16802 results for "sec+and+unspecified+malignant+neoplasm"

in 32.67 milliseconds.

• Parallel CRISPR Editing of Familial ALS Mutations

  Induced pluripotent stem cells (iPSCs) provide a modeling system for human disease within the critical context of the human genome. CRISPR editing of iPSCs allows the construction of isogenic pairs where the cells have nearly identical genomes except for the desired edited change. Here, we used CRISPR editing on a healthy control line to generate three new isogenic iPSC lines that each contains a different familial amyotrophic lateral sclerosis (fALS) mutation (TARDBP[G298S/+], SOD1[G85R/+], and PFN1[G118V/+]). As controls for each mutation, we retained iPSC lines that went through the editing process but did not have the desired heterozygous mutation. We have also performed editing in a patient cell line with a hexanucleotide repeat in C9ORF72. This edit mutates a non-canonical start codon upstream of the hexanucleotide repeat. These edited lines have been used in three different studies:(1) In “Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions” (PMID: 34362895), we performed exome sequencing to confirm the absence of off-target CRISPR events. We also performed single-cell sequencing on sensorimotor organoids from a second healthy control iPSC line, which is deposited alongside the exome sequencing data.(2) In “iPSC motor neurons, but not other derived cell types, capture gene expression changes in postmortem sporadic ALS motor neurons (PMID: 37651231), we differentiated these isogenic lines into motor neurons, sensory neurons, cortical neurons, and astrocytes and then performed bulk RNA-sequencing. We then assessed similarities between fALS mutations, differences between cell types, and the capacity of iPSC modeling to capture differentially expressed genes in postmortem sporadic ALS motor neurons.(3) In "Blocking RAN translation without altering RNA foci rescues C9ORF72-related ALS/FTD phenotypes" (Jiang et al. 2025), we mutate a non-canonical start codon upstream of a hexanucleotide repeat in C9ORF72. This mitigates several phenotypes related to neurodegeneration.

  Study phs002440

• Intra-tumor heterogeneity of localized lung adenocarcinomas defined by multi-region sequencing

  Background: Intra-tumor heterogeneity (ITH) may have profound impacts on biopsy strategy, characterization of actionable targets, treatment planning, and drug resistance. ITH of lung cancers has not been well studied. Methods: We performed multi-region whole exome sequencing (average sequencing depth 277x) on 48 tumor regions from 11 resected lung adenocarcinomas (8 stage I, 2 stage II and one stage III tumors) followed by deep sequencing validation (average sequencing depth 863x). Results: All tumors showed clear evidence of spatial ITH. On average, 76% of all mutations and 20/21 known cancer gene mutations were present in all regions of individual tumors (trunk mutations). Copy number analysis did not show substantial difference in large-scale chromosome aberrations. A canonical KRAS p.G12C mutation was detected in only 1 of 4 tumor regions (branch mutations) at exome depth but detected in all four tumor regions (trunk mutations) at increased sequencing depth. In addition, many heterogeneous branch mutations defined by exome sequencing were detectable in all regions of individual tumors with increasing sequencing depth. Significant differences in mutational spectrum were observed in 6 tumors indicating that specific mutational processes were likely operative at different times during development of these tumors. With a median follow up of 21 months post surgery, 3 patients have relapsed and all 3 patients presented with significantly larger fractions of subclonal mutations in their primary tumors. Conclusions: Although multi-region sampling is still required to fully assess ITH complexity, single biopsy analysis at appropriate depth might be sufficient to identify the majority of known cancer gene mutations in localized lung adenocarcinomas. Larger subclonal mutation fractions may be associated with increased likelihood of postsurgical relapse in patients with localized lung adenocarcinomas. Studies on larger cohort, ideally with comprehensive clinical annotation and repeat biopsy at relapse are needed to fully understand the clinical impact of ITH.

  Study EGAS00001000930

• Primary ER-positive Breast Cancer Treated with Neoadjuvant Letrozole

  These are tumor biopsies and corresponding normal samples from patients with early stage ER+/HER2- breast cancer who had received the aromatase inhibitor letrozole for 10-21 days prior to surgery.

  Study phs000857

• PEDS-PLAN - Pediatric Precision Laboratory Advanced Neuroblastoma Therapy

  A multi-center clinical trial for newly diagnosed high-risk neuroblastoma patients. Molecular tumor boards selected one of six targeted agents based on tumor-normal whole exome sequencing and tumor RNA sequencing data.

