3855 results for "*geneti*"

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• University of Zurich (UZH) - Snedeker lab

  Authorised Personnel: The individuals at the User Institution to whom University of Zurich (UZH) grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: UZH and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. UZH: University of Zurich, Raemistrasse 71, 8001 Zurich, Switzerland

  Dac EGAC50000000817

• Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer

  Study EGAS00001007188

• Accessibility Over Transposable Elements Reveals Genetic Determinants of Stemness Properties in Normal and Leukemic Hematopoiesis

  Study EGAS00001007191

• Construction of endoscopic biopsy banking for understanding the intestinal environment in colorectal diseases and exploratory studies using these banking systems.

  Colorectal cancer is the most common type of cancer in Japan. Although some colorectal cancers have a genetic background, most colorectal cancers are sporadic. Known risk factors for colorectal cancer include smoking, obesity, lack of exercise, and red and processed meat. Furthermore, although it has been suggested that changes in the intestinal environment due to changes in diet and lifestyle may be involved in the increased incidence of colorectal cancer in Japan, the molecular mechanism has not yet been fully elucidated. The main objective of this study is to elucidate the changes in the intestinal environment that cause colorectal tumors, and also to contribute to the establishment of colorectal mucosal tissue banking in Japan.

  Study JGAS000655

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001141

• Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

  Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two-thirds will relapse with fatal disease within five years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure, and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known about the genetic determinants driving their stemness properties. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC) 6, we investigated accessible chromatin unique across normal hematopoietic and cancer cell states and identified transposable elements (TEs) as genetic determinants of both primitive populations in comparison with their downstream mature progeny. A clinically-relevant TE chromatin accessibility-based LSCTE121 signature was developed that enabled patient classification based on survival outcomes. Through functional assays, primitive cell specific-TE subfamilies were found to serve as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors, including LYL1 in LSCs. Finally, using chromatin editing tools, we establish that chromatin accessibility at LTR12C elements in LSCs are necessary to maintain stemness properties. Our work identifies TEs as genetic drivers of primitive versus mature cell states, where distinct TE subfamilies account for stemness properties in normal versus leukemic hematopoietic stem cells.

  Study EGAS50000001147

• Clonal evolution of metastatic colorectal cancer under anticancer therapies

  To investigate the clonal evolution of metastatic CRC at the single-cell level, we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC.

  Study EGAS50000001023

• DAC for human-derived clonal organoid studies

  This is the DAC for human-derived clonal organoid culture studies. It includes the study to investigate the clonal evolution of metastatic CRC at the single-cell level, where we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC.

  Dac EGAC50000000628

• Molecular profiles in early onset prostate cancer

  Paired germline (blood) and tumour samples were collected from prostate cancer cases <65 years at diagnosis to identify genetic changes in early onset prostate cancer.  Whole exome sequencing was performed on these samples. The aim was to determine if these changes are associated with more aggressive disease and to identify targets for treatment and screening by identifying associations with family history, DNA repair germline mutations, and clinical features.

  Study EGAS50000001467

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• RNA sequencing of genetically modified human iPSCs modeling patients with autism spectrum disorders (ASD)

  We generated two genetically modified iPSC lines. In each line, a single promoter variant identified in a patient with autism spectrum disorder (ASD) was introduced by using the CRISPR/Cas9 system. These mutant lines were analyzed by RNA-seq together with control lines to assess the impact of the introduced variant.

  Study JGAS000651

• Research for genetic causes and mechanisms of Hirschsprung's or Hirschsprung's related diseases

  Hirschsprung's disease (HD) is an abdomen disorder which is caused by absence of enteric neurons. HD is a complex genetic disorder and several causing gene mutations have been identified including the receptor tyrosine kinase gene. However, the whole mechanism of HD remains unknown and additional genetic causalities are implicated. To further investigate the genetic causalities of HD, we conducted whole-exome sequencing of patients with HD and unaffected patient's families.

  Study JGAS000007

• Phylogenetic analysis of combined lobular and ductal carcinoma of the breast

  Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, we analyzed two combined lobular and ductal carcinoma (CLDC) cases, including one mixed ductal-lobular carcinoma (MDL) lesion, by next generation sequencing.

  Study JGAS000300

• Whole genome, whole exome and transcriptome sequencing of 10 ccRCC with Von Hippel-Lindau disease

  The aim of this study is to investigate genetic and transcriptomic profiles of inherited ccRCC with Von Hippel-Lindau disease.

