apoptosis and fibrosis, suggesting that these two processes are responsible for the transition. To our knowledge, no study has analysed the impact of the rate of myocardial diffuse fibrosis, non-invasively estimated by ECV, in the risk of LV dysfunction during MR and AR, especially after surgery. The measurement of ECV could become an important tool for risk stratification in left-sided regurgitant VHD. Thus, it would provide an early marker of LV myocardial involvement before the occurrence of global remodeling, might help physicians in surgical decision, and would improve prognosis. This is an innovative original project because it uses modern imaging modalities to answer to a crucial question. The clinical implications would be important because this work would modify the international surgical indications of MR and AR in order to finally improve the prognosis of patients with this frequent heart disease. Moreover, investigators will analyze the genetic factors that can influence the myocardial reaction resulting from these regurgitations, which will improve the quality of this work and offer new future perspectives. Investigators hypothesize that the ECV measurement could be used as an early predictor of LV dysfunction in the left-sided valve regurgitations.

Conduct a prospective study to confirm blood and urine ctDNA detection value in non-small-cell lung cancer patients.