16490 results for "sec+and+unspecified+malignant+neoplasm"

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• CIDR: Molecular Pathological Epidemiology of Colorectal Cancer

  Colorectal cancer, the second most commonly diagnosed cancer is a biologically heterogeneous disease. To characterize the molecular attributes of colorectal tumors, we conducted targeted sequencing at the Center for Inherited Disease Research (CIDR) on 4,518 tumor and matched normal DNA samples from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colon Cancer Family Registry (CCFR). These consortia are based on cohort and population-based case-control studies.

  Study phs001905

• Whole genome sequencing of neuroendocrine tumors of the small intestine

  This dataset contains whole genome sequences for 13 patients with neuroendocrine (unique/multiple) tumor(s) of the small intestine. There are in total 25 tumor and 12 matched normal genomes. Libraries were prepared using a Illumina DNA PCR Free kit following the manufacturer’s recommendations and sequencing was performed on Illumina Novaseq6000 machine with a 2x151bp paired-end fashion. It contains data for : - 1 patient with 4 tumors and 1 matched normal - 1 patient with 3 tumors and 1 matched normal - 1 patient with 2 tumors, 1 liver metastasis and 1 matched normal - 2 patients with 1 tumor, 1 mesenteric nodule and 1 matched normal - 7 patients with 1 tumor and 1 matched normal - 1 patient with 3 tumors and 1 mesenteric nodule

  Dataset EGAD50000000907

• Transcriptome-Wide Association Study (TWAS) to Identify Susceptibility Genes for Colorectal Cancer

  This study included genotype data from 420 study participants of East Asian descent, along with RNA-seq (n=300) and small RNA seq data (n=400) generated from their colorectal tissue samples. We used the transcriptome data and genotype data from these individuals to build a prediction model for each coding gene and long non-coding RNA, and perform a Transcriptome-Wide Association Study (TWAS) of colorectal cancer in East Asian populations.

  Study phs002813

• Understanding Determinants of Racial Disparities in Lung Cancer Incidence

  This is a nested case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The study included 1258 cases and 1252 controls selected from the Southern Community Cohort Study (SCCS), a large, prospective observational cohort. Cases were identified from cancer registries across the catchment area of the SCCS. Cases and controls were frequency matched on age, sex, race, and enrollment site (community health center vs general population).

  Study phs003789

• RNA sequencing of serial samples from patients enrolled in the NA-PHER2 trial

  Improved outcomes in HER2+ breast cancer have resulted from chemotherapy and anti-HER2 therapies. However, HER2+ER+ cancers exhibit lower response rates. The NA-PHER2 trial investigated chemo-free preoperative HER2 and CDK4/6 blockade with or without endocrine therapy in HER2+ER+ breast cancer. Through RNA sequencing and tumour infiltrating lymphocytes (TIL) assessment in serial biopsies we identified predictive biomarkers of pCR, Day 14 Ki67 response, and unveiled treatment-induced molecular changes.

  Study EGAS50000000248

• Whole genome sequencing of PDAC tissues an PDOs

  whole genome sequencing (WGS) on 48 PDOs (established from 39 tumors) and 4 tissues samples. The majority of PDOs were established from treatment-naive and localized tumors. Histopathologically, the majority of PDAC tumors from which PDOs were established displayed a conventional morphological pattern, with two containing squamous components (defined as adenosquamous), and one classified as a signet-ring tumour. 7 of the PDOs were grown in a culture medium lacking both WNT3A and RSPO1.

  Study EGAS50000000193

• Genomic landscape of poorly differentiated thyroid carcinoma

  Poorly differentiated thyroid carcinoma (PDTC) is a rare and aggressive subtype of thyroid cancer with limited molecular characterization. This study aims to define the somatic mutational landscape of PDTC using whole-genome sequencing. Paired tumour and matched normal blood samples were collected from six patients undergoing surgery. The overarching goal is to identify recurrent mutations, structural variants, and other genomic alterations associated with tumour aggressiveness and poor clinical outcomes.

  Study EGAS50000001134

• scRNAseq of acute myeloid leukemia

  This study analyzes T-cell transcriptional state in acute myeloid leukemia (AML) and healthy donors. The goal of the study is to correlate T-cell transcriptional states abundances with response to chemotherapy. 12 samples (5 baseline and post-treatment, 2 baseline-only) from AML patients and 3 samples from healthy donors were collected and sequenced on Illumina platforms. The files were created using the GRCh38 reference through CellRanger count (10xGenomics).

  Study EGAS50000000357

• Whole genome sequencing data of pediatric TCF3::PBX1 acute lymphoblastic leukemia

  TCF3::PBX1 leukemia is a rare subtype of B-cell acute lymphoblastic leukemia (B-ALL), occurring in approximately 3–5% of pediatric cases. It results from a chromosomal translocation t(1;19)(q23;p13), generating the TCF3::PBX1 fusion gene, which disrupts normal transcriptional regulation and contributes to leukemogenesis. Although historically associated with poor prognosis, contemporary risk stratification and intensified therapy have significantly improved outcomes, and both 5-years DFS and OS are nowadays ≥ 0.96.

  Study EGAS50000001257

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001888