12233 results for "fc 26 coins pc Visit Buyfc26coins.com for latest FC 26 coins news..z7ux"

in 34.69 milliseconds.

• A combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancer

  The earlier diagnosis of cancer is one of the keys to reducing future cancer deaths. Here we describe our efforts to develop a non-invasive, blood test for the detection of pancreatic ductal adenocarcinoma. We combined blood tests for KRAS gene mutations with carefully thresholded protein biomarkers to determine whether the combination of these markers was superior to any single marker. The cohort tested included 221 patients with resectable pancreatic ductal adenocarcinoma and 185 control patients without known cancers. KRAS mutations were detected in the plasma of 66 patients (30%) and every mutation found in the plasma was identical to that subsequently found in the patients' primary tumor (100% concordance). The use of KRAS in conjunction with two thresholded protein biomarkers (CA19-9 and prolactin) increased the sensitivity to 67%. Only one of the 185 plasma samples from the control cohort were positive for any of the three markers (99.5% specificity). This combinatorial approach may prove useful for the earlier detection of many cancer types.

  Study EGAS00001002444

• An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

  We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena

  Study EGAS00001005974

• dbGaP Collection: NHLBI Heart Failure Related dbGaP Data (No IRB requirement)

  The National Heart, Lung, and Blood Institute (NHLBI) Big Data Analysis Challenge: Creating New Paradigms for Heart Failure Research has concluded. The NHLBI will continue to make this collection of data available to the research community.Past information regarding the Data Collection for the NHLBI Big Data Analysis Challenge: Creating New Paradigms for Heart Failure Research is below.The National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health (NIH), is inviting novel Solutions for the NHLBI Big Data Analysis Challenge: Creating New Paradigms for Heart Failure Research. The goal of the challenge is to foster innovation in computational analysis and machine learning approaches utilizing large-scale NHLBI-funded datasets to identify new paradigms in heart failure research. The challenge aims to address the need for new open source disease models that can define sub-categorizations of adult heart failure to serve as a springboard for new research hypotheses and tool development in areas of heart failure research from basic to clinical settings. NHLBI has a history of making considerable investments in the creation of deep data resources including: long-standing, deeply-phenotyped epidemiological cohorts, innovative clinical trials, and large-scale precision medicine efforts that have generated whole genome sequencing and "other omics" data for more than one-hundred thousand individuals. To provide challenge participants with streamlined access to data across NHLBI's numerous studies containing heart failure data, the NHLBI has created this dbGaP study collection. Data access for this collection is controlled by NHLBI's Data Access Committee. Challenge participants are required to follow the use restrictions and acknowledgement instructions from the original dataset(s). Please note that the data in this collection are not harmonized across studies or otherwise altered from the original study. The NHLBI Big Data Analysis Challenge: Heart Failure Data Collection contains all NHLBI studies currently in dbGaP that contain data that may be relevant to research on heart failure. The studies in this collection are approved for General Research Use (GRU), Health/Medical/Biomedical Use (HMB), or Disease-Specific Use (DS) that permits research on heart failure. These studies span a variety of study designs, inclusion and exclusion criteria, sample sizes, and provide a wide breadth and depth of phenotype data on study participants. The available genomic data in these studies also varies, including genotyping arrays, sequencing (targeted, exome, whole genome), and additional -omic data (e.g., RNA or metabolite profiles). Please refer to each study's individual accession page to learn more about how study data were collected. Challenge participants are reminded that in addition to dbGaP, NHLBI's Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) contains other studies that have collected data relevant to heart failure and may wish to utilize BioLINCC data in the development of their Solution. Please refer to the individual accession page for each study in this collection to learn more about the history of each study.

  Study phs001991

• Whole Exome Sequencing for Colorectal Cancer

  This project was designed to use next generation sequencing technology to screen the protein coding regions of the genome for low frequency variants in a panel of high-risk colorectal adenocarcinoma cases. Blood and cell-line DNA for colorectal cancer patients and a subset of quality control samples that had existing whole exome sequence data were analyzed using Illumina HiSeq sequencers. Samples from this project were from participants in the Women's Health Initiative (WHI) and the Diet, Activity, and Lifestyle Study (DALS).

  Study phs000410

• Circulating Tumor DNA Sequencing Provides Comprehensive Mutation Profiling for Pediatric Central Nervous System Tumors

  Tumor molecular profiling is increasingly important for the diagnosis and clinical management of childhood brain tumors, including diffuse midline glioma (DMG). We established a targeted deep sequencing approach using the TruSight Oncology 500 ctDNA exome panel to detect tumor genomic mutations and copy number variations in circulating tumor DNA from children diagnosed with DMG. In this study, we present the sensitivity, specificity, and clinical implications of our liquid biopsy sequencing approach for tumor genome profiling in children with DMG.

