12534 results for ""non-traditional+communal+storytelling+approach"+novel+segment+noted+in+critical+commentary"

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• 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

• Leukemic evolution of donor-derived cells harboring IDH2 and DNMT3A mutations after allogeneic stem cell transplantation

  An individual with acute myeloid leukemia (AML) received peripheral blood stem cell (PBSC) transplantation, but later experienced relapse. Whole-exome sequencing of bone marrow cells obtained from different stages of this patient as well as PBSC of the donor revealed that relapsed AML was not the regrowth of the original leukemic clones, but donor cell leukemia (DCL). Interestingly, some of the oncogenic mutations found in DCL were already present at a low frequency in the donor PBSC. Target deep sequencing of these genes indeed confirmed this observation, and revealed that the emergence of additional oncogenic mutations triggered leukemic evolution.

  Study JGAS000017

• Single-cell RNA sequencing of SI-NET

  Small intestinal neuroendocrine tumors (SI-NETs) arise from hormone-producing cells in the gut, yet the molecular changes driving malignant transformation remain poorly understood. Bulk tissue-based analyses make it challenging to distinguish signals derived from normal cells from those of normal hormone-producing cells. In this study, we analyzed SI-NETs at single-cell resolution and directly compared tumor cells with their corresponding normal hormone-producing counterparts using single-cell RNA sequencing. Tissue samples were obtained from two patients undergoing tumor resection surgery. Cells from corresponding normal intestinal mucosa and SI-NET tumors were isolated using specific markers and analyzed for direct comparison.

  Study EGAS50000001584

• North American Brain Expression Consortium (NABEC) Exome Sequencing

  A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on mRNA expression distinct human brain regions. We show that brain tissues may be readily distinguished based on expression profile. We find an abundance of genetic cis regulation mRNA expression. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation.

  Study EGAS00001002110

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD43291_Novaseq__WG_

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from lung tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will deeply sample from individuals with smoking-related lung diseases (COPD, pulmonary fibrosis, lung cancer) and those without smoking history. This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumor development.

  Study EGAS00001003502

• Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden

  Profiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we developed a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions was strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients.

  Study EGAS00001004657

• Targeted sequencing of follicular lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Follicular lymphoma displays morphological and clinical heterogeneity, underpinned by shared molecular pathogenesis. Mutations in epigenetic regulators alongside t(14;18) have been identified as disease initiating events. Additional mutational diversity suggests disease heterogeneity. Whether this resolves into mechanistically distinct subsets remains an open question. Targeted sequencing was applied to an unselected population-based FL cohort (n=548) diagnosed in a catchment population of ~4 million (14 centers), with full clinical follow-up (n=538) that included 96 DLBCL transformations. We investigated whether molecular subclusters of FL can be identified, and whether mutational data provide predictive information relating to transformation.

  Study EGAS00001005238

• 2014_Lung_sq_WES

  Purpose Lung squamous cell carcinoma (SqCC) is the second most prevalent type of lung cancer. Currently, no targeted-therapeutics are approved for treatment of this cancer, largely due to lack of systematic understanding of the molecular parthenogenesis of the disease. To identify therapeutic targets and comparatively analyze them in lung SqCC, we probed somatic alterations of Korean lung SqCC. Patients and Methods We performed massively parallel whole-exome sequencing of 104 Korean lung SqCC patients’ samples with matched normal samples. In addition, copy number analysis and transcriptome analysis were conducted for a subset of these samples. Clinical association with cancer-specific somatic alterations was investigated.

  Study EGAS00001002844

• Genomic and ecologic characteristics of the airway microbial-mucosal complex

  Lung diseases due to infection and dysbiosis affect hundreds of millions of people world-wide. Microbial communities at the airway mucosal barrier are conserved and highly ordered, reflecting symbiosis and co-evolution with human host factors. We show here the results of the first systematic culture and whole-genome sequencing of the principal airway bacterial species. We match the gene content of bacterial isolates to human transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways that can sustain host interactions with the microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosal immunity in lung diseases of global significance.

  Study EGAS00001006689

• Linked-read based analysis of Medulloblastomas

  Medulloblastoma (MB) is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases of medulloblastomas. The molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants (SVs) in recurrently affected gene typically requires the application of long-read technologies. Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements.

  Study EGAS00001007064