15013 results for "cancer studies using rna-seq"

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• Genome-wide Association Study for Non-syndromic Clefts in the African Population: CIDR

  The focus of this project is to identify genetic variants that are associated with orofacial clefts in African populations in sub-Saharan Africa. Most genetic studies of CLP (including the vast majority of GWAS) have been conducted in populations of European origin with only a few focused on Asian or African populations. We choose to study the genetics of these complex traits in African populations because, African populations have the greatest genetic variation amongst the various populations in the world by virtue of being the primary ancestral population to modern humans (Cavalli-Sforza and Feldman, 2003; Ramsay et al., 2011). Therefore, the potential for finding novel loci for CLP is quite high. To date 6 genome wide association studies (GWAS) for cleft lip with or without cleft palate (CL/P) have been conducted and 18 risk loci identified (Birnbaum et al., 2009; Grant et al., 2009 ; Beaty et al., 2010; Mangold et al., 2010; Ludwig et al., 2012; Sun et al., 2015). All these studies have either been conducted in European populations, Asian populations or both. There is currently no published GWAS for clefts in African populations. African populations represent a novel and richly productive populations for genetic and environmental exposure studies for CL/P. Investigating the presence of genetic variants in diverse population groups can identify novel variants and candidate genes that are population specific. Environmental factors may also increase the risks in certain population groups due to genetic susceptibility and/or specific exposures. Understanding the role these susceptibility genes play in the effects of environmental risk factors can inform strategies designed towards reducing the outcome of these complex traits, e.g. through the modification of the environmental influences. The study population comprises a large number of individuals (3205 individuals) from Africa (Ghana, Ethiopia and Nigeria). There are cases, case triads (nuclear families), as well as controls with no history of OFC nor other developmental defects.

  Study phs001090

• ARDSnet and the iSPAAR Consortium: Genomic Basis of Susceptibility and Outcomes in Patients with the Acute Respiratory Distress Syndrome (ARDS)

  Acute Respiratory Distress Syndrome (ARDS)/ Acute Lung Injury (ALI) is a syndrome defined by the presence of acute hypoxemic respiratory failure, bilateral pulmonary infiltrates on chest radiograph, a known clinical risk factor (e.g. sepsis, pneumonia, trauma, gastric fluid aspiration, pancreatitis, massive transfusion), and the absence of physiologic or clinical evidence of congestive heart failure. The Identification of SNPs Predisposing to Altered ALI Risk (iSPAAR) study is a multi-institutional cooperative study, funded through the NHLBI Recovery Act, that assembled samples and phenotype information from existing cohorts. The consortium included samples from patients with ARDS from the NIH NHLBI ARDS Clinical Trials Network (ARDSNet). Samples were obtained from 3 interventional treatment trials in patients with ARDS, including the Fluid and Catheter Treatment Trial (FACTT), the Albuterol to Treat Acute Lung Injury (ALTA) trial, and the Omega-3 Fatty Acid/Antioxidant Supplementation for ALI trial (Omega). In addition to ARDSnet samples, samples from the other cohorts included cases of established ARDS but also controls: critically ill patients who were at-risk for ARDS but who did not develop ARDS during their hospital course. These cohorts included the Molecular Epidemiology of Acute Respiratory Distress (MEA) Study enrolled at the Harvard University/Massachusetts General Hospital, the Systemic Inflammatory Immune Response Syndrome (SIRS) Patient Database and ICU Traumatic Injury cohorts from Harborview Medical Center, and cohorts collected from the ALI research programs at the University of Pennsylvania and the University of California, San Francisco. The Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs000631 ARDSnet iSPAAR Consortium. phs000334 ESP_LungGO_ALI phs000686 ALI_GeneticRisk

  Study phs000631

• Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

  Sample cohort (n=48) is consisted of healthy, atrophic gastritis and gastric cancer patients. Some of the gastric cancer patients samples are collected at the separate time points: -1 before the operation; -2 after the operation; -3 during the control visit. For the hybridisation capture of the genes unique 15 gastric cancer-related gene panel was developed and very deep sequencing using TruSight Oncology Unique Molecular Identifier (UMI) Reagents (Illumina) was used.

