2965 results for "愛の戦士完全破壊2-re-imagination-version-鞭首絞め・電撃・ヘソか"

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• Whole genome and transcriptome sequencing of lung cancer patients and cell lines at Genentech

  Version 1 Whole genome sequencing was applied to tumor and adjacent normal lung tissue in an individual non-small-cell lung cancer patient. We present an analysis of somatic changes identified throughout the tumor genome, including single-nucleotide variants, copy number variants, and large-scale chromosomal rearrangements. Over 50,000 high-confidence single-nucleotide variants were identified, revealing evidence of substantial smoking-related DNA damage as well as distinct mutational pressures within the tumor resulting in uneven distribution of somatic mutations across the genome. Version 2 Lung cancer is a highly heterogeneous disease in terms of both underlying genetic lesions and response to therapeutic treatments. We performed deep whole genome sequencing and transcriptome sequencing on 19 lung cancer cell lines and 3 lung tumor/normal pairs. Overall, our data show that cell line models exhibit similar mutation spectra to human tumor samples. Smoker and never-smoker cancer samples exhibit distinguishable patterns of mutations. A number of epigenetic regulators are frequently altered by mutations or copy number changes. A systematic survey of splice-site mutations identified over 100 splice site mutations associated with cancer specific aberrant splicing, including mutations in several known cancer-related genes. Differential usages of splice isoforms were also studied. Taken together, these data present a comprehensive genomic landscape of a large number of lung cancer samples and further demonstrate that cancer specific alternative splicing is a widespread phenomenon that has potential utility as therapeutic biomarkers.

  Study phs000299

• Molecular Characterization of Prostate Cancer Specimens by Bulk and Single Cell Analysis

  Version 1: We performed single-cell RNA-sequencing (scRNA-seq) of fresh biopsies from metastatic castration resistant prostate cancer. Additionally, where available, we performed matched bulk whole exome sequencing (WXS; tumor and normal paired) and whole transcriptome sequencing for the same individuals. We also performed bulk whole exome (WXS) and RNA-sequencing (RNA-Seq) from FFPE pre-treatment biopsies from patients with clinically localized high-risk prostate cancer.Version 2: We added data from a randomized phase 2 trial of radium-223 with or without pembrolizumab in patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) to bone. After enrollment, study participants underwent bone biopsy and were randomized 2:1 to receive radium-223 at 55 kBq/kg every 4 weeks + pembrolizumab at 200 mg every 3 weeks (Arm A, R223+P) or radium-223 at 55 kBq/kg every 4 weeks alone (Arm B, R223). Stratification factors were alkaline phosphatase ≥220 vs. Data generated includes bulk whole exome sequencing (WXS), ultra-low pass whole genome sequencing (WGS) at 0.1X coverage, and targeted-capture sequencing. The ultra-low pass sequencing was used as part of the selection criteria for the target capture sequencing. Note: Two subjects in this study are linked to phs001577 and phs000915 respectively.

  Study phs001988

• Neoadjuvant_Breast_Cancer_Validations

  This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced.

  Study EGAS00001000428

• Deciphering Maternal-Fetal Crosstalk in the Human Placenta During Parturition Using Single-Cell RNA-Sequencing

  Labor is a complex physiological process requiring a well-orchestrated dialogue between the mother and fetus. However, the cellular contributions and communications that facilitate maternal-fetal crosstalk in labor have not been fully elucidated. In this latest version (#5), scRNA-seq was applied to decipher maternal-fetal signaling in the human placenta and chorioamniotic membranes during term labor. Samples were obtained from women who underwent spontaneous labor (n = 24) or who were delivered in the absence of spontaneous labor (n = 18) at term. Samples from previous versions (#1-3) of this study include the placental villous tree, basal plate, and chorioamniotic membranes of women across a range of pregnancy physiologic and pathologic conditions, including the processes of labor (term labor and preterm labor), and COVID-19 (version #3). Version #4 includes samples from the human myometrium during spontaneous term labor.

