3796 results for "*oma"

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• Viral integration analysis of hepatocellular carcinoma using virus capture sequence.

  Hepatitis B viral (HBV) DNA is frequently integrated into the genome of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas it is yet to be clarified in patients after HBV disappearance (prior HBV, hereafter). This study aimed to identify viral integration such as HBV and adeno-associated virus type 2 (AAV2) into the HCC genome as oncogenic event.

  Study JGAS000194

• Single cell sequences in patients with malignant tumors

  We perfomed single cell RNA and TCR sequencing of 2 lung adenocarcinoma patients and 3 head and neck squamous cell carcinoma to assess the detailed biological mechanisms of resistance to immune checkpoint inhibitors.

  Study JGAS000480

• 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

• Pilot study of adoptive cell therapy using cultured tumor infiltrating lymphocytes for Japanese melanoma patients refractory to immune-checkpoint inhibitors

  To evaluate feasibility of the adoptive cell therapy (ACT) using tumor infiltrating lymphocytes (TIL) in Japanese melanoma patients who failed the immune checkpoint inhibitors (ICIs) and investigate the immune components and immunologic milieu within the pretreatment tumor and expanded TILs from there.?Three patients whose clinical subtype were mucosal, superficial spreading, and acral melanoma were treated and the all completed the TIL-ACT. Clinical response were one short-partial response, one relatively long-stable disease, and one progression disease. Whole-exome and transcriptional analysis of pretreatment tumor revealed the various?immunophenotypes including tumor mutation burden with immunogenic neoantigens and upregulation of immunosuppressive gene signatures.

  Study JGAS000249

• Whole-genome sequencing on hepatocellular carcinoma with nodule-in-nodule appearance reveals stepwise cancer evolution

  We examined five cases with hypovascular early HCC with hypervascular foci, so-called nodule-in-nodule HCC. Multiregional sampling was performed from both the inner hypervascular region and outer hypovascular region, together with noncancerous liver tissue and lymphocytes as controls. Comprehensive analysis of genomic aberrations, such as single nucleotide variants (SNVs) and structural variations (STVs), was performed by whole-genome sequencing.

  Study JGAS000190

• Paediatric Hepatic International Tumour Trial (JPLT2: PHITT)

  Hepatoblastoma (HBL) is the most common primary liver tumor in children. Despite their diversity in histopathological phenotype and clinical outcome, the underlying molecular aberrations have not been fully understood. Here we describe a comprehensive landscape of genomic, epigenomic, and transcriptomic heterogeneity among the 163 cases of HBLs and transitional liver cell tumors (TLCTs) collected in the multicenter clinical trial JPLT-2. The total numbers of mutational events in HBLs are very few (0.52 SNVs/Mb on exonic regions) but show a positive correlation with the age of onset. While dysregulation of Wnt-pathway related genes was observed (somatic deletion or mutations of CTNNB1 and germline or somatic mutations of APC) in 83.6% of the HBL cases, TERT promoter mutations are mainly in the elderly HBLs (> 8 years old), meeting with the proposed criteria of TLCT. These TLCT cases are clustered in the hypermethylated epigenotype in promoter and enhancer regions. Copy number analyses also revealed recurrent 11p15.5 UPD/LOHs including the IGF2/H19 region (31.6%), focal deletions in 4q35 (15.8%) and focal amplifications in 2q24.3 (7.0%) predominantly in the child and infant HBLs. Motif enrichment analysis of the specific hypomethylated enhancers in these HBL subtypes suggests specific binding of ASCL2, the regulatory transcription factor for definitive endoderm and digestive systems. Transcriptome and histochemical analysis revealed that ASCL2 is upregulated not in HCC and TLCT but in child and infant HBL, suggesting their ?cell of origin? derived from the premature hepatoblast with high proliferative potential such as intestinal epithelial cells. Systematic molecular profiling of HBL will provide a fundamental understanding of hepatoblast carcinogenesis and clues for risk stratification.

  Study JGAS000236

• 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 exome sequencing and RNA-seq of esophageal squamous cell carcinoma

  We perform integrative genome-wide analyses such as whole-exome sequencing, copy number variant(CNV) analysis, and gene expression analysis using next-generation sequencing and other methods to elucidate driver genes and signaling pathways causing tumorigenesis and cancer progression, leading novel molecular diagnostics and molecular therapies.

  Study JGAS000367

• Whole genome analysis of liver cancer by long-read sequencing

  Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

  Study JGAS000361

• Research of factors related to diagnosis, progression, prognosis and treatment of hepato-biliary-pancreatic malignancies

  Advanced cancers with metastasis and/or recurrence are usually resistant and refractory to treatment. In our studies, whole exome sequencing analysis, comprehensive epigenetic analysis and genome-wide expression analysis were performed using cancerous and non-cancerous tissues derived from multicentric cohort study of hepatocellular carcinoma (HCC). The aim of the studies is identification of the refractoriness-related deriver genes for application to novel molecular targeted therapy and preventive medicine. The studies are intended for refractory HCC. High frequency of the tumor recurrence even after curative resection is one of the major difficulties in the treatment of HCC. According to our previous studies, not the recurrence itself, but the recurrence pattern has critical effects on prognosis of the patient with HCC. Then, we analyzed the cancerous and non-cancerous tissues of primary HCC on the point of the recurrence patterns in accordance with or without Milan criteria. The materials were obtained from thirty three patients underwent curative hepatectomy for HCC at Department of Hepato-Biliary-Pancreatic Surgery, Tokyo Medical and Dental University Hospital. Written informed consent from these patients, as well as the institutional review board approved was obtained. The determination of the refractory HCC group (16 cases) was based on the point of the recurrence patterns in accordance with Milan criteria for the recurrent tumor (solitary <5cm, or up to 3 nodules <3 cm, without major vascular invasion or distant metastasis) that has been proposed as the useful criteria of the liver transplantation for HCC. The cellular DNA was extracted from the cancerous and non-cancerous tissues of primary HCC by the phenol-chloroform method. After SNP certification using Genome-Wide Human SNP Array 6.0 (Affymetrix), whole exome sequencing was performed at the Cancer Institute of JFCR, as the support infrastructure. Exome sequencing was performed using HiSeq 2000 (Illumina), and the obtained reads were mapped to the human reference genome (hg19) using BWA software. GATK software was used for local realignment base call recalibration. Single nucleotide variants (SNVs) and indels were analyzed by MuTect and SomaticIndelDetector, as well as visual confirmation by IGV software.

  Study JGAS000052