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Institute for Refractory Cancer Research (IRCR) Data Access Committee

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Do-Hyun Nam
nsnam@skku.edu

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This DAC controls 10 datasets

Dataset ID	Description	Technology	Samples
EGAD00001001424	We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases).	Illumina HiSeq 2000 Illumina HiSeq 2500	141
EGAD00001002143	We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases).	Illumina HiSeq 2500	86
EGAD00001002248	Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors.	Illumina HiSeq 2500	104
EGAD00001002249	Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).	Illumina HiSeq 2500	355
EGAD00001003441	Total of 584 tumor specimens and/or patient-derived cells across 14 cancer types were subjected for whole-exome/targeted-exome and/or whole-transcriptome sequencing.	Illumina HiSeq 2500	584
EGAD00001004862	Glioblastoma multiforme (GBM) is clinically highly aggressive as a result of evolutionary dynamics induced by cross-talk between cancer cells and a heterogeneous group of immune cells in tumor microenvironment. The brain harbors limited numbers of immune cells with few lymphocytes and macrophages; thus, innate‐like lymphocytes, such as γδ T cells, have important roles in antitumor immunity. Here, we characterized GBM‐infiltrating γδ T cells, which may have roles in regulating the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor‐infiltrating and blood‐circulating γδ T cells from four patients were analyzed by next-generation sequencing-based T-cell receptor (TCR) sequencing in addition to mutation and immune profiles in four GBM cases. In all tumor tissues, abundant innate and effector/memory lymphocytes were detected, accompanied by large numbers of tumor‐associated macrophages and closely located tumor‐infiltrating γδ T cells, which appear to have anti-tumor activity. The immune-related gene expression analysis using the TCGA database showed that the signature gene expression extent of γδ T cells were more associated with those of cytotoxic T and Th1 cells and M1 macrophages than those of Th2 cells and M2 macrophages. Although the most abundant γδ T cells were Vγ9Vδ2 T cells in both tumor tissues and blood, the repertoire of intratumoral Vγ9Vδ2 T cells was distinct from that of peripheral blood Vγ9Vδ2 T cells and was dominated by Vγ9Jγ2 sequences, not by canonical Vγ9JγP sequences that are mostly commonly found in blood γδ T cells. Collectively, unique GBM‐specific TCR clonotypes were identified by comparing TCR repertoires of peripheral blood and intra‐tumoral γδ T cells. These findings will be helpful for the elucidation of tumor-specific antigens and development of anticancer immunotherapies using tumor-infiltrating γδ T cells.	Illumina HiSeq 2500	18
EGAD00001005331	Total of 180 gynecologic tumor specimens were subjected for targeted-exome and/or whole-transcriptome sequencing.	Illumina HiSeq 2500	180
EGAD00001005709	To identify what factors cause a different reactivity to MLN4924, 15 cells were categorized into high, intermediate, and low MLN4924 resistance groups based on the half-maximal inhibitory concentration (IC50) of MLN4924. PDC1, PCD2, PDC3, PDC4, and PDC5 showed high MLN4924 sensitivity, whereas PDC12, PDC13, PDC14, and PDC15 showed low MLN4924 sensitivity. Whole-transcriptome sequencing of these 9 patient-derived glioblastoma stem cells was performed.	Illumina HiSeq 2000	9
EGAD00001005766	Newly generated 52 gastric tumor specimens were subjected for targeted-exome and/or whole-transcriptome sequencing	Illumina HiSeq 2500	52
EGAD00001006877	RNA-seq dataset for Mutation-specific non-canonical pathway of PTEN as a distinct therapeutic target for glioblastoma	Illumina HiSeq 2500	42