  Study phs001886

• Solve-RD_GENTURIS_cohort-1_DF1+2_V1

  Solve-RD data submitted to the ERN-GENTURIS cohort for re-analysis (Data freeze 1+2) v1

  Dataset EGAD00001009767

• Timing chromosomal amplification events using patterns of somatic mutations in high hyperdiploid acute lymphoblastic leukemia

  This dataset included samples with high hyperdiploid acute lymphoblastic leukemia (ALL) collected from the Division of Clinical Genetics, Lund University, Sweden. All samples were subjected to whole genome sequencing using the Illumina HiSeqX platform. Paired-end sequencing (2x150bp) was done to ~60x coverage for diagnostic samples and ~30x coverage for remission samples. The paired-end reads were aligned to the human reference genome GRCh37 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/) by the Burrows-Wheeler Aligner tool (version 0.7.17). Duplicate reads marking and local realignment were performed by GATK (version 4.0.11.0).

  Study EGAS00001007052

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• Y90 radioembolization followed by intravenous Nivolumab for advanced hepatocellular carcinoma

  To evaluate the efficacy of combination therapy with ICI and RT in patients, a Phase II trial (CA209-678) was conducted to investigate the efficacy and safety of Y90-RE followed by nivolumab in patients with advanced HCC (NCT03033446, n = 36). Interestingly, the ORR was found to be 30.6% in all patients and 43.5% when restricted to patients with only intrahepatic tumors, suggesting possible synergism between Y90-RE and ICI. Here we present whole exome sequencing (WES) and RNA-seq data for 33 patients treated with Y90 radioembolization followed with Nivolumab.

  Study EGAS00001006834

• 24 Chordoma samples (WES,WGS)

  Case series of the rare tumor entity chordoma. 9 cases sequenced with Whole Exome Sequencing (WES) and 2 cases sequenced with Whole Genome Sequencing (WGS) were recruited from the personalized oncology program NCT-MASTER/DKTK-MASTER at the German Cancer Research Center. One of the WES patients was re-sequenced at a later time point when he relapsed, this resequencing was done by WGS. Therefore there are 11 patients, one of which with two samples, all of which were sequenced with matched normal controls, amounting to a total number of 24 NGS samples.

  Dataset EGAD00001004825

• single cell RNA-seq of peripheral blood from analysis in infants with MLL-rearranged Acute Lymphoblastic Leukemia

  This dataset contains two experiments. 1) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with SORT-seq (see cell systems, 2016, doi:10.1016/j.cels.2016.09.002). For some of the patients, multiple indipendent plates were produced (each plate is a sample). Barcode-well correspondence can be found here: https://bitbucket.org/princessmaximacenter/sharq/src/master/data/celseq2_bc384-v4.csv . 2) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with10x Genomics Version 2.

  Dataset EGAD00001007752

• PDX_HTA2.0_Guergen2022

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) and RCC metastases related to Guergen et al, Front Oncol 12:2022 889789. Microarrays were normalized individually using the SCAN method from the R package SCAN.UPC (version 2.34.0). Probe sets were summarized on the Entrez GeneID level using the annotation provided by BrainArray (version 25).

  Dataset EGAD00010002392

• 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

• Role_of_Epigenetic_Memory_in_Human_Induced_Pluripotent_Stem_Cells_Pilot

  Fibroblasts have been shown to re-program into induced pluripotent stem (hiPS) cells, through over-expression of pluripotency genes. These hiPS cells show similar characteristics to embryonic stem cells including cell surface markers, epigenetic changes and ability to differentiate into the three germ layers. However it is unclear as to the extent of changes in gene expression through the re-programming process.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000742

• Characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  RNA was extracted from eight diagnostic ETV6-RUNX1 positive acute lymphoblastic leukemia samples collected in PAXgene blood RNA tubes using PAXgene Blood RNA kit (cat #762174, Qiagen GmbH, Hilden, Germany), following the version 2 instructions for manual purification. Samples were processed with Globin-Zero Gold rRNA Removal Kit (Illumina) and directional libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs). The library preparation and paired end (150 bp) sequencing were performed by Novogene (HK) Company Limited (Hong Kong, China) using Illumina Novaseq 6000 aiming at 70 million read pairs per sample.