  Dataset EGAD00001011153

• Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers: multi-timepoint exome sequencing of a single patient's disease

  This dataset is a time-series of EGFR-mutant NSCLC clinical specimens from an individual patient profiled using tumor-based whole exome sequencing and the data is in BAM format. DNA was extracted from FFPE for primary tumor and frozen tumor tissue samples and matched non-tumor tissue using the Qiagen Allprep DNA/RNA Mini Kit.  The library preparation protocol was based on the Agilent SureSelect Library Prep and Capture System. DNA was resuspended in a low TE buffer and sheared (Duty Cycle 5%; Intensity 175; Cycles/Burst: 200; Time: 300s, Corvaris S2 Utrasonicator).  Bar-coded exome libraries were prepared using the Agilent Sure Select V5 library kit per manfucaturer’s specifications. The libraries were run on the HiSeq2500. Raw paired end reads (100bp) in FastQ format generated by the Illumina pipeline were aligned to the full hg19 genomic assembly obtained from USCS, gencode 14, using bwa version 0.7.12. Picard tools version 1.117 was used to sort, remove duplicate reads and generate QC statistics. Tumor DNA was sequenced to median depth of 303X (range 114.39-383.41) and the matched germline DNA to average depth of 231.65.

  Dataset EGAD00001003769

• CNCD Recall by Genotypes

  This is a DAC to handle recall by genotype studies by the conducted by the Center for Non-Communicable Disease Karachi, Pakistan.

  Dac EGAC50000000937

• Examination of Engineered LINE-1 Integration Events in HeLa Cells

  Long Interspsesed Element-1 (LINE1 or L1) encodes two proteins (ORF1p and ORF2p) required for its mobilization (i.e. retrotransposition) in the human genome. Human ORF2p, a 150kDa protein, has endonuclease (EN) and reverse transcriptase (RT) activities. L1 EN is classified as apurinic/apyrimidin-like endonuclease (APE) and is responsible for initiating target-site primer reverse transcription (TPRT) during the L1 retrotransposition cycle. During canonical TPRT, the L1 EN activity makes a single-strand endonucleolytic nick at a double-strand DNA target sequence in genomic DNA. The endonucleolytic nick is typically made at an L1 EN degnerate consensus cleavage sequence (5'-TTTT/A-3') exposing a free 3' hydroxy group that can be used as a primer by the ORF2p L1 RT activity to reverse transcribe the associated L1 RNA. Here, we characterized over 21,000 de novo engineered L1 retrotransposition events in HeLa cells to determine if L1 exhibits overt integration preferences in the human genome. Bru-seq of HeLa cells to determine actively transcribed regions of the genome was also performed. This Bru-seq data was used to determine if engineered L1 integration events preferentially integrate into transcribed regions of the genome, and to determine which strand during transcription may present itself as preferential during L1 retrotransposition.

  Study phs001669

• 10X whole single cell RNA-seq from pre-frontal cortex biopsy

  The biopsy procedure was performed by a standard operative procedure under general anaesthesia. The placement of burr hole on the frontal lobe, opening of dura and cortex was performed in a routine fashion for VP shunt or VCS surgery. The biopsy was sharp dissected with knife through the leptomeninges, forming a tissue block consisting of cortex and subcortex, and placed in a sterile tube containing CSF. Fresh tissue sample processing was performed within the hours after surgery. The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics). After dissociation only non neuronal cells were retrieved.

  Study EGAS50000001058

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

  ONT whole-genome sequencing data for "HPV integration induces gene fusions" . We sequenced five HPV-positive head and neck cancer samples using Oxford Nanopore platform. The sequences was submitted in fastq format.

  Dataset EGAD50000001302

• FFPE CPA Accreditation Study

  FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Dataset EGAD00001000678

• CRISPR transduction of iPS cells

  Genome engineering using CRISPR/Cas9 technology enables simple, efficient and precise genomic modifications in human cells. Conventional immortalized cell lines can be easily edited or screened using genome-wide libraries with lentiviral transduction. However, cell types derived from the differentiation of induced Pluripotent Stem Cells (iPSC), which often represent more relevant, patient-derived models for human pathology, are much more difficult to engineer as CRISPR/Cas9 delivery to these differentiated cells can be inefficient and toxic. Here, we present an efficient, lentiviral transduction protocol for delivery of CRISPR/Cas9 to macrophages derived from human iPSC with efficiencies close to 100%. We demonstrate CRISPR/Cas9 knockouts for three non-essential proof-of-concept genes - HPRT1, PPIB and CDK4. We then scale the protocol and validate for a genome-wide pooled CRISPR/Cas9 loss-of-function screen. This methodology enables, for the first time, systematic exploration of macrophage involvement in immune responses, chronic inflammation, neurodegenerative diseases and cancer progression, using efficient genome editing techniques.

  Study EGAS00001005102

• National Cancer Institute (NCI) Prostate Cancer Genome-Wide Association Study for Uncommon Susceptibility Loci (PEGASUS)

  This genome-wide association study was funded by the National Cancer Institute (NCI) to identify uncommon susceptibility loci for prostate cancer. A total of 4,600 prostate cancer cases and 2,840 controls of European ancestry from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial were genotyped using the Illumina HumanOmni2.5 and passed rigorous quality control filters. Additional genotype data (available in dbGap under other accession numbers) from 101 independent controls of European ancestry scanned with the HumanOmni2.5 were also included, resulting in a total of 4,600 cases and 2,941 controls for the published analysis. SNPs from the most promising regions, as determined by rank p-value, under multiple different models as well as select candidate genes were taken forward for replication using a custom Iselect chip in 6,575 cases and 6,392 controls of European ancestry. Results from the primary scan after imputation were then meta-analyzed with the Iselect results as well as results from previous GWAS. In a combined meta-analysis of the primary scan together with the custom Iselect replication and a previous GWAS, thirteen loci reached genome-wide significance (P < 5 x 10-8) for prostate cancer overall; however, each of them confirmed a previously reported locus. Although they did not reach genome-wide significance, we found evidence for two new suggestive loci at chromosome 16q22.2 (PKD1L3, rs12597458, P = 9.67 x 10-8) and 6p22.3 (CDKAL1, rs12198220, P = 2.13 x 10-7). In a combined case-only analysis of 12,518 prostate cancer cases, we identified two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49x10-9) and rs78943174 at 3q26.31 (NAALADL2, P=4.18x10-8). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85x10-5) with no association for non-aggressive prostate cancer compared to controls (P=0.57). Only the cases and controls genotyped on the HumanOmni2.5 specifically for this study are included under this accession number. Controls (n=101) genotyped with the HumanOmni2.5 for another study are posted under a different accession number. Please note that the majority of prostate cancer cases and controls genotyped in CGEMS (and posted under a different accession number) are included in this study.

  Study phs000882

• The chemotherapeutic CX-5461 is extremely mutagenic and may increase cancer risk

  Deposited here are whole-genome sequencing bam or fastq files from the experimental isogenic cell lines used in the study "The chemotherapeutic CX-5461 is extremely mutagenic and may increase cancer risk, Koh, Gene (2023)". The bam files were aligned to GRCh38/hg38 using BWA-MEM. The corresponding variant call data have been deposited on Mendeley Data, V2, doi: 10.17632/d58cv549v6.2

  Dataset EGAD50000000036

• WES and RNAseq dataset

  This dataset includes WES and RNAseq for 7 patients with metastatic melanoma (4), non-small cell lung adenocarcnioma (1), cervix adenocarcinoma (1), and Epidermoid nasophaeyngeal carcinoma (1), enrolled in phase I clinical trials (NCT03475134m NCT04643574 and NCT05195619). WES was performed on matched cancer and healthy tissues, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 4000/6000 and Illumina NextSeq 500/550 systems.

  Dataset EGAD50000000337

• Cancer initiation organoids BAM files

  This dataset contains whole-genome sequencing data files from colon organoid cultures, which were mutated using CRISPR-Cas9 for specific genes (APC, KRAS, TP53 and SMAD4) to generate in vitro transformed cancer cells. After introducing each mutation, the resulting cultures were subjected to whole-genome sequencing. In addition, some cultures were xenotransplanted in recipient mice. The resulting primary tumors and corresponding metastases were subjected to whole-genome sequencing.

  Dataset EGAD00001002719

• Paired ONT and downsampled Illumina cfDNA dataset

  The dataset contains 12 lung cancer plasma cfDNA samples, 8 bladder cancer and 2 healthy control urine cfDNA samples collected in EDTA collection tubes. Shallow WGS was performed using both Oxford Nanopore Technologies' MinION platform with an R9.4.1 flow cell and the SQK-PBK004 kit (22 files) and Illumina Novaseq platform with an S4 flow cell in PE150bp configuration (2x22 files).

  Dataset EGAD00001009392

• Genetic and immune landscape evolution defines subtypes of MMR deficient colorectal cancer

  Genomic data from a cohort of 19 MMR deficient colorectal cancers and 1 MMR proficient colorectal cancer. All cases were target gene DNA sequenced using multiple primary and where available metastatic tumour regions from surgical resection samples.

  Dataset EGAD00001008334