3855 results for "*geneti*"

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• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• Detroit Research on Cancer Survivors (ROCS) and Disparities and Cancer Epidemiology - Colorectal Cancer (DANCE)

  The goals for this study were as follows:1. Enroll a total of 5,060 African Americans newly diagnosed with cancer into the Detroit Research on Cancer Survivors (Detroit ROCS) Cohort. These population-based cases will be ascertained through the Detroit Metropolitan Detroit Cancer Surveillance System (MDCSS), a founding member of the NCI SEER Program. Participation at baseline will include a written, web-based, or telephone interview, saliva and/or blood collection, and tumor block retrieval, with detailed cancer-related information coming from the MDCSS registry and medical records.2. Enroll a subgroup of colorectal cancer patients identified through the Louisiana Tumor Registry (LTR). An additional 500 colorectal cancer patients, approximately half non-Hispanic white and half African American, will be identified through the LTR and enrolled into the ROCS protocol. The survey is the same survey administered to the ROCS cohort. The Louisiana (“DANCE-CRC”) cohort will not be followed beyond baseline, and blood will not be collected (tumor tissue, however, will be collected, deidentified, and sent for processing through Dr. Rozek's laboratory at Georgetown University).The proposed cohorts will provide for a broad research agenda evaluating cancer outcomes in African Americans across a variety of factors from individual, provider, health care system and community perspectives. These factors include tumor characteristics driving individualized treatment planning, quality of life after a diagnosis and recurrence. Utilizing the MDCSS registry, we will enroll a large population-based sample of African-American cases with lung, breast, colorectal, and prostate cancers and their caregivers resulting in a cohort that will provide substantial benefit to the cancer research community. KCI has a strong history of research in the African-American community and the faculty represents a breadth of experience that includes clinical oncology, genetic epidemiology, environmental exposures, quality of life, treatment decision making, racism/discrimination, and health behaviors. Drs. Schwartz and Beebe-Dimmer have been and will continue to be generous collaborators with other institutions to ensure that this resource will be extensively utilized. The proposed overall cohort will be the only one of its kind, to our knowledge, filling a substantial gap in our understanding of the determinants driving cancer outcomes in African Americans. In addition to registry data detailing cancer specifics, yearly surveys have collected information about individualized treatment experiences, heath histories, family histories, quality of life after a diagnosis, recurrence and caregiving. Population: Adult cancer survivors (see inclusion criteria in next section) Molecular Technologies: Genotyping: Infinium Expanded Multi-Ethnic Genotyping Array (MEGAEX) DNA Sequencing: Illumina NovaSeq X Plus using XLEAP-SBS (sequencing by synthesis) Whole genome sequencingPrincipal Findings: The preliminary data collected reinforces differences by race in factors affecting cancer outcomes. Variants in DNA damage repair genes and HOXB13 may be important cancer risk factors for Black men diagnosed with prostate cancer, and are more frequently observed in men with a family history of cancer. ROCS participants reported high rates of a family history of cancer. The high rate of eligibility for Cancer genetic counseling among ROCS participants supports the need for interventions to increase referrals and uptake of genetic counseling among African Americans 60% of ROCS participants reported participating in regular physical activity (PA), with 24% reporting ≥150 min/wk. There were no differences by sex, but prostate cancer survivors were the most likely to report participating in regular PA, whereas lung cancer survivors were the least likely. Survivors who reported participating in regular PA reported higher health-related quality of life and lower depression. More African American than White survivors reported financial hardship and limiting care. More White than African American survivors reported utilizing assets, while more African American survivors reported cancer-related debt. Data available in dbGaP: Individual phenotype data Individual genotype data Individual sequencing dataSample types: Germline DNA

  Study phs003116

• Risk Factors for Asymptomatic Diverticulosis

  Data for this analysis came from a prospective study of colonic diverticulosis at the University of North Carolina Hospital in Chapel Hill, North Carolina (NIH R01DK094738). This is a case-control genetic and transcriptomic study to identify the genetic and cellular determinants underlying colonic diverticulosis and the relationship with other gastrointestinal disorders. The study inclusion and exclusion are described below. DNA and RNA sequencing were performed on colonic tissue from 404 patients with (N=172) and without (N=232) diverticulosis. We assessed variation in the transcriptome associated with diverticulosis and integrated this variation with human intestine single-cell RNA-seq data. We integrated our expression quantitative trait loci with GWAS using Mendelian Randomization. A polygenic risk score analysis examined associations between severity of diverticulosis and other gastrointestinal disorders. We identified 38 genes with differential expression and 17 genes with varied transcript usage linked to diverticulosis. Our results suggest tissue remodeling as a primary mechanism for diverticula formation. The presence of diverticulosis was linked to stromal and epithelial cells in the colon including endothelial cells, myofibroblasts, fibroblasts, goblet, tuft, enterocytes, neurons, and glia. MR highlighted five genes including CCN3, CRISPLD2, ENTPD7, PHGR1, and TNFSF13. In diverticulosis cases, ENTPD7 upregulation was confirmed. A greater burden of diverticula was positively correlated with genetic predisposition to diverticulitis. The data related to the study including total RNA-Seq, SNP array and imputed genotypes will be available through dbGaP.