  Study phs002303

• Mutational Profile in Newly Diagnosed Diffuse Large B-Cell Lymphoma: Insights from the GAINED Study

  The GAINED study (NCT01659099) is a randomized phase 3 trial comparing obinutuzumab (G) to rituximab (R) in combination with ACVBP or CHOP14 induction, followed by PET-guided consolidation. This post-hoc analysis focuses on primary mediastinal B-cell lymphoma (PMBL) patients, confirmed through expert pathological review and characterized using gene-expression profiling (GEP) and Next-Generation Sequencing (NGS).

  Dac EGAC50000000540

• Establishment of iPS cells from Japanese healthy volunteers

  We performed whole exome sequencing of Japanese volunteers. We established iPSCs from those volunteers, and the iPSCs were deposited to Riken Bioresource Bank. The whole exome sequencing were performed using their PBMCs.

  Study JGAS000287

• Effects of GATA4-inhibiting compound 3i-2012 on HB-243 hepatoblastoma cells

  In order to study the effects of GATA4 inhibition, HB-243 hepatoblastoma cells were treated with GATA4-inhibiting compound 3i-2012 for 24 hours. Total RNA was extracted and sequenced.

  Study EGAS50000000999

• DAC Wachten Laboratory and Toma Laboratory, University of Bonn/University Hospital Bonn

  DAC for collaborative projects of the Wachten Laboratory (Institute of Innate Immunity, University of Bonn, University Hospital Bonn) and the Toma Laboratory (Institute of Pathology, University Hospital Bonn). Contact: Prof. Dr. Dagmar Wachten dwachten@uni-bonn.de Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany Prof. Dr. Marieta I. Toma Marieta.Toma@ukbonn.de Institute of Pathology, University Hospital Bonn, Germany

  Dac EGAC50000000916

• Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment

  Genomic data from FFPE tumor samples of 258 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS) at 1x. The study aimed to characterize somatic copy number alterations (SCNAs) and SCNA burden to assess their clinical relevance for patient stratification across different first-line treatments.

  Dac EGAC50000000929

• Genome-wide association scan in psoriasis

  To identify novel susceptibility loci for psoriasis, we undertook a genome-wide association scan of of 594,224 SNPs in 2,622 individuals with psoriasis and 5,667 controls.

  Study EGAS00000000108

• Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma

  We analyzed the genome of plasma cells collected from bone marrow samples or plasmocytoma from patients prior to (when available) and progression on anti-GPRC5D T cell engagers.

  Study EGAS50000001148

• Identification of phenotype-modifier genes

  Patients were stratified at the extremes of the renal phenotype according to their estimated glomerular filtration rate annual decline and subjected to whole exome sequencing (WES) aiming to find candidate phenotype-modifier genes.

  Study EGAS50000000829

• The Jackson Laboratory for Genomic Medicine APML DAC (rare disease research)

  This Data Access Committee oversees access to genomic data from rare disease research conducted by the Advanced Precision Medicine Laboratory (APML) at The Jackson Laboratory for Genomic Medicine. The DAC reviews data access applications to ensure compliance with patient consent agreements, institutional policies, and ethical guidelines. Access decisions are made based on scientific merit and data security capabilities of the requesting institution.

  Dac EGAC50000000845

• Prospective Lynch Syndrome Database entries

  These data have been used to produce cancer incidence results for https://pubmed.ncbi.nlm.nih.gov/37181409/ , https://pubmed.ncbi.nlm.nih.gov/40231433/ and https://plsd.eu as available in March 2026. The tables contain demographic information at individual level, individual cancer events with given age, as well as prophylactic and therapeutic surgeries to remove organs. The data have been de-identified to ensure anonymity.

  Dataset EGAD50000002468

• Indigenous American Genomic Diversity Project (IAGDP).

  Here we present the Indigenous American Genomic Diversity Project (IAGDP), comprising 128 newly generated high-coverage (NGS; ~44X) whole genomes from Indigenous individuals across eight Latin American countries, representing 45 populations and 28 language families. This dataset expands Indigenous representation in genomics, with emphasis on geographically and linguistically diverse populations, particularly from the South American lowlands.

  Dataset EGAD50000002396

• Integrated whole-genome and transcriptome sequencing reveals divergent evolutionary processes across biliary tract cancer subtypes (WTS data from biliary tract cancer molecular subtype study)

  WTS data for biliary tract cancer samples (Consensus molecular subtypes define distinct evolutionary trajectories of biliary tract cancers). The dataset includes tumour bam files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=85 tumours)

  Dataset EGAD50000002529

• Dynamic human admixture histories over the past ~1,300 years at the northern Himalayan frontier

  Whole-genome sequencing data from ten present-day individuals from Himachal Pradesh, India. DNA from these ten present-day individuals was converted to double-stranded libraries and sequenced on Illumina NovaSeq 6000 in 150 bp paired-end mode. The dataset consists of raw fastq and bam (hg19) files.

  Dataset EGAD50000001925

• Bulk 3' mRNA-Sequencing of human ASC-derived kidney tubuloids

  Bulk 3' mRNA-Seq raw files (FASTQ) from human kidney tubuloids derived from 4 separate donors in collagen-based dome culture and suspension culture. Samples were collected for sequencing on day 7 of passage 3, 4, and 5. Total = 24 samples.

  Dataset EGAD50000002335

• Spatial Dynamics of the Developing Human Heart

  68 paired-end raw FASTQ files obtained from 38 tissue sections across 16 hearts, spanning embryonic human heart development between 5.5 and 14 postconceptional weeks. Some libraries were re-sequenced for better coverage. The tissue sections were processed using the 10x Genomics Visium Gene Expression kit, and libraries were paired-end sequenced using Nextseq2000 (Illumina).

  Dataset EGAD50000001615

• Human Paraganglioma

  This dataset comprises single-nucleus transcriptomic profiles from 9 human paraganglioma samples. Nuclei were isolated and processed using the SMART-Seq2 protocol to enable full-length, high-resolution RNA sequencing at the single-nucleus level. cDNA libraries were generated and sequenced on the Illumina HiSeq 2500 platform. The resulting raw sequencing data are provided as .fastq files for downstream analysis.

  Dataset EGAD50000001689

• Dataset for "HPV integration induces gene fusions" (RNA)

  RNA-seq data for "HPV integration induces gene fusions" We performed RNA-seq analysis of five HPV+ head and neck cancer samples using Illumina short reads. Sequenced are submitted in bam format. We also sequenced one samples with pacBio long reads, and the reads are submitted in fastq format.

  Dataset EGAD50000001303

• Human Neuroblastoma

  This dataset comprises single-nucleus transcriptomic profiles from 10 human neuroblastoma samples. Nuclei were isolated and processed using the SMART-Seq2 protocol to enable full-length, high-resolution RNA sequencing at the single-nucleus level. cDNA libraries were generated and sequenced on the Illumina HiSeq 2500 platform. The resulting raw sequencing data are provided as .fastq files for downstream analysis.

  Dataset EGAD50000001596

• Hi-C in breast healthy, primary cancer and metastatic tissues

  Hi-C libraries have been prepared by enzymatic digestion with MboI restriction enzyme and sonication (Covaris). Illumina single-indexig primers have been use to amplify ligated fragments. Hi-C experiments have been performed on 10 slices (50um thick) of fresh-frozen tissues or 10x10e6 Pleural Effusion cells. Raw paired-end fastq.gz files are provided.

  Dataset EGAD50000000643

• TOTHER3 dataset

  This dataset contains the FASTQ and BAM files for TOTHER3 study. Targeted DNA-Seq experiment were realized with 49 samples. Since this data was obtained with a panel of genes protected by Intellectual Property (IP), these files only contain information to validate the results published and, in consequence, sensible data had to be specifically removed.

  Dataset EGAD50000000562

• RNAseq Data Cyr61-MAC and HUVEC

  Gene expression of MAC enriched by adhesion to Cyr61 in comparison to HUVEC. This dataset includes RNAseq Data from myeloid angiogenic cells (MAC) enriched from peripheral blood by adhesion to Cyr61 (4 samples prepared from different donors) and of human umbilical vein endothelial cells (HUVEC) (4 samples). Illumina NextSeq500 technology was used. FASTQ data are provided.

  Dataset EGAD50000000758