14980 results for "cancer studies using rna-seq"

in 17.11 milliseconds.

• Exome Sequencing of familial and sporadic Meniere disease patients

  This study aims to characterize the genetic architecture of spanish patients diagnosed with Meniere disease (MD), focusing on both familial (FMD) and sporadic (SMD) forms, by analyzing coding variants. Whole-exome sequencing was performed on these patients, and variants were called and annotated using the nf-core/sarek bioinformatics pipeline, including alignment to the GRCh38 reference genome. The resulting data provide a curated resource for investigating the potential genetic contribution to the pathophysiology of MD. All data will be made available for reuse under controlled access.

  Study EGAS50000001178

• Identification of new molecular targets with profiling of malignant mesothelioma

  Aims: Malignant mesothelioma which is associated with asbestos exposure is highly aggressive and refractory to conventional therapeutic modalities. The aim of this study is identification of new targets for molecular target therapy by next generation sequencing and application of the genomic data to new diagnostic and therapeutic strategies for malignant mesothelioma patients. Methods: We extracted genomic DNAs from surgical specimens or established mesothelioma cell lines from Japanese malignant mesothelioma patients. We also extracted control DNAs from peripheral blood of the same patients. We performed whole exome sequencing using these DNAs.

  Study JGAS000062

• Nanopore whole-genome sequencing of sample RK067 and variant-call data (SNVs and intermediate-sized deletions) of 174 Japanese samples.

  We performed whole-genome sequencing of a human samples using Oxford Nanopore MinION sequencer, so as to be able to establish methods to detect and identify structural variations in Japanese individuals. Intermediate-sized deletions were identified from 174 Japanese samples��� short-reads whole-genome sequencing data. Variant call information of these intermediate-sized deletions were joined with SNVs identified in a previous study (Fujimoto, A et al., Nat Genet, 2016) to create a reference panel for use in imputation.

  Study JGAS000180

• WES of Mino-VEN-R Mantle Cell Lymphoma Cells

  This project investigates the genetic basis of therapy resistance in mantle cell lymphoma (MCL) using whole exome sequencing (WES) of the Mino_VEN_R cell line, a model of resistance to pirtobrutinib, a non-covalent BTK inhibitor. Our study suggested that drug-tolerant persister (DTP) cells evade therapy through metabolic and phenotypic reprogramming. By analyzing the exome profile of resistant cells, this study aims to identify mutations associated with treatment escape and cellular plasticity. The findings will contribute to a better understanding of resistance mechanisms and support the development of more effective therapeutic strategies.

  Study EGAS50000001088

• The DIRECT study: A roadmap for ctDNA-based risk prediction, molecular profiling and MRD detection in Diffuse Large B Cell Lymphoma

  DIRECT was a prospective, multisite study assessing the feasibility and utility of circulating tumor DNA (ctDNA) in 188 patients with aggressive B-cell non-Hodgkin lymphoma using capture panel sequencing and an open-source computational pipeline. The aims of the study were 1)baseline risk stratification, 2)genetic profiling and 3)ultrasensitive minimal residual disease (MRD) assessment. This study highlighted the considerable potential, but also the caveats and limitations, of ctDNA technology when applied to aggressive B-cell lymphoma.

  Study EGAS50000000968

• Whole genome sequencing of colon organoid cultures with artificially induced oncogenic mutations

  Using the CRISPR-Cas9 genome editing system, various oncogenic mutations were introduced in the genome of normal adult stem cells derived from the colon. The resulting clonal cultures were subjected to whole genome sequencing. In addition, the cultures were transplanted in a mouse and the resulting primary and metastatic tumors were also subjected to whole genome sequencing. The initial bulk culture, which was used to generate the mutations, was also whole genome sequenced and served as a reference sample to filter germline variants.

