14480 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Single cell resolution of human CNV body map (2019-10-02)

  12 tissues from the warm autopsy are selected for this project. Using 10X Chromium technology we will generate ~1000 single cell/nulei genomic libraries per tissue. Each tissue will be whole genome sequenced (~2 lanes per 1000 cells) on hiseq X10. per single cell we will generate CNV profile and we investigate the level of genomic heterogenity with in tissue and across different tissues. . This dataset contains all the data available for this study on 2019-10-02.

  Dataset EGAD00001005372

• Bam files from Whole exome sequencing (WES, ~50x mean read depth) of metachronous bladder tumors

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors) Data provided here consist of 122 Bam files for WES (83 Tumors and 39 blood)

  Dataset EGAD00001002716

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007854

• Hip OA Functional Genomics RNAseq (2017-06-09)

  From 9 patients undergoing hip joint replacement surgery for osteoarthritis, we collected 3 cartilage samples each: a low-grade sample (no obvious evidence of damage or fibrillation); a high-grade sample (damaged and fibrillated cartilage); an osteophytic sample (overlaid bony protrusions mainly around the margins of the articular surface). Multiplexed libraries were sequenced on Illumina HiSeq 2000 (75bp paired-end read length) and a cram file was produced for each sample. This dataset contains all the data available for this study on 2017-06-09.

  Dataset EGAD00001003354

• Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer

  The dataset for the study “Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer” includes 171 bam files from targeted next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 33 individuals with small cell lung cancer, alongside 10 bam files from whole exome sequencing of tumor and matched normal DNA for 5 individuals with small cell lung cancer.

  Dataset EGAD00001009860

• subset of DEEP IHEC release 2016 (EGAS00001001937), as used in EGAS00001001656 (bidirectional promotors paper, Fatemeh et al. 2018)

  part of the DEEP project results resulted in the publication of 'Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters', Epigenetics & Chromatin (2018), Fatemeh et al., DOI: 10.1186/s13072-018-0236-7, PMID: 30414612, PMCID: PMC6230222. This dataset contains the subset of DEEP data related to that study.

  Dataset EGAD00001005953

• Pseudotime ordering of cell cycle state (2020-01-29)

  We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005919

• Prevalence of transthyretin amyloidosis in patients with heart failure and no left ventricular hypertrophy

  The study prospectively enrolled patients admitted for HF with LV ejection fraction (LVEF) ≥ 50% and LV wall thickness <12 mm. TTR cardiac amyloidosis was diagnosed according to accepted criteria, which include positive cardiac 99-Tc-DPD scintigraphy in the absence of monoclonal protein expansion in blood. In a cohort of patients with HFpEF without LVH, the prevalence of TTR cardiac amyloidosis was 5%. Transthyretin gene sequencing was performed in positive patients.

  Dataset EGAD00001007787

• CRUK Accelerator: Non-small cell lung cancer whole exome and RNA sequencing

  Whole exome and RNASeq raw sequencing data for a cohort 24 patients with non-small cell lung cancer, 15 adenocarcinoma (8 female, 7 male) and 9 squamous cell carcinoma(5 female, 4 male). Median age at diagnosis was 69. Tumour tissue and PBMCs were used for whole exome sequencing and RNA sequencing. This data was generated as part of a study funded by a Cancer Research UK Centres Network Accelerator Award Grant (A21998).

  Dataset EGAD00001007934

• Evolutionary Genome Analysis of Transformation into Small Cell Carcinomas from Lung Adenocarcinomas

  This dataset includes the high-throughput sequencing data from a study entitled "Clonal History and Genetic Predictors of Transformation into Small Cell Carcinomas from Lung Adenocarcinomas". Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X or HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

  Dataset EGAD00001003315

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• Dataset for Sarcoma-WGS linked from study EGAS00001004813

  Sequencing data of 77 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010257

• Mapping genetic variants underlying gene regulation in healthy intestinal cell types to identify novel IBD drug targets (2020-05-12)

  Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-12.

