5735 results for "canc*"

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• Global Architecture of anti-Tumor B-Cell Immunity against Gastric Cancer

  Recent successes in tumor immunotherapies have warranted the importance of tumor immunity. Compared to the T-cell immunity, B-cell immune system in cancer is largely elusive. Here we immunogenetically profiled tumor-infiltrating B-cell and T-cell repertoires for exome- characterized diffuse-type gastric carcinoma (DGC), which is remarkable for its B-cell infiltrations, unraveling previously un-defined architectures of B-cell immunity and its interplays with T-cell immunity in cancer. We also performed transcriptome analysis to enumerate the proportions of tumor-infiltrating immune cells in the gastric cancer environment .

  Study JGAS000141

• Integrated copy number and expression analysis identifies profiles of whole-arm chromosomal alterations and subgroups with favorable outcome in ovarian clear cell carcinomas

  Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism arrays in 57 (31 CCCs, 14 SCs, and 12 ECs) and expression microarrays in 55 epithelial ovarian cancers (25 CCCs, 16 SCs, and 14 ECs), and then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%) (P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the others (CCC-1and CCC-3) (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%) (P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis.

  Study JGAS000022

• Genomics characterization of primary central nervous system lymphoma

  Primary central nervous system lymphoma (PCNSL) is a rare malignancy confined to the central nervous system (CNS). Despite low tendency of systemic dissemination, its prognosis is poor with median overall survival of 2?4 years. Due to its rarity, knowledge of genomic alterations underling PCNSL pathogenesis is severely limited. Here we performed whole-exome sequencing on 44 PCNSL and paired normal specimens, revealing high penetrance of nonsynonymous somatic mutations in PIM1 (95.5%), BTG2 (88.6%) and MYD88 (81.8%). Interestingly we found oncogenic mutations in GRB2, and this effect was cancelled when transformed cells are treated with inhibitors to downstream kinases MAP2K1/2. Further, when tumor cells carries MYD88 mutations, the same mutations were also found at low frequency in peripheral blood mononuclear cells (PBMNC), implying that MYD88 mutation?positive precancerous cells originate outside CNS and develop to lymphoma with additional genetic hits that fit the CNS environment.

  Study JGAS000021

• Target sequencing of 27 cancer-predisposing genes and 13 renal cell carcinoma-related genes in Japanese renal cell carcinoma patients

  Identifying causative genes via genetic testing is useful for the screening, prevention, and treatment of cancer. Several hereditary syndromes are known to occur in renal cell carcinoma (RCC). However, these evidences came from the European population; it remains unclear how the RCC-related genes and other cancer-predisposing genes contribute to the development RCC in the Japanese population. A case-control study of 14 RCC-related genes and 26 cancer-predisposing genes was performed using 1,563 Japanese patients with RCC and 6,016 controls. Patients were divided into two major histological subtypes of clear cell RCC (ccRCC) or non-clear cell RCC (nccRCC). Gene-based analysis of germline pathogenic variants in patients with each subtype and cancer-free subjects was performed. Following quality control, 1,532 patients with RCC and 5,996 controls were further analyzed. For ccRCC, 52 of 1,283 (4.05%) patients carried pathogenic variants mainly in the cancer-predisposing genes such as TP53 (P = 1.73 �� 10-4; OR, 5.8; 95% CI, 2.2���15.7). Approximately 80% of patients with pathogenic variants in TP53 had p.Ala189Val that was specific in East Asian population. For nccRCC, 14 of 249 (5.62%) patients carried pathogenic variants mainly in the RCC-related genes such as BAP1 (P = 6.27 �� 10-5; OR, Inf; 95% CI, 10.0���Inf), and FH (P = 6.27 �� 10-5; OR, Inf; 95% CI, 10.0���Inf). Our study showed different and population-specific contributions of risk genes between ccRCC and nccRCC in Japanese for better-personalized medicine.

  Study JGAS000414

• Intractable Cancer Therapy Development through a New Target Identification by Molecular Profiling

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

  Study JGAS000075

• Homozygous inactivation of CHEK2 is linked to a familial case of multiple primary lung cancer with accompanying cancers in other organs

  In clinical practice, there are a number of cancer patients with clear family histories, but not belonging to existing familial malignancies. Recent advances in genomic technologies have enhanced the possibility of identifying causative genes in such cases. Two siblings, an elder sister and a younger brother, were found to have multiple primary lung cancers at the age of 60. The former subsequently developed breast cancer, and had a history of myoma uteri. The latter had initially developed prostate cancer at the age of 59, and had a history of colon cancer. SNP genotyping revealed that approximately 10% of the genomes were homozygous in both patients. Exome sequencing revealed non-synonymous mutations in four genes in the runs of homozygosity: CHEK2, FCGRT, INPP5J, and SFI1. Evolutionary conservation of primary protein structures suggested the functional importance of the CHEK2 mutation, R474C. This mutation altered the tertiary structure of CHK2 by disrupting the salt bridge between R474 and E394. No such structural changes were observed with the other three mutated genes. Subsequent cell-based transfection analysis revealed that CHK2 R474C was unstable and scarcely activated. We concluded that CHEK2 is a causative gene in this case of familial cancer. Although homozygous inactivation of CHEK2 in mice led to cancers in multiple organs, accumulation of additional human cases is needed to establish its pathogenic role in humans.