  Study EGAS00001001969

• Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing

  A genetic diagnosis of autosomal dominant polycystic kidney disease (ADPKD) is challenging. However, long-read single-molecule sequencing has been shown to be a reliable alternative strategy that could overcome PKD1 complexities. Using long-read sequencing to characterize a cohort of 19 patients with ADPKD, we developed an approach that provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. Reliable screening of ADPKD patients in a single test without interference of PKD1 homologous sequences is now possible.

  Study EGAS00001002106

• Whole Genome Sequences of 18th century African descended individuals from Charleston, South Carolina.

  This study presents Whole Genome Sequencing results from the Anson Street African Burial Ground Project, which is a community-based initiative aimed at understanding the histories of 37 Ancestors found during construction in Charleston, South Carolina. Here we report fastq files for all 37 Ancestors. DNA was extracted at the University of Tennessee-Knoxville following Dabney et al. 2013, and dual index libraries prepared using a modified NEBNext Ultra II kit with partial USER enzyme digestion. Libraries were then enriched for human genomic DNA (MyBaits) and sequenced on Illumina Platforms.

  Study EGAS00001006693

• ALPI deficiency and inflammatory bowel disease

  Inflammatory bowel diseases (IBDs) are complex and severe disorders ascribed to alterations in the dialogue between the microbiota and the host immune system (Bouma & Strober, 2003; Maloy & Powrie, 2011). By using whole‐exome sequencing (WES), we report the identification of compound heterozygous ALPI mutations in two unrelated patients displaying severe intestinal inflammation and autoimmunity. ALPI encodes the Intestinal alkaline phosphatase, a brush border metalloenzyme that catalyses phosphate hydrolysis of the lipid moiety of LPS and thereby drastically reduces LPS pro‐inflammatory activity (Schromm et al, 1998; Goldberg et al, 2008).

  Study EGAS00001002847

• KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

  The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 818 Finnish biobank samples genotyped for 5774 KIR-region SNPs and analysed for KIR gene content with targeted sequencing.

  Study EGAS00001005457

• Whole genome sequencing based on short and long reads from GM09237 cell line with and without folate depletion

  To asess changes in the DNA-sequence occurring as a result of folate deprivation, DNA extracted from the GM09237 cell line grown with and without folate was sequenced using short read and long read sequencing. The DNA was extracted from cells cultured with either normal medium or medium with no folic acid for 5 days, and then sequenced by BGI PE100 platform (100 bp paired-end sequencing 60x coverage; performed by BGI), or PacBio Sequel system (SMARTbell; performed by BGI) respectively.

  Study EGAS00001005345

• Chromatin accessibility changes in hiPSC-derived neurons after BDNF and KCl stimulations

  Brain-Derived Neurotrophic Factor (BDNF) is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. Molecular mechanisms of BDNF promoting cellular survival and synaptic plasticity have been intensely studied, yet its role in genome regulation is obscure. Using human induced pluripotent stem cell (hiPSC)-derived neurons via lentiviral delivery of the neuronal transcription factor Ngn2, we performed a temporal profiling (1h, 6h and 10h) of chromatin accessibility upon BDNF treatment or depolarization (KCl) to identify BDNF-specific chromatin-to-gene expression programs.

  Study EGAS00001006394

• Leukemia sequencing study

  A custom single-cell amplicon DNA sequencing panel was designed to cover relevant somatic mutations and common single nucleotide polymorphisms (panel CO303). Frozen bone marrow mononuclear cells were thawed, stained using the antibody-derived tags panel TotalSeq™-D Human Heme Oncology Cocktail, V1.0 (Biolegend) and loaded into Tapestri single-cell DNA genotyping platform (Mission Bio) to perform microfluidic encapsulation, lysis, and barcoding according to the manufacturer’s protocol (Chemistry V2, PN_3360A). DNA and ADT libraries were prepared and underwent 2x150bp paired-end sequencing on a NextSeq 500 platform (Illumina).

  Study EGAS00001006784

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Study EGAS00001006989