15028 results for "cancer studies using rna-seq"

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• WTCCC case-control study for T1D and RA - combined cases

  WTCCC genome-wide case-control association study using two disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000013

• SNP_array

  33 ETMR samples were genotyped using Illumina HumanOmni2.5M array. Hybridization and scanning was done according to the manufacturer's instructions (Illumina). Copy number (Log R) and B allele frequency estimates were obtained sing the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina). Normalized and log2-transformed copy number measurements were imported from genomestudio and analysed using R package CopyNumber to identify segments with similar copy number.

  Dataset EGAD00010001667

• RCC_HTA2.0_Buettner2022

  GeneChip HTA 2.0 data of primary renal cell carcinoma (RCC) related to Buettner et al, Genome Med 2022. Microarrays were normalized individually using the SCAN method from the R package SCAN.UPC (version 2.26.0, R version 3.6.1). Probe sets were summarized on the Entrez GeneID level using the annotation provided by BrainArray (version 23).

  Dataset EGAD00010002353

• 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

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Dataset EGAD50000000199

• WTCCC2 case-control study for Ulcerative Colitis

  WTCCC2 project genome-wide case-control association study for Ulcerative Colitis (UC) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000084

• NanoSeq of buccal swab samples

  16 buccal swab samples were analyzed by Nanoseq. S3 in the file names indicates 28 mm^2 swab size, and S5 indicates 254 mm^2 swab size. We analyzed 28 mm^2 swab samples using paired 254 mm^2 swab samples as controls. The files were generated by the Nanoseq pipeline using GRCh37 as the reference genome.

  Dataset EGAD50000000999

• Whole Exome Sequencing Data of indolent primary renal B-Cell lymphomas

  We used sequenced 34 iNHL samples using whole exome sequencing (WES) data to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

  Study EGAS50000000774

• Whole genome sequencing data of pediatric hypodiploid B cell acute lymphoblastic leukemia

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) bone marrow samples of one hypodiploid ALL patient (ALLT-351). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001856

• Impact of DIS3 Aso on BCR repertoir in human buffy coat purified B-Cells

  The aim is to identify difference in the BCR of Aso DIS3 treated cells compared to Control Aso. Using extracted DNA from human B-cells

  Study EGAS50000001107

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set4)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-389, ALLK-124). Sequencing library was made using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002159

• GWAS genotype data of Japanese

  GWAS genotype data of the Japanese population (N=2,380) were collected at Osaka University and the affiliated medical institutes. GWAS genotyping was performed using Infinium Asian Screening Array (Illumina, USA).

  Study EGAS00001006423

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set4)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one hyperdiploid ALL patient (ALLK-134). Sequencing libraries were made using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq X Plus.

  Dataset EGAD50000002429

• Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations

  Whole Exome Sequencing was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 6). Library prep was done by exon capture using the Illumina Truseq Exome kit and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

  Dataset EGAD00001006107

• Abnormal foetal development exome trios

  This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group

  Dataset EGAD00001001442

• Targeted MCC-seq

  The capture panel targets the functional methylome in human whole blood. Regions incorporated in the panel design included hypomethylated windows generated from merged WGBS data.

  Dataset EGAD50000000286

• NICHE - DNA-seq of MMR proficient and MMR deficient early stage colon cancers

  The dataset includes 174 FASTQ files from paired-end WXS sequencing on Illumina HiSeq2500 for 39 patients.

  Dataset EGAD00001006041

• SCNA-Seq of tumor DNA samples

  Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping of corresponding tumor material

  Dataset EGAD00001002150

• EGAD00010000578

  Gencode case samples using 550K

  Dataset EGAD00010000578

• EGAD00010000580

  Gencode control samples using 550K

  Dataset EGAD00010000580

• EGAD00010000764

  Ovarian tumor samples using Illumina

  Dataset EGAD00010000764

• EGAD00010000456

  Leukemia samples using 450K DNA methylation

  Dataset EGAD00010000456

• EGAD00010000458

  Controls using 450K DNA methylation

  Dataset EGAD00010000458

• BHD-associated kidney cancer

  Background Birt-Hogg-Dub? (BHD) syndrome is a hereditary kidney cancer syndrome, which predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas and pulmonary cysts. The responsible gene, FLCN is a tumor suppressor for kidney cancer which plays an important role for energy homeostasis through the regulation of mitochondrial oxidative metabolism. However, how FLCN-deficiency leads to renal tumorigenesis is unclear. Results Whole-exome sequencing analysis of BHD-associated kidney cancer revealed that copy number variations (CNV) of BHD-associated kidney cancer are considerably different from those already reported in sporadic cases. Somatic mutation analysis revealed BHD-associated kidney cancer has quite few common mutations in specific genes; however, chromatin remodeling genes in total were frequently mutated in BHD-associated kidney cancer (17/29 tumors, 59%). Metabolite analysis revealed that glycolysis, pentose phosphate pathway and lipid metabolism were upregulated whereas the rate of beta oxydation and TCA cycle is decreased in BHD-associated kidney cancer compared to normal adjacent kidney. Conclusions BHD-associated kidney cancer displays a unique molecular characteristics which is totally different from that of sporadic kidney cancer, providing the mechanistic insight into tumorigenesis under FLCN deficiency as well as the foundation for the development of novel therapeutics for kidney cancer.

  Study JGAS000115

• Whole exome sequencing of colorectal cancer

  To elucidate immune status of solid tumors including gastrointenstinal cancer, we performed whole exome sequencing of colorectal cancer 7 patients.

  Study JGAS000279