  Dataset EGAD00001006406

• Genome-wide Identification of Variants Affecting Early Human Brain Development

  This is a genome-wide association study (GWAS) of global brain tissue volumes in human infants. The published study for this project includes 561 infants, and 239 parents gave consent for data sharing through dbGaP. An intronic single-nucleotide polymorphism (SNP) in IGFBP7 (rs114518130; GeneID: 3490) met genome-wide significance for gray matter volume (P=4.15x10-10). An intronic SNP in WWOX (rs10514437; GeneID: 51741) neared genome-wide significance for white matter volume (P=1.56x10-8). Additional loci with small P-values include psychiatric GWAS associations and transcription factors expressed in the developing brain. Genetic risk scores for schizophrenia and ASD, and the number of genes affected by rare copy number variants (CNV burden) did not predict global brain tissue volumes. Integrating these results with large-scale GWAS in adolescents [Philadelphia Neurodevelopmental Cohort (PNC)] and adults [Enhancing Neuro Imaging Genetics through Meta-Analysis version 2 (ENIGMA2)] suggested minimal overlap between common variants impacting brain volumes at different ages.

  Study phs001122

• Starting Treatment with Agonist Replacement Therapies (START): A Randomized Trial of Methadone vs Buprenorphine/Naloxone for the Treatment of Opioid Dependence

  The Starting Treatment with Agonist Replacement Therapy (START) study was a 24-week, open-label, randomized trial of methadone versus Suboxone (buprenorphine/naloxone) for the treatment of opioid dependence. Patients were over the age of 18 and met DSM-IV qualifications for opioid dependence. The primary goal of the study was to determine if either medicine was associated with liver toxicity issues in this vulnerable patient population. Liver enzymes were measured at four time points. Urinalysis for opioids, cocaine, cannabis, benzodiazepines, and methamphetamine were performed on a weekly basis. A flexible dosing scheme was used during which physicians could alter medication dose based on withdrawal symptoms and urinalysis results. Neither medication was found to be associated with liver enzyme levels. In version 2 of this study, a text file containing 7704 SNPs with large allele frequency discrepancy as compared to 1000 Genomes is included. Users have the option to exlude these 7704 SNPs.

  Study phs001135

• cfMeDIP-seq for 18 patients with pleural mesothelioma

  The dataset contains cfMeDIP-sequencing data (bam files) for 18 plasma samples from pleural mesothelioma patients. The libraries were prepared according to the published protocol (Shen, S. Y., Burgener, J. M., Bratman, S. V. & De Carvalho, D. D. Preparation of cfMeDIP- seq libraries for methylome profiling of plasma cell-free DNA. Nat. Protoc. 14, 2749–2780 (2019)). Whole genome sequencing (WGS) was performed for pre-made libraries on NovaSeq X Plus with a 150 paired-end strategy. Low-quality reads and adapters were removed with Trim Galore version 0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). The trimmed reads were aligned to hg38 with Bowtie2 version 2.3.4.3. SAMTools version 1.9 was used to convert the SAM alignment files to BAM files, sort and index reads, and remove duplicates.

  Dataset EGAD50000002126

• Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study - Maternal Glycemia and Birthweight GEI Study