  Study phs003556

• Replication data for RNA-SEQUENCING: A RELIABLE TOOL TO UNVEIL TRANSCRIPTIONAL LANDSCAPE OF PAEDIATRIC B-OTHER ACUTE LYMPHOBLASTIC LEUKAEMIA

  This dataset contains the raw data of the RNA-seq experiments described in the paper "RNA-Sequencing: a reliable tool to unveil transcriptional landscape of pediatric B-other acute lymphoblastic leukemia" It contains the raw data from 60 pediatric patients diagnosed with B cell progenitor acute lymphoblastic leukemia lacking the main genetic alterations. RNA material was extracted from bone marrow or periphereal blood and RNA libraries were prepared using Illumina® TruSeq™ stranded mRNA kit following manufacturer's instructions and were sequenced in a NextSeq 550 using a v2 HighOutput 150 cycle kit 2x75bp. Funding: Instituto de Salud Carlos III (ISCIII), PI21/00213 

  Dataset EGAD50000000981

• Mapping Genotypes to Chromatin Accessibility Profiles in Single Cells

  In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1–3. Therefore, somatic mutations likely alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. To chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed Genotyping of Targeted loci with single-cell Chromatin Accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution, across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from myeloproliferative neoplasm (MPN) patients with JAK2V617F-mutated hematopoiesis.

  Study EGAS50000000164

• Raw sequencing files from WGS and RNA-Seq

  Acute leukemias are the most common malignancies in children with an onset of the disease among 0-6 years-old. The early development of theses malignancies has been proposed as an indicator of their prenatal origin, hypothesis that has been confirmed especially in the case of acute lymphoblastic leukemia. For acute myeloid leukemia (AML), comprising an heterogenous group of different cytogenetics subtypes, this prenatal origin has also been confirmed specially for MLL-rearranged and t(8;21) subgroups. AMLs carrying t(7;12) constitute up to 30% of cases under 2-years-old, frequently being associated with a trisomy of chromosome 19 and an overexpression of MNX1 gene. An in utero origin of this specific subgroup has been suggested but not clearly confirmed. Here, we present the case of a 5-months-old AML patient with t(7;12) in which we have fully characterized a novel breakpoint occurring among ETV6 and NOM1 genes. We demonstrate the presence of this specific ETV6-NOM1 fusion in CD34+ hematopoietic stem and progenitor cells isolated from the cord blood unit from the same patient and stored at birth. Moreover, trisomy +19 present at diagnosis was not detected at birth. Together, our results demonstrate the prenatal origin of the t(7;12) in infant AML, and establish trisomy +19 as a secondary event in this leukemia.

  Study EGAS50000000186

• Whole-genome sequences of Korean populations generated by using long- and short-read sequencing technologies.

  We newly sequenced whole-genome of Korean participants by using long- and short-read sequencing platforms (n = 3 and n = 100 for long- and short-read sequencing, respectively). With these data, generated by Sequel II HiFi system (Pacific Bioscience) and DNBSEQ-T7 (MGI) sequencers, we identified a set of structural variations common in Korean population as well as the genetic features distinct from other ethnicities.

  Study EGAS50000000375

• Changes in CRISPR/Cas9 Outcomes depending on the usage of Pifithrin-alpha

  Study of the effects of Pifithrin-alpha in the context of genetic-engineering in primary human T cells.

  Study EGAS50000000656

• Clinical evaluation of long read sequencing-based episignature detection in developmental disorders

  Some developmental disorders (DD) are marked by specific genome-wide methylation changes, known as episignatures, which can support diagnosis and reveal underlying mechanisms. Current methods rely on indirect methylation profiling. Here, we assessed whether long-read whole genome sequencing with nanopore technology could directly detect both episignatures and genetic variants. We sequenced forty controls and twenty DD patients, using clustering and dimensional reduction to compare methylome patterns with microarray-based signatures. Our classifiers accurately identified episignatures in 17 of 19 patients with pathogenic variants, matching microarray results. This study shows nanopore sequencing enables comprehensive, haplotype-aware genomic and epigenomic analysis for DD diagnostics.

  Study EGAS50000000719

• The landscape of somatic mutations in epigenetic regulators across 1000 pediatric cancer genomes

  Study EGAS00001000449