  Dataset EGAD00001006139

• Healthy human B-lymphopoiesis RNA-Seq reference using FACS sorted bone marrow aspirates

  To define a transcriptomic reference of human B lymphopoiesis, bone marrow aspirates were obtained from n=4 healthy donors (study registration DRKS00023583). After immunodensity cell separation, samples were FACS-sorted into 7 established lymphopoietic differentiation stages. RNA was extracted from 5,000-320,000 cells per differentiation stage and subjected to ultra-low-input RNA sequencing after generation of stranded sequencing libraries.

  Dataset EGAD00001010917

• Whole-genome and transcriptome sequencing of NUT midline carcinoma

  In this study, we sequenced three NUT midline carcinoma genomes and their transcriptomes (NMC1, NMC2 and Ty-82), and two paired normal blood samples (for NMC1 and NMC2). Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X machines. Transcriptome (mRNA) sequencing was performed in HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

  Dataset EGAD00001003117

• Indonesian Genome Diversity Project

  High-coverage whole genome sequences were collected to study patterns of genomic variation across the broad geography of Indonesia and New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. We have sequenced the genomes of 161 individuals from 14 populations spanning this geographical region, from communities close to mainland Asia through to New Guinea.

  Dataset EGAD00001004156

• Deep WGS of matched tumor-normal pairs for HGSOC copy-number signatures study

  This dataset includes 111 bam files from WGS sequence data aligned to human genome assembly GRCh37 (hg19) from 56 tumour and matched normal samples. Libraries were constructed with ~350-bp insert length using the TruSeq Nano DNA Library prep kit (Illumina) and sequenced on an Illumina HiSeq X Ten System in paired-end 150-bp reads mode. The average depth was 60× (range 40-101×) in tumours and 40× (range 24-73×) in matched blood samples.

  Dataset EGAD00001004189

• Identification of low frequency variants associated with ulcerative colitis using whole-genome sequencing

  2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD.

  Dataset EGAD00001000409

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Dataset EGAD00001006239

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• Transcriptome of CD4+ T cells and CD8+ T cells in glioblastoma multiforme

  Patients included in this study were over 18 years of age and had a histology-confirmed diagnosis of glioblastoma multiforme (GBM). Exclusion criteria were the previous administration of any anti-tumor therapy including radiation therapy. All patients gave written informed consent. The study was approved by the local ethics committee (TUM Medical school) and conducted following the Declaration of Helsinki. During resection of the tumors, tumor tissue and tissue from normal appearing brain within the operative channel was collected. Blood was drawn during the surgical procedure. Single cell suspensions were prepared from the tumor tissue, the normal appearing brain, and the blood. CD4+ T cells and CD8+ T cells were sorted by flow cytometry. Only patients with a complete set of specimens (CD4+ tumor infiltrating lymphocytes (TIL), CD8+ TIL, CD4+ T cells from normal appearing brain, CD8+ T cells from normal appearing brain, blood-derived CD4+ and CD8+ T cells) containing a minimum of 1000 cells in each sorted sample were further analyzed (n=9). Total RNA was isolated from sorted cell populations using the RNAeasy Plus micro kit (Qiagen, 74034). Quality and integrity of total RNA was controlled on a Bioanalyzer 2100 (Agilent Technologies). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (ThermoFisher Scientific, EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated and 3'-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read 1 and barcodes and UMIs in read 2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 59 cycles for the cDNA in read 1 and 16 cycles for the barcodes and UMIs in read 2. Data were processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to the Genecode Annotation Version 35.