  Study phs003022

• ctDNA multigenic panel for non-small cell lung cancer

  Detection of actionable mutations in liquid biopsies constitute an important tool for management of non-small cell lung cancer (NSCLC) patients in the era of oncology precision medicine. We aimed to evaluate the actionable alterations using a commercial multi-gene panel in circulating tumor DNA (ctDNA) derived from plasma samples of treatment naïve and prior-treated non-small cell lung cancer (NSCLC) patients. For this, we analyze plasma samples of 30 subjects with non-small cell lung cancer.

  Study EGAS50000000643

• WGS data for EBiSC iPSC lines

  The European Bank for Induced Pluripotent stem cells (EBiSC) is designed to address the increasing demand by iPSC researchers for quality-controlled, disease-relevant research grade iPSC lines, data and cell services. In this study Whole Genome Sequencing was performed on a selection of lines from the project.

  Study EGAS50000000742

• A GWAS for cutaneous leishmaniasis in Brazil

  Our goal was to identify genetic risk factors for cutaneous leishmaniasis (CL) caused by Leishmania braziliensis. Genotyping 2066 CL cases and 2046 controls using Illumina HumanCoreExomeBeadChips provided data for 4,498,586 imputed single nucleotide variants (SNVs). Genome-wide association testing using linear mixed models took account of genetic diversity/ethnicity/admixture. Post-GWAS positional, expression quantitative trait locus (eQTL), and chromatin interaction mapping was performed in FUMA. Transcriptional data were compared between lesions and normal skin, and cytokines measured using flow cytometry and Bioplex assay.

  Study EGAS00001004596

• Single cell RNA sequencing of normal endometrial derived organoids uncovers novel cell type markers for prognostication

  Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed single cell sequencing on endometrial and ovarian tumors and found both secretory-like and ciliated-like tumor cells.

  Study EGAS00001004466

• Investigation of different library preparation and tissue of origin deconvolution methods for urine and plasma cfDNA methylome analysis

  In this study, a single- and a double-stranded library preparation approach was evaluated with respect to their technical biases when applied on cfDNA from plasma and urine. This study thus outlines potential limitations of double-stranded library preparation for methylation analysis of cfDNA especially for urinary cfDNA. While the double-stranded method allows jagged end analysis in addition to TOO analysis, it leads to significant methylation bias in urinary cfDNA, which single-stranded methods can overcome.

  Study EGAS00001007314

• The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

  Tumor infiltration by T cells is paramount for effective anti-cancer immune responses. We hypothesized that the T cell receptor (TCR) repertoire of tumor infiltrating T lymphocytes (TIL/Tc) could determine disease course at different stages in cancer progression. We show that the diversity of the TIL/Tc TCR at baseline is prognostic in various cancers, whereas in metastatic melanoma TIL/Tc TCR clonality at baseline is predictive for activity and efficacy of PD1 blockade immunotherapy.

  Study EGAS00001005201

• Annotated VCF Files for WGS of ASD Cohort with 68 Individuals from 22 families, enriched for recent shared ancestry

  We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. Samples were sequenced using Illumina HiSeq X platform, and Variants (single nucleotide variants (SNVs) and insertions or deletions (indels)) were detected using GATK with HaplotypeCaller. Quality control checks for (i) duplicate samples, (ii) samples per platform, (iii) genome call rate, (iv) missingness rate, (v) singleton rate, (vi) heterozygosity rate, (vii) homozygosity rate, (viii) Ti/Tv ratio, (ix) inbreeding coefficient, and (x) sex inference were performed as previously described. Variant call format (VCF) files for SNVs and indels were annotated with ANNOVAR using allele frequencies from the 1000 Genomes project (2015; 1000G), the Genome Aggregation Database (gnomAD), and the Greater Middle East Variome Project (GME).

  Dataset EGAD00001008634

• Genome Database of Latvian Population

  Access policy for the samples and data from Genome Database of Latvian Population: https://www.genomadatubaze.lv/en/conditions-for-the-issue-of-biological-materials-and-data

  Dac EGAC50000000624

• TOPARP-B patient cell-free DNA WGS

  Sequencing files for TOPARP-B patients as described in manuscript

  Study EGAS50000000280

• Human_Developmental_Cell_Atlas_HDCA___WGS

  Single cell + bulk genomics study for immune and hematopoietic organs during human fetal development

  Study EGAS00001002929

• Ewing's sarcoma sequencing data

  This study shares DNA and RNA sequencing data for patients with Ewing's sarcoma

  Study EGAS00001005689

• Lund HPI data access committee for Inspire

  Phenotype data from human pancreatic islets from 191 donors, Lund University. Processed for the Inspire consortium.