  Low and high birth weight are not only major causes of neonatal morbidity and mortality, but epidemiological data have established an association between birth weight and later life risk of adult metabolic diseases. Fetal growth is determined by complex interactions between fetal genes and the maternal uterine environment. Subtle or overt variation in maternal glucose tolerance, which is, in part, genetically determined, is related to fetal size at birth. Moreover, new emerging data suggest that genetic variation in the fetus can impact maternal metabolism (e.g., blood pressure and glucose tolerance). Given the above, we are addressing the hypothesis that, during pregnancy, gene-environment interactions in the context of the maternal-fetal unit impact fetal size at birth and maternal metabolism. Genes that control fetal growth or maternal metabolism during pregnancy are largely unknown, so the first step to address our hypothesis will be to identify genetic variation that impacts fetal growth and maternal metabolism and to determine the interaction of that variation with the intrauterine and fetal environment. To accomplish this, we are performing genome wide association (GWA) mapping on a subset of ~37,000 DNA samples that were collected from mothers and their offspring as part of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study. HAPO is a multicenter, international study in which high quality phenotypic data related to fetal growth and maternal glucose metabolism has been collected from 25,000 pregnant women of varied racial and socio-demographic backgrounds using standardized protocols that were uniform across centers. For these studies, we are genotyping 1,500 infants and their mothers of European descent, 1,250 Afro-Caribbean infants and mothers, 800 Hispanic (Mexican-American) infants and mothers, and 1200 Thai infants and mothers. Genotyping is being performed using the Illumina Human610 Quad (European ancestry participants), Human1M Duo (Afro-Caribbean and Hispanic participants), and Omni1-Quad_v1-0_B (Thai participants). The specific aims for the project are as follows: (1) To apply analytic approaches for conducting GWA mapping studies on quantitative phenotypes related to offspring size at birth (birth weight, ponderal index, head circumference and adiposity) allowing for other known influences such as gestational age, parity, and maternal weight gain. (2) To apply the above approaches to identify genetic variation that impacts maternal glucose tolerance at ~28 weeks of gestation (fasting glucose, glucose during an oral glucose tolerance test, and insulin sensitivity expressed as quantitative traits) allowing for other known influences such as maternal weight gain, parity and age. (3) To examine the interaction between maternal genes, the intrauterine environment, and fetal genes to identify interactions that modulate genetic regulation of size at birth and fetal genetic variation that impacts on maternal glucose tolerance. GWA mapping will provide initial evidence for association of specific SNPs with the quantitative traits outlined above. As low and high birth weight are not only major causes of neonatal morbidity and mortality but have also been associated with increased risk of metabolic diseases in adults, identification of genes that regulate fetal growth and maternal metabolism will provide novel information about the pathways that regulate these processes as well as important insight into susceptibility genes for chronic diseases like type 2 diabetes. The Version 1 (v1) dbGaP release will include data only from the Hispanic study participants. The Version 2 (v2) dbGaP release will include data from the Hispanic and European ancestry study participants. The Version 3 (v3) dbGaP release will include data from the Afro-Caribbean, Hispanic and European ancestry participants. The Version 4 (v4) dbGaP release will include data from all participants (i.e., Afro-Caribbean, Hispanic, European ancestry, and Thai participants). This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to maternal metabolism and birthweight through large-scale genome-wide association studies of infants and their mothers at multiple international sites. Genotyping was performed at the Broad Institute of MIT and Harvard, and at CIDR of Johns Hopkins University, GENEVA genotyping centers. Data cleaning and harmonization was performed at the GEI-funded GENEVA Coordinating Center at the University of Washington.

  Study phs000096

• Re-aligned BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for Copy Number Variant Calling.

  Re-aligned BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for Copy Number Variant Calling.

  Dataset EGAD00001012638

• Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

  The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying ‘personal’ gene regulatory network. We validated μ-cisTarget by re-analyzing the TAL1 and LMO1 enhancer mutations in T-ALL, and the TERT promoter mutation in melanoma. Next, we re-sequenced the full genome of ten cancer cell lines and used matched transcriptome data and motif discovery to identify master regulators with de novo binding sites that result in the up-regulation of nearby oncogenic drivers.

  Study EGAS00001002571

• Lung_Multi_site_Targeted_Sequence_Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000436

• Multisite_Primary_Breast_Cancer

  DNA extracted from multiple biopsies taken from different areas of primary breast tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Study EGAS00001000891

• Paired-end Whole Exome-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.

  Dataset EGAD00001005386

• Exome sequencing in CLL re-treated with venetoclax

  Study EGAS00001006158

• LIFESTYLE atlas - dietary intervention - methylation data - buccal sample

  Dataset EGAD00010002674