  Study EGAS50000000156

• A Genome-Wide Association Analysis in Angiotensin-Converting Enzyme (ACE) Inhibitor-Associated Angioedema and ACE Inhibitor-Exposed Controls; A Collaboration between the NIH Pharmacogenomics Research Network and the RIKEN Yokohama Center for Genomic Medicine

  The purpose of this study is to identify genetic predictors of ACE inhibitor-associated angioedema. In addition to preventing the formation of the pressor angiotensin II, ACE inhibitors prevent the carboxyl-terminal degradation of the vasoactive substances bradykinin and substance P. Angioedema is hypothesized to result from defective amino-terminal degradation of bradykinin or substance P in patients in whom ACE is inhibited. For example, activity of dipeptidyl peptidase IV (DPP-IV), the enzyme responsible for the inactivation of substance P when ACE is inhibited, is decreased in patients with angioedema. In preliminary studies, we have identified SNPs in the DPP4 gene that associate with DPP-IV activity and, in blacks, with risk of angioedema. This project will use genome-wide genotyping to compare 250 cases and 568 ACE inhibitor-exposed control subjects (131 cases and 288 controls ascertained at Vanderbilt and 70 cases and 280 controls ascertained at the Marshfield Clinic). We plan a 2-stage analysis of associations between SNPs and angioedema - first, we will study DPP4 SNPs for association with angioedema and, second, we will explore associations using the full GWAS data set. Depending on the platform, additional DPP4 SNPs will be used to fully tag common genetic variants in both African American and European American samples. Based on the HapMap data, there are 14 tagging SNPs in people of European descent and 34 in Yoruba (selection criteria MAF>0.05 and r2>0.8). Cases were defined as having ACE inhibitor-associated angioedema if they had had swelling of the lips, throat, tongue or face while taking an ACE inhibitor but had never had angioedema while not taking an ACE inhibitor. For simplicity, intestinal edema was excluded. Control subjects were treated for at least 6 months with an ACE inhibitor without angioedema. Because black Americans are known to be overrepresented among patients with ACE inhibitor-associated angioedema, control subjects were prespecified to be 50% black American, 50% white American, and 50% female. At Vanderbilt, the medical history, including the history of angioedema, was confirmed by a research nurse or physician using a detailed case report form. Characteristics of Vanderbilt cases appear in the Table. At Marshfield, medical history will be confirmed by chart review. The Marshfield cohort is 98% white American and 57% female with a mean age of 47.2 years.

  Study phs000438

• Therapeutic Trial of Potassium and Acetazolamide in Andersen-Tawil Syndrome

  Andersen-Tawil syndrome (ATS) is an ion channel disorder that causes episodes of muscle weakness and potentially life-threatening heart arrhythmias. The majority of ATS cases are caused by a mutation in the KCNJ2 gene, which is linked to potassium channels in the heart, brain, and skeletal muscle; other cases are presumed to be caused by an undetermined gene lesion. To date, the treatment for ATS has been largely anecdotal, and no treatments have been formally assessed in a controlled clinical trial. This study will determine whether potassium supplements and/or acetazolamide, which is a diuretic medication, affect the duration of muscle weakness and heart rhythm abnormalities in people with ATS. Participation in this study will last about 11 months. Participants will first attend a 3-day inpatient visit that will include a medical history, physical examination, blood work, heart rhythm testing by an electrocardiogram (ECG) and Holter monitor, strength testing, a health questionnaire, and daily potassium supplementation. Participants will also track the number and length of weakness episodes that they experience while in the hospital. On the last day of the inpatient visit, participants will be provided with multiple bottles containing either potassium or placebo. Participants will then return home for an 18-week treatment period that will consist of six 3-week-long treatments of either potassium or placebo, with the treatment schedule being randomly determined. Upon completing the first 18-week treatment period, participants will attend a second 3-day inpatient visit that will include the same tests and procedures as the first. The only difference will be that participants will receive acetazolamide along with potassium. This will be followed by a second 18-week treatment period that will consist of six 3-week-long treatments of either acetazolamide or placebo. At the end of the second treatment period, participants will fill out another health questionnaire. Throughout both 18-week treatment periods, participants will phone in daily to track any muscle or heart problems. They will also provide blood samples on a weekly basis. At Weeks 2, 5, 8, 11, 14, and 17 of both treatment periods, participants will wear a Holter monitor for 24 hours and then mail it in. A final outpatient visit will occur 8 weeks after the end of the second treatment period and will include heart rhythm testing, muscle strength testing, and blood work.