  Dataset EGAD00001005523

• RNASeq files for Roussel-ATRT-TM

  RNASeq files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00001009302

• High-throughput 3D engineered paediatric tumour models for precision medicine

  Paired fastqs for DNA and RNA from Illumina TSO500 targeted sequencing from PDX.

  Dataset EGAD00001015753

• PACA-CA Whole Exome Sequence bam files

  Merged bam files for PACA-CA Whole Exome Sequencing, for DCC release 25

  Dataset EGAD00001003592

• DATA FILES FOR Histone-NSD2_RNASeq

  DATA FILES FOR Histone-NSD2_RNASeq

  Dataset EGAD00001000655

• HCC.GNE exome dataset

  Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma".

  Dataset EGAD00001000885

• McGill EMC Release 4 for assay "ChIP-Seq Input"

  McGill EMC Release 4 for assay "ChIP-Seq Input"

  Dataset EGAD00001001293

• WTCCC case-control study for Hypertension - Combined Controls

  WTCCC genome-wide case-control association study for Hypertension (HT) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000010

• Exome sequencing data for the DIRECT study.

  This dataset contains all available fastq files for gemline, baseline plasma/biopsy, and response assessment patient samples for the DIRECT study. The total number of samples was 729 (188 germline, 190 baseline plasma, 159 baseline biopsy, and 192 response assessment). The dataset files were generated from targeted (exome) Illumina sequencing performed on paired biopsy tissue and plasma cell free DNA.

  Dataset EGAD50000001409

• Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

  Development of a novel machine learning guided ctDNA detection platform for use in liquid biopsy detection and therapeutic monitoring of solid tumors in several clinical contexts. Included are WGS alignments from our study.

  Study EGAS00001007306

• Metadata and count matrix

  The dataset contains metadata for all cells before scRNA-seq quality control and for cells passing quality control. It also contains a count matrix with Salmon gene counts for all cells passing quality control, and reconstructed B-cell receptor sequences using the computational tool BraCeR. The scRNA-seq data was generated using the Smart-seq2 protocol and sequenced on Illumina NextSeq500.

  Dataset EGAD00001006435

• Sequencing data for the Genomic Autopsy Study

  The .cram files of the Trio or Quad sequencing data used for generation of the genomic autopsy study. This contains a mix of genome sequencing and exome sequencing data for probands and their parents. A subset of families (n=32) did not provide consent to publicly sharing their data.

  Dataset EGAD00001009737

• Dataset of transcriptomic, whole genome and whole exome sequencing to identify predictive biomarkers in pediatric solid tumors

  This Dataset contains whole genome sequencing data for 148 sample, transcriptome sequencing for 66 samples and exome sequencing for 123 samples from pediatric solid tumors. Sequencing was performed on Illumina NovaSeq 6000 and Illumina HiSeq 4000. The sequencing was paired.

  Dataset EGAD00001015701

• eMERGE: Northwestern (NUgene) WGS

  The NUgene Project is a biorepository with longitudinal medical information from participating patients at Northwestern Medicine affiliated hospitals and outpatient clinics. Participants' DNA samples are coupled with data from a self-reported questionnaire (2 versions were used, 1 before and 1 after February 2006, both are included) and continuously updated data from our Electronic Medical Record (EMR) representing actual clinical care events. Northwestern has a state-of-the art, comprehensive inpatient and outpatient EMR system of over 3 million patients. NUgene has broad access to participant data for all outpatient visits as well as inpatient data via a consolidated enterprise data warehouse. NUgene participants consent to distribution and use of their coded DNA samples and data for a broad range of genetic research by third-party investigators. The electronic MedicalRecords and Genomics (eMERGE) Network is a consortium of 9 clinical sites with EMR linked DNA biobanks, including Northwestern University and its NUgene biobank, funded by the NHGRI (National Human Genome Research Institute) to investigate the use of electronic medical record systems for genomic research. The goal of eMERGE is to conduct genome-wide association studies in approximately 100,000 individuals using EMR-derived phenotypes and DNA from linked biorepositories. Using electronic phenotyping methods, the consortium has been and is using DNA samples from all participating sites to explore the genetic determinants of approximately 80 phenotypes, including both diseases and traits, for which the electronic phenotyping algorithms have or are being published on PheKB.org. Thus, for the eMERGE network, ~900 NUgene subjects were selected, as described in the study inclusion/exclusion criteria section below, to be genotyped using whole genome sequencing (WGS), for use in the eMERGE network as eMERGE subjects. The criteria used below were selected so that these subjects will likely meet the criteria to be cases and/or controls, of diverse races and/or ethnicities, for at least 1 of the ~80 phenotypes being studied within eMERGE, and could be recontacted for future research if needed.