  Study JGAS000057

• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Identification of genetic mutations characteristic for recurrence and metastasis of gastric cancer.

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

  Study JGAS000086

• Systematic identification of long non-coding RNAs potentially involved in gastrointestinal carncer

  Recent work has suggested various important functions and molecular mechanisms for long non-coding RNAs (lncRNAs) and they are also thought to play critical roles in cancer. However the importance of lncRNAs in cancer biology is still unclear. In this study, we aim to comprehensively identify novel lncRNAs that are critically involved in tumorigenesis and progression in gastrointestinal cancer.

  Study JGAS000011

• comprehensive genetic analysis and database construction for head and neck cancer

  The main purpose is to conduct comprehensive genetic analysis of head and neck malignant tumor tissue and patient-derived blood, and to construct a database for it. By analyzing these databases, we aim to clinically identify recurrence and metastasis prediction markers and establish new molecular target therapies.

  Study JGAS000214

• Comprehensive analyses of genetic aberrations in gastroenterological tumors

  Intestinal metaplasia (IM) is a risk factor of gastric cancer in gastric mucosa with Helicobacter pylori infection. To explore the susceptibility to the cancer development in pure gastric IM, we investigated landscape of genetic alterations in gastric single-glands with IM.

  Study JGAS000269

• Research for biological features by gene expression analysis and biomarkers at diagnosis/therapeutics in lung cancer

  WGS, WES, ATAC-seq and methylation analysis with DNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients. RNA-seq analysis with RNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients.

  Study JGAS000610

• Genomic features of Helicobacter pylori-na��ve diffuse-type gastric cancer.

  Helicobacter pylori (HP) is a major etiologic driver of diffuse-type gastric cancer (DGC). However, improvements in hygiene have led to an increase in the prevalence of HP-na��ve DGC; that is, DGC that occurs independent of HP. Although multiple genomic cohort studies for gastric cancer have been conducted, including studies for DGC, distinctive genomic differences between HP-exposed and HP-na��ve DGC remain largely unknown. Here, we employed exome and RNA sequencing with immunohistochemical analyses to perform binary comparisons between 36 HP-exposed and 27 HP-na��ve DGCs from sporadic, early-stage, and intramucosal or submucosal tumor samples. Among the samples, 33 HP-exposed and 17 HP-na��ve samples had been preserved as fresh-frozen samples. HP infection status was determined using stringent criteria. HP-exposed DGCs exhibited an increased single nucleotide variant burden (HP- exposed DGCs; 1.97 [0.48���7.19] and HP-na��ve DGCs; 1.09 [0.38���3.68] per megabase; p=0.0003) and a higher prevalence of chromosome arm-level aneuploidies (p&lt;0.0001). CDH1 was mutated at similar frequencies in both groups, whereas RHOA���ARHGAP pathway misregulation was exclusive to HP-exposed DGCs (p=0.0167). HP-exposed DGCs showed gains in chromosome arms 8p/8q (p&lt;0.0001), 7p (p=0.0035) and 7q (p=0.0354), and losses in 16q (p=0.0167). Immunohistochemical analyses revealed a higher expression of intestinal markers such as CD10 (p&lt;0.0001) and CDX2 (p=0.0002) and a lower expression of the gastric marker, MUC5AC (p=0.0305) among HP-exposed DGCs. HP-na��ve DGCs, on the other hand, had a purely gastric marker phenotype. This work reveals that HP-na��ve and HP-exposed DGCs develop along different molecular pathways, which provide a basis for early detection strategies in high incidence settings.

  Study JGAS000575

• Establishment of an integrated database for clinical and genomic data in cancer

  In this study, to clarify the genomic varieties of MM in Asian population, we planned to investigate the genomic features in Japanese population, represented as an Asian cohort, and preformed the comprehensive genomic analysis of MM cells with newly diagnosed multiple myeloma (NDMM) by means of targeted capture sequencing (TCS) method. In our TCS assay, MM cells are subjected to the detection of following genomic abnormalities; IG rearrangements, IG associated translocations, CNAs, and somatic mutations from 340 genes related to the pathogenesis and therapeutic agent of MM.