  Study phs001316

• Genetics of Human Inherited Retinal Diseases (GHIRD)

  The goal of this project is to identify novel mutations and genes involved in human retinal disorders, a stated priority of the National Eye Institute. To accomplish this, additional genes whose mutations cause inherited retinal diseases (IRD) will be identified by combining targeted gene panel sequencing, whole exome sequencing, and whole genome sequencing. We have collected about 1050 patient families around the world. In this proposal, we will identify the underlying mutations in these patients using a combination of targeted gene panel sequencing, whole exome sequencing, whole genome sequencing, bioinformatics, statistics, and functional studies. Genes targeted for gene panel sequencing are: ABCA4; ASIC2; JAG1; ABCC6; ARL3; ATP1B2; BBS1; BBS2; BBS4; OPN1SW; CAPN5; C21orf2; CA4; CACNA1F; CDH3; CHM; ERCC8; CLCN2; CLCN3; CLCN7; TPP1; CLN3; CLN5; CNGB1; CNGA1; CNGA3; COL2A1; COL9A1; COL11A1; CRX; VCAN; CTSD; TIMM8A; DMD; CLN8; ERCC6; EFEMP1; OPN1MW; GNAT1; GNAT2; GNGT1; GRM6; GUCA1A; GUCA1B; GUCY2F; GUCY2D; HARS; CFH; HK1; IDH3B; IMPDH1; IMPG1; KCNJ13; KIF11; LRP5; MAK; MITF; TRPM1; MTTP; MVK; MYO7A; NDP; NEK2; NEUROD1; NPHP1; NRL; OAT; OPA1; OTX2; PAX2; PAX6; PDCL; PCYT1A; PDE6A; PDE6C; PDE6G; PDE6H; PDE6B; PEX1; PEX6; PEX7; PEX10; PEX12; PEX13; PEX14; PFDN5; PGK1; PHYH; PIN1; PLA2G5; PPT1; PRKCZ; PEX19; PEX2; PEX5; RB1; RBP3; RBP4; OPN1LW; RDH5; PRPH2; RGR; RHO; GRK1; RLBP1; ROM1; RP9; RP1; RP2; RPGR; RPE65; RS1; SAG; ATXN7; CCL2; SLC6A6; ELOVL4; TEAD1; NR2F1; TIMP3; NR2E1; TTPA; TUB; TULP1; UCHL3; USH2A; CLRN1; VLDLR; BEST1; WFS1; ALMS1; MKKS; FZD4; OFD1; PEX3; CTSF; GBF1; ADAM9; RGS9; PEX11B; PROM1; UNC119; PRPF4; PRPF3; AIFM1; SLC24A1; LRAT; ASIC3; RAB28; PEX16; ITM2B; SLC4A7; IQCB1; CROCC; IFT140; DHX38; MFN2; NR2E3; USH1C; TOPORS; MERTK; FBLN5; CIB2; PRPF8; SDCCAG8; IFT27; TREX1; RRAS2; CEP164; ATF6; TRIM32; RIMS1; SNRNP200; CLUAP1; EMC1; ZNF423; TTLL5; AGTPBP1; RPGRIP1L; CRB1; TSPAN12; ARL2BP; AIPL1; PRPF6; FSCN2; ABHD12; PRPF31; TCTN3; IFT172; CNNM4; NPHP3; INVS; BBS9; FLVCR1; RDH8; IMPG2; WDPCP; RDH11; TMEM216; TMEM138; LZTFL1; CNGB3; AHI1; MKS1; CLN6; BBS7; POMGNT1; PEX26; SPATA7; KIZ; KLHL7; INPP5E; MDM1; CABP4; RPGRIP1; MCOLN1; CC2D2A; KIAA1549; SLC7A14; WDR19; NYX; CDH23; SEMA4A; MPP5; NMNAT1; TMEM237; PCDH15; C5orf42; GNPTAB; TMEM231; TCTN1; SRD5A3; BBS10; ZNF408; TTC21B; CSPP1; LPCAT1; DHDDS; PDZD7; PANK2; CEP290; OPA3; DNAJC5; PITPNM3; MFRP; HMCN1; ADGRV1; ARL6; FAM161A; TMEM126A; GNPTG; GJA10; RAX2; TUBGCP6; TMEM67; ACBD5; C12orf65; CDHR1; BBIP1; REEP6; CACNA2D4; RP1L1; CEP41; C1QTNF5; NXNL1; TTC8; USH1G; BBS5; ZNF513; RDH12; SLC38A8; C8orf37; VPS13B; NXNL2; BBS12; ADGRA3; LCA5; KCNV2; ADAMTS18; ARL13B; ATOH7; MFSD8; NPHP4; CCDC66; CYP4V2; CRB2; RD3; LRIT3; EYS; KIF7; CERKL; RGS9BP; C2orf71; GDF6; DTHD1; GPR179; CISD2; CCR2; PRCD; WHRN; ADGRA3. The current dbGaP study release makes available all sequencing-derived vcf data of study participants.