  Study phs001191

• Molecular defects in pseudohypoparathyroidism or related disorders

  Maintaining calcium levels within a narrow normal range is of critical importance for numerous different cellular functions. One of the most important regulators of blood calcium levels is parathyroid hormone (PTH), which mediates its actions through the PTH/PTHrP receptor, a Gαs-coupled receptor. Few inherited disorders are characterized by diminished blood calcium levels and elevated blood phosphate levels; some of these disorders are caused by too little PTH synthesis and/or secretion (hypoparathyroidism, HP), while others are caused by resistance towards PTH (pseudohypoparathyroidism, PHP). Only few of the inherited forms of HP (<10%) have been defined at the molecular level. In contrast, genetic mutations have been identified for several inherited forms of PHP. For example, PHP type Ia (PHP-Ia) is caused by maternally inherited mutations in those GNAS exons that encode Gαs, while autosomal dominant PHP type Ib (AD-PHP-Ib) is caused by maternal inherited deletions within or up-stream of GNAS, which are associated with abnormal GNAS methylation. However, a large number of patients with PTH-resistance and thus hypocalcemia show GNAS methylation changes, but their underlying genetic defects have not yet been defined at the DNA level. These "sporadic" patients may be affected by an autosomal recessive form of PHP-Ib (AR-PHP-Ib), which is most likely not linked to the GNAS locus. In our studies, we propose to search through exome sequence analyses for novel genetic mutations responsible for novel autosomal dominant forms of HP that are not caused by mutations in the known disease-causing genes; some of these families are large enough to perform genetic linkage studies. We furthermore propose to search for the genetic mutation(s) responsible for the autosomal recessive variant of PHP-Ib through the analysis of whole exome sequences; for these studies we focus particularly on patients, whose parents are likely to be consanguineous. The proposed efforts are expected to lead to the identification of novel genes that are involved in parathyroid development and function (HP) and genes that are involved in the establishment or maintenance of GNAS methylation (AR-PHP-Ib).

  Study phs000476

• NIDDK IBD Genetics Consortium Crohn's Disease Genome-Wide Association Study

  This dataset contains data from a genome-wide association study performed with 968 Inflammatory Bowel Disease (IBD) affected cases and 995 unrelated controls using the Illumina HumanHap300 Genotyping BeadChip. Cases were selected to have Crohn's disease with ileal involvement, and controls were matched to cases based on sex and year of birth. Subjects were drawn from two cohorts: (1) persons with non-Jewish, European ancestry (561 cases and 563 controls), and (2) persons with Jewish ancestry (407 cases and 432 controls). Genotyping was performed at the Feinstein Institute for Medical Research. Seven-hundred fifty-four of the samples (468 cases and 286 controls) were taken from the NIDDK IBD Genetics Consortium cell line repository. These samples are identified in the IBD_Sample file. The subject IDs for these individuals may be used to request corresponding samples for follow-up research through the repository. In addition, complete phenotype data for these individuals are available, together with the Consortium's phenotyping manual and the forms used to collect the data. The remaining 1,209 samples were obtained from pre-existing collections ascertained through Cedars-Sinai Medical Center, Johns Hopkins University, University of Chicago, University of Montreal, University of Pittsburgh, University of Toronto, and the New York Health project (controls only). For these samples, only sex, cohort (Jewish vs. non-Jewish), and age at diagnosis (cases only) are available. Two-hundred three individuals from among the pre-existing samples did not provide consent to release their genotype data (designated as consent group 2 in the file IBD_Subject). Thus, individual genotype data are only provided for 1,760 samples. To compensate for this, we have provided summary results for each SNP. These are based on a stratified analysis testing case/control association. Fifty-one samples had a call rate less than 93% and were therefore excluded from this analysis, leaving an overall sample size of 1,963 - 51 = 1,912. X Chromosome Heterozygosity Nine samples have X chromosome heterozygosity that is neither consistent nor inconsistent with their phenotypic sex. One of these samples was found to have Turner Syndrome. The remaining 8 samples have heterozygosity ranging from 35-76%.

  Study phs000130

• National Institute on Aging (NIA) SardiNIA Study

  Sardinia is the second largest island in the Mediterranean and constitutes a genetically isolated founder population. This population has aided in the identification of genes involved in several Mendelian disorders and is attractive for genetic studies due to its organization in long