  Study JGAS000544

• Identification of genetic mutations characteristic for recurrence and metastasis of lymphoma.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent B cell lymphoma, and the purpose of this study is to find the characteristics of recurrent B cell lymphoma by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000087

• Study for establishment for effective screening and diagnosis of Lynch syndrome

  The purpose of this study is to establish efficient diagnostic procedure of the Lynch syndrome in Japan and to determine the MMR gene mutation spectrum and clinicopathologic characteristics.The person who is suspected Lynch Syndrome and gives informed consent for participation in this study .To carry out the project ?Construction of clinical and genetic integral information database to help Lynch syndrome management?, the following three are required. 1) screening for Lynch syndrome-suspected cases, 2) genetic testing to define Lynch syndrome, 3) integration of detailed clinical data of Lynch syndrome, and 4) The case which has not been diagnosed Lynch syndrome, is investigated causing gene.

  Study JGAS000638

• New classification of occlusive cerebrovascular diseases by combining diagnostic imaging and genetic analysis of RNF213

  The aim of the study is to unravel the genetic and environmental background of moyamoya disease and to understand the pathophysiology of the disease by utilizing radiological evaluations. We will identify susceptibility genes other than RNF213. We also assess whether genetics affects radiological characteristics including collateral development, tortuosity of the main trunk of the arteries and the extent of stenosis. Environmental factors will be evaluated such as feces, urea, and cerebrospinal fluid.

  Study JGAS000540

• Whole Genome Sequencing Analysis of Adult T-cell Leukemia/Lymphoma

  In this study, we have performed the whole genome sequencing (WGS) for primary tumors from adult T-cell leukemia/lymphoma (ATL) to identify recurrent genetic mutations and structural variants.

  Study JGAS000320

• Comprehensive genomic analysis for AYA with acute lymphoblastic leukemia

  AYA with B-ALL showed extremely inferior outcomes when compared to children. Genetic basis undelying AYA B-ALL is largely unknown. We performed integrated analysis of RNA-seq (hum0045���JGAS000047) and target DNA-seq.

  Study JGAS000276

• Neuron-specifc methylome analysis of Alzheimer's disease brain

  Neuron-specific methylome analysis of Alzheimer's disease brain to detect epigenetic changes related to the pathomechanism.

  Study JGAS000125

• Research for candidate genes of splenic epidermoid cyst

  Splenic epidermoid cyst is a very rare benign tumor-like lesion filled with fluid or semi-fluid material. It occurs mostly in 2nd or 3rd decades of life with some female dominance. Most cases are asymptomatic and the clinical symptoms are dependent on the size of the cyst. Exome re-sequencing is an efficient strategy to selectively sequence the protein-coding regions of the genome, and has increasingly been used to identify novel genetic variants underlying Mendelian diseases. In this study, exome re-sequencing of 8 Japanese patients with splenic epidermoid cyst were conducted.

  Study JGAS000008

• Genetic analysis in monozygotic twins discordant for bipolar disorder

  To identify genes relevant to bipolar disorder, an exome sequence analysis was conducted in 3 pairs of healthy monozygotic twins as control twins in this study. In addition to this data set, an exome sequence analysis was also conducted in several monozygotic twins discordant for bipolar disorder.

  Study JGAS000014

• Comprehansive analysis of somatic mutations and genetic variations with whole genome sequencing

  Indetification of stractural variations by using of long read whole genome sequencing data

  Study JGAS000516

• Identification of genetic polymorphism on aggressive periodontitis

  Periodontitis is an inflammatory disease with loss of gingival tissue and alveolar bone. Aggressive periodontitis is rapidly progressive form of periodontitis in young people. It has been demonstrated that the susceptibility to AgP is influenced by genetic risk factors. However few were established as a risk factor for aggressive periodontitis. To identify genetic risk factors for aggressive periodontitis in Japanese population, we conducted the exome sequence of unrelated patients.

  Study JGAS000040

• Identification of RNA biomarkers in Parkinson's disease patients

  Parkinson?s disease (PD) is an age-related, chronic and progressive neurodegenerative disorder characterized by a loss of dopaminergic neurons and subsequent motor symptoms. These overt motor symptoms are often preceded by prodromal non-motor symptoms. Though a number of genetic and environmental factors have been identified to play a role in PD, more exact methods for both diagnosing and assessing prognosis are yet to be discovered. By analyzing the transcriptome of early-stage PD patients, this study aims to identify genes (including important non-coding RNAs) and pathways altered at disease onset that may be used as novel biomarkers for PD diagnosis as well as potential new drug targets. The study consists of three main sources of data: first year blood transcriptomes, second year blood transcriptome and matched neural stem cell (NSC)/neuron transcriptomes. All transcriptome libraries were synthesized and sequenced using no-amplification non-tagging cap analysis of gene expression (nAnT-iCAGE) on the Illumina HiSeq 2500 platform. Resulting data was mapped to the human genome annotation (hg38), processed CAGE tags were clustered ready for differential expression analyses. First year blood sequencing consisted of 22 PD patients and 10 healthy controls across four lanes. In the second year, a further four lanes were sequenced containing 17 PD patients (12 patients from the first year and 5 new patients) along with 10 healthy controls and 5 first year blood samples matching the new second year patients.

  Study JGAS000119