  Study phs001517

• MP2PRT: Evaluation of an Inflammation Polygenic Risk Score (iPRS) to Predict Cancer Related Cognitive Impairment and Fatigue in Patients Receiving Chemotherapy for Non-Metastatic Breast Cancer in URCC0701 and URCC10055

  This study is a secondary analysis of cancer related cognitive impairment (CRCI) and cancer related fatigue (CRF) among participants in URCC0701 and URCC10055 from the University of Rochester NCI Community Oncology Research Program (NCORP) Research Base. CRCI and CRF are common, troublesome, and dose-limiting toxicities reported by patients undergoing breast cancer chemotherapy that have an etiologic basis linked to low-grade systemic inflammation. Chronic, low-grade systemic inflammation is, in part, genetically determined with common single nucleotide polymorphisms (SNPs) capturing variation across individuals. This study aimed to 1) determine whether an inflammation polygenic risk score (iPRS) is associated with CRCI or CRF, 2) determine whether the relationship between the iPRS and CRCI or CRF is modified by exercise at the time of cancer treatment, 3) identify SNPs associated with serum cytokines measured at the time of cancer treatment, and 4) identify novel CRCI- and CRF-associated risk SNPs via genome-wide association analyses. We found that there was a significant inverse correlation between the iPRS and change in fatigue score from pre-chemotherapy to post-chemotherapy while there was no statistically significant association between the iPRS and cognitive impairment score. The inverse relationship between the iPRS and fatigue may be explained in part by the finding that the iPRS was also significantly associated with greater pre-chemotherapy fatigue, suggesting that women with a genetic predisposition to low-grade systemic inflammation (i.e., high iPRS) have more fatigue at the time of breast cancer diagnosis and, therefore, are less likely to worsen over the course of treatment. In contrast, women with a low iPRS had significantly less fatigue pre-chemotherapy and a significant worsening of fatigue from pre- to post-chemotherapy. The relationship between the iPRS and fatigue remained after adjustment for patient and cancer treatment covariates and was most pronounced in women who reported regularly exercising for at least 6 months prior to starting their cancer treatment. Exploratory genome-wide analysis identified a novel risk locus on chromosome chr6q27, tagged by rs9365961, associated with CRCI. This locus is upstream of TBXT, which encodes an embryonic nuclear transcription factor previously associated with susceptibility to neural tube defects. The genome-wide SNP data, patient-reported CRCI and CRF outcome measures, and covariate data used in this analysis are available through dbGaP.

  Study phs003688