53c5f7c5-620a-4a44-bd46-fa0f2eae23b3 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005116 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Interethnic variability in chemotherapy response is becoming increasingly evident, making approaches for customizing chemotherapy treatment to different ethnic populations desirable. At the same time, significant genetic variation has also been observed between ethnic groups, including many germline and somatic pharmacogenetic variants involved in chemotherapy pharmacology. Recently, based on meta-analyses of studies on germline pharmacogenetic variant frequencies and clinical trials, the investigators found that chemotherapy outcomes between Asians and Caucasians colorectal cancer (CRC) patients could potentially be inferred from the frequencies of variants between the ethnic groups and their respective biological functions. In this study, the investigators seek to further clarify the validity of using pharmacogenetic variants to customize chemotherapy between ethnicities through the following specific aims: (1) To verify the differences observed in the frequency of germline pharmacogenetic variants related to chemotherapy between Asian and Caucasian CRC patients, (2) To test whether variations in the frequency of somatic pharmacogenetic gene mutations between Asian and Caucasian CRC patients could be used to infer differences in clinical outcomes between the two ethnicities. (3) (4) For Aim 1, DNA samples from approximately 1000 Asian and Caucasian CRC patients each will be analyzed for the frequency of a panel of germline pharmacogenetic variants identified in our meta-analyses using high-throughput methodology. For Aim 2, meta-analyses will be performed on pharmacogenetic studies and clinical trials to establish the relative frequencies of somatic variants and clinical outcomes in Asian and Caucasian CRC patients. These frequencies will be verified on the same series of DNA samples used in Aim 1. The clinical outcomes inferred from the frequency differences and biological functions will then be compared to those summarized from clinical trials. This data could provide a basis for developing a rational approach to customizing chemotherapy in non-Caucasian populations and improve assessment of drug feasibility in different ethnic populations.If validated, this working hypothesis would be of high clinical interest, giving the opportunity to use this as a DNA prognosis biomarker in CRC.
Pharmacogenetic frequencies could be a potentially useful approach for predicting likely chemotherapy outcomes in non-Caucasian populations
| 2125182 | ecrin-mdr-crc
Project description:Panel-based next-generation sequencing data of 211 human CD4 T cells, CD8 T cells and genomic DNA. The panel was designed to capture 260 SNVs in high linkage disequilibrium with multiple sclerosis susceptibility SNVs. NGS was carried out using PE300 reads on the Illumina MiSeq (Illumina Inc., San Diego, CA, United States).
| EGAS00001004139 | EGA
Project description:Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes were filtered when not in Hardy-Weinberg equilibrium. The genomes were phased with IMPUTE using the 1000 Genomes reference panel. NB: for the Y chromosomes, only the 44 Aboriginal Australian males are included.
| EGAD00001004155 | EGA
Project description:Natural variants of the Drosophila melanogaster foraging (for) gene as a popular model to understand behaviour, plasticity, and pleiotropy at an evolutionary and molecular level. The effects for variants on phenotype, fitness, stimulus-response (e.g., food deprivation), and tissue-specific for expression are well characterized. In contrast, the transcriptome-wide influence that for variants have across different tissues and stimuli remains unknown. In this study, we collected fed and 4-hour food-deprived D. melanogaster samples from the genetic null, the natural sitter variant, and the natural rover variant in the CNS (brain and brain stem), gut, and fat (89 samples total, N=4-5 per condition/genotype/tissue). Paired-end bulk RNA sequencing was then completed in one experimental batch at Genome Quebec using the NovaSeq6000 S4 PE100 Sequencing Lane. Briefly, samples were aligned to the dm6 genome using STAR, duplicates were marked with Picard, and reads that were non-chromosomal, low-quality, or unpaired were filtered with samtools. High-quality reads were then counted to the dm6 genome with the "Drosophila_melanogaster.BDGP6.22.96" genome annotation with featurecounts. These RNA-seq data elucidated how the for locus, and the natural variants of for can influence gene expression and cellular function across tissues and conditions.
2023-03-15 | E-MTAB-12688 | biostudies-arrayexpress
Project description:Purpose: the goal of this study is to determine the changes in gene expression during EB differentiation after BPA, BPF and BPS treatments, as indications of potential developmental toxicity. Methods: Transcriptomics profiling for EB samples treated with 100 nM BPA, BPF, BPS or DMSO control at different time points were generated by RNA-seq, using a BGISEQ-500 platform. Reads were filtered and aligned to the reference genome with Bowtie2. Results: BPA, BPF and BPS disrupted many processes, during mESC global and neural differentiations, in very similar manners. In fact, analogous gene categories were differentially regulated by the three chemicals, at each time point, particularly the ones involved in cell-matrix and cell-cell adhesions, signal transduction pathways, and medical conditions such as cardiovascular diseases and cancer.