  Study JGAS000206

• Genomic profiling identified ERCC2 helicase domain mutations respond to platinum-based neoadjuvant therapy in urothelial bladder cancer

  Genomic profiling of tumours enables therapeutic decisions, and identifying drug-matched mutations will prolong survival and prognosis. Here, we generated a custom panel for detecting genetic alterations in 19 patients with urothelial bladder cancer. This panel targeted 71 genes associated with urological cancer. Targeted sequencing was performed on formalin-fixed paraffin-embedded tumour tissues. In this study, we revealed genome profiles and actionable mutations in patients with urothelial bladder cancer.

  Study JGAS000241

• Loss of presentation of estimated neoantigens from mutated genes in ctDNA was essential for fostering primary to recurrent tumors in postoperative colorectal cancer cases

  Specific parameters regarding mutations at primary sites for the detection of postoperative recurrence using circulating tumor (ct)DNA liquid biopsy are lacking. In the current retrospective study, we conducted target resequencing of ctDNA using 47 plasma samples and established a cancer panel carrying the commonly mutated genes between primary and recurrent tumors. We found that mutated genes in ctDNA indicated immune-resistance traits with respect to the impaired ability to present neoantigens by loss of expression or binding affinity to HLA in the primary tumor. Compared with the estimated neoantigens from all mutated genes in primary tumors, the neoantigen peptides from commonly mutated genes between primary and recurrent tumors showed abundant and significant expression with no binding affinity to HLA. Therefore, ctDNA mutations can be frequently and postoperatively detected to identify recurrence; however, these mutated genes were derived from immune-tolerated clones owing to the loss of neoantigen presentation in primary CRC tumors.

  Study JGAS000549

• Prediction of response to preoperative chemoradiotherapy in rectal cancer based on whole-exome sequencing and transcriptomic analysis

  Accumulating evidence suggests that radiotherapeutic success has an immune-associated component. We aimed to investigate the immunogenomic profiles associated with response to preoperative chemoradiotherapy (CRT) in patients with locally advanced rectal cancer.

  Study JGAS000158

• Common and rare germline variants in Japanese prostate cancer patients

  Study JGAS000487

• Defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Germline structural variants (SVs) are challenging to identify by conventional genetic testing assays. Long-read sequencing has improved the global characterization of SVs, but its sensitivity at genetic loci associated with high- and moderate-penetrance cancer susceptibility has not been reported. This study used long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Study EGAS50000000286

• single-cell RNA-Seq of colorectal cancer patient samples

  Study EGAS00001006665

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___DNA_sequencing

  This study will reconstruct the single cellular phylogeny of tumour and immune cells in relation to both genomic, functional, and spatial location. 20 tumours in total will be studied, including non-progressing small renal masses, progressing small renal masses, relatively indolent larger tumours, and high risk tumour with metastatic sampling. We aim to: Generate a focused, comprehensive phylogenetic characterisation of tumour cells Understand the dependencies of the cancer genome, transcriptome, tissue architecture and the single cellular micro-environment Quantify the single cellular composition and functional intra- and inter- tumoural heterogeneity Determine the phylogeny of tumour associated lymphocytes and their relationship to neo-epitopes and the immune microenvironment Investigate the mechanisms by which the tumour-normal interface constrains tumoural growth

  Study EGAS00001003517

• WTCCC case-control study for Breast cancer

  WTCCC genome-wide case-control association study for Breast cancer (BC) using the 1958 British Birth Cohort collection as controls.

  Study EGAS00000000024

• WTCCC case-control study for Breast cancer - Combined Controls

  WTCCC genome-wide case-control association study for Breast cancer (BC) - Combined Controls.

  Study EGAS00000000025

• Sequencing_of_rare_human_histiocytic_tumour

  Sequencing of rare human histiocytic tumour

  Study EGAS00001000591

• MutWP4__CRUK_Grand_Challenge_Mutographs_of_Cancer__Pancreatic_Organoids

  The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge. Different patterns of somatic mutation are generated by the different environmental, lifestyle and genetic factors that cause cancer, many of them are still unknown. Within Mutographs, Kings College London will characterise the mutational signatures induced by putative human carcinogens in order to identify the origins of mutational signatures found in human cancers. To achieve this human organoid cell cultures will be exposed to a representative catalogue of known or suspected human carcinogens and mutagens and, using whole genome sequencing, the patterns of mutations induced by them will be determined. Somatic mutational signatures will be subsequently extracted by non-negative matrix factorisation methods and correlated with exposure data. Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development.

  Study EGAS00001003520