8224 results for "canc*"

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• NGS in FACSorted populations from AML patients

  FACS-enriched bone marrow cell populations from 22 AML patients were analyzed using a custom panel targeting 56 genes recurrently mutated in myeloid neoplasms. DNA was released from a median of 60,000 sorted cells by incubation with 2.5 μL proteinase K and 2 μL RNase A (Thermo Fisher Scientific) for 30 minutes at 37°C, purified using 2× AMPure XP beads (Beckman Coulter, Brea, CA), and stored in pH 8 elution buffer at −20°C. DNA quantity was measured using the Qubit dsDNA BR Assay on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), and quality was assessed using the Genomic DNA ScreenTape assay on a 4200 TapeStation system (Agilent Technologies, Santa Clara, CA). Libraries were prepared from at least 20 ng of DNA according to the SOPHiA GENETICS protocol and sequenced on an Illumina MiSeq using 2 × 251-cycle paired-end reads. At least 95% of target bases achieved ≥1,000× coverage. FASTQ files were analyzed in SOPHiA DDM using the GRCh37/hg19 reference genome for alignment, variant calling, and annotation. Variants were retained when the variant allele frequency was ≥2%, coverage was ≥100 reads, and the alternate allele was supported on both strands. Synonymous, intronic, intergenic, 5′ untranslated-region, and recurrent panel-artifact calls were excluded. The remaining variants were classified according to Association for Molecular Pathology and American College of Medical Genetics and Genomics guidance using VarSome, ClinVar, COSMIC, and dbSNP. Only pathogenic or likely pathogenic variants were analyzed. All retained calls were visually confirmed in Integrative Genomics Viewer v2.11.3, and only variants previously reported as somatic in hematopoietic or myeloid neoplasms were retained.

  Study EGAS50000002132

• Single-Cell Multiomic and Whole-Genome Profiling of Primary and Metastatic Colorectal Cancer

  This study contains controlled-access single-cell multiomic sequencing (scRNA-seq and scATAC-seq) data generated from patients with colorectal cancer, including 33 primary tumours, 11 metastatic lesions, and 7 adjacent normal tissue samples. Whole-genome sequencing (WGS) data are available for the tumour samples. These data were generated to investigate the genomic and epigenomic landscape of colorectal cancer and to identify recurrent regulatory alterations associated with tumour progression and metastasis.

  Study EGAS50000002048

• Weizmann Breast Cancer Epigenetics Data Access Committee

  Data Access Committee responsible for reviewing requests for controlled access to human sequencing data generated in the study "Epigenetic Heterogeneity in Breast Tumors with Implications for Disease Diagnosis and Monitoring".

  Dac EGAC50000001136

• Committee of human data related to Livanova et al. paper submission

  This DAC controls access to single-cell multiomic (scRNA-seq and scATAC-seq) and matched whole-genome sequencing (WGS) data generated from colorectal cancer patient samples, including 33 primary tumours, 11 metastatic lesions, 7 adjacent normal tissues. The data were generated to investigate recurrent somatic chromatin accessibility alterations (SCAAs) associated with tumour progression and metastasis

  Dac EGAC50000001117

• UNICORN Visium HD spatial transcriptomics of colorectal cancer

  This controlled-access dataset contains raw paired-end sequencing data generated from 56 human colorectal cancer tissue samples using the 10x Genomics Visium HD spatial gene expression workflow. The dataset comprises 324 paired-end sequencing runs represented by 648 FASTQ files. Libraries were sequenced on an Illumina platform and are intended for spatial transcriptomic analysis of the colorectal cancer tissue microenvironment.

  Dataset EGAD50000002908

• Transcriptome Sequencing Data of High Grade Serous Ovarian Cancer

  Study EGAS00001004714

• Long-read whole genome sequencing of gastric cancer

  Gastric cancer (GC) remains a significant health challenge globally, with a particularly high incidence in Asia, including Singapore. Understanding the genomic landscape of normal gastric and the different GC subtypes along with its precursor lesions such as intestinal metaplasia (IM) as well as GC metastatic sites is crucial for advancing diagnostics, prognostics, and therapeutics. Long-read sequencing technologies offer an opportunity to delve deeper into the genomic and epigenetic alterations underlying these conditions and to complement existing short-read omics data. By integrating these data with previously generated in-house multi-omics data (such as RNA sequencing and whole exome sequencing), we hope to better elucidate the molecular mechanism underlying GC initiation and progression.

  Study EGAS50000001607

• scRNA-seq profile of three ATC and three lethal PTC samples

  To elucidate molecular and immunological characteristics distinguishing anaplastic thyroid cancer (ATC) from aggressive papillary thyroid cancer (PTC), we performed single-cell RNA sequencing on three ATC and three lethal PTC samples.

  Study JGAS000942

• NoSarC -- Norwegian Sarcoma Consortium. Towards individualized therapy for orphan cancer.

  This study is initiated and conducted by the Norwegian Sarcoma Consortium - a collaboration between 5 Norwegian hospitals and universities, coordinated by Oslo University Hospital. The NoSarC project was initiated in 2014 and aimed to perform molecular characterization of samples from a national, population-based cohort of sarcoma patients, to identify tumors which are sensitive to therapies already developed and approved for more common cancers. The NoSarC cohort in this study consists of Tumor-Normal pairs from 287 subjects that has been Whole Exome Sequenced.

  Study EGAS50000002163

• Recommended Text: Plasma cfChIP-seq profiling of cell-free nucleosomes in Small-Cell Lung Cancer and neuroendocrine carcinomas

  This dataset contains raw, encrypted Crypt4GH paired-end Fastq files from cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) targeting histone modification H3K4me3 in plasma samples. The cohort includes small-cell lung cancer (SCLC) cases, neuroendocrine carcinomas (NEC) and non-small-cell lung cancer (NSCLC) samples. Access is restricted exclusively to non-commercial, duplicate-prevention SCLC research protocols approved by the Data Access Committee.

  Dataset EGAD50000002783