2019-09-30 | GSE120224 | GEO
Project description:In-depth information regarding the DFCI OncoPanel sequencing panel has been described previously. Briefly, sequencing is performed using an Illumina HiSeq 2500 system (RRID:SCR_016383) with 2×100 paired-end reads. Samples must meet an average 50X coverage and minimum of 30X coverage for 80% of targets for analysis. For all samples, a board-certified molecular pathologist evaluates alterations and writes interpretations of the results. The three generations of OncoPanel use Mutect (RRID:SCR_000559) and GATK (RRID:SCR_001876) to interrogate possible alterations in the complete exonic DNA sequences of 275, 309, and 447 cancer-related genes, respectively, including substitutions, insertions, and deletions. Because tumor tissues are tested without a paired normal from individual patients, additional informatics steps are taken to identify common single nucleotide polymorphisms (SNPs). Any SNP present at >0.1% in Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) (RRID:SCR_012761), or present in dbSNP (RRID:SCR_002338) is filtered; however, variants also present in at least twice in COSMIC (RRID:SCR_002260) are rescued for manual review. Variants that appear two or more times in a panel of 150 normal samples sequenced in-house and are not present in COSMIC are also filtered. For copy number alteration (CNA) analysis, the workflow employs an in-house algorithm (RobustCNV) to cover exonic regions of targeted genes as well as select intronic regions. The depth of coverage of these regions is determined by counting the number of reads aligning within defined genomic intervals and then normalized against a panel of normals and corrected for GC bias. The copy number for a segmented genomic interval is calculated as a log2 ratio of the depth of coverage of this sample compared to a panel of normal (non-cancer) samples that are run on the same plate. In parallel (samples not included), additional cases were previously sequenced via the MSK-IMPACT platform. To ensure maximum overlap between the platforms, only single nucleotide variants (SNVs), dinucleotide/oligonucleotide variants (DNVs/ONVs), insertions/deletions (indels), high copy gains (amplifications), and homozygous deletions from 182 genes shared between all versions of both platforms were evaluated in our analyses involving samples from both platforms. To filter pathogenic and passenger mutations, missense, truncating (nonsense, frameshift, and splice site), and in-frame indel mutations from the 182 genes overlapping between the DFCI OncoPanel and MSK-IMPACT panels were subjected to analysis in the Cancer Genome Interpreter (CGI) suite (RRID:SCR_023752) with cancer type set to “Skin Cutaneous Melanoma (SKCM)”. Known pathogenic mutations, defined as those listed as pathogenic in ClinVar (RRID:SCR_006169), OncoKB (RRID:SCR_014782), and/or CGI databases, were included in downstream analyses. Mutations which had not been previously annotated but were predicted to be pathogenic mutations by CGI were also included. Missense SNV mutations called passengers in CGI were subjected to another round of analysis in the ChasmPlus suite with cancer type set to SKCM. Missense mutations called pathogenic via this approach (p < 0.05; FDR Q < 0.3) were salvaged and included in further analyses. All other mutations were excluded. TERT promoter mutations were evaluated via FATHMM-MKL. Mutations called pathogenic via this tool were included in downstream analyses. Clinical data for these cases is available in a supplementary file from the associated publication. OF NOTE, THE RAW SEQUENCING DATA FROM THESE SAMPLES CANNOT BE MADE PUBLICLY AVAILABLE BECAUSE THE RESEARCH PARTICIPANT CONSENT DOES NOT INCLUDE AUTHORIZATION TO SHARE IDENTIFIABLE DATA.
2024-11-21 | E-MTAB-14575 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to investigate the effect of the cytarabine treatment on the transcriptional profiles of U2OS cells retrovirally expressing DNMT3A R882C isoform, compared to DNMT3A WT and empty vector controls Methods: U2OS DNMT3A WT, R882C, and empty vector cells were treated with 10uM cytarabine or vehicle control for 24 hours. Biological triplicates were generated, ie each replicate was performed on different day using a new batch of cells. Total RNA was collected and QC'd; mRNA was enriched using Poly-T oligo attached to magnetic beads and Illumina libraries were prepared and sequenced on Novaseq6000 (PE 150). Library construction and sequencing were performed by Novogene Corporation, Inc according to standard workflow. Results: Using a custom built pipeline in PartekFlow, the reads were aligned to human (build hg38) genome with the STAR aligner 2.6.1d and low quality alignments were filtered. About 25 million sequence reads per sample were mapped to the human genome. We identified 5714 transcripts/sample and low expression genes with counts less than 10 were filtered and the raw read counts were normalized using TMM model with an offset of 1 to avoid zero counts. Unsupervised hierarchical clustering was performed on the top 2000 genes with highest variance Conclusions: The study identifies gene networks involved in cytarabine response that are deregulated by presence of mutant DNMT3A.
2021-06-02 | GSE153871 | GEO
Project description:Purpose: The study aimed to characterize the molecular phenotype of bone marrow macrophages in NHL with RNA sequencing analysis. Methods:RNA of sorted femur macrophages (CD11b+F4/80+) were extracted with an RNA extraction kit (Qiagen). The samples were submitted to Novogene Inc. for library preparation and subsequent RNA sequencing. RNA was used for cDNA library construction using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s protocol. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina) using a paired-end 150 run (2×150 bases). Reads containing adapter or poly-N and those of low quality were trimmed, after which gene counts were obtained though mapping the clean reads to reference genome mm10 using STAR 2.5.3a.
2021-12-12 | GSE190598 | GEO
Project description:In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.
2015-05-27 | GSE69225 | GEO
Project description:The Akirin (AKR) family are transcription cofactors without catalytic or DNA-binding capability with a conserved function in the regulation of multiple biological processes (BPs) throughout the metazoan. Human akirin2 (AKR2) is involved in various BPs in cell type and stimulus-dependent manner by acting as a link between NF-κB and chromatin remodeling complexes (remodelers) for transcriptional regulation. The regulome (transcription factors/cofactors-target genes interactions) plays an important role in the regulation of these BPs and the application of transcriptomics studies can be critical to better understanding the role of this transcription factors/cofactors as AKR2. In this study, we focused in AKR2 regulome to clarify its function as conserved regulatory cofactor. To assess this, RNA-seq analysis were conducted in wild type (WT) and AKR2-knock down (KO) human Caucasian promyelocytic leukemia HL60 cells. Results have shown a different gene expression profile that allowed us to identify immune response genes as putative AKR2 functional complements providing a better understanding of AKR2 regulome and its possible chromatin remodeling function.
2020-10-02 | GSE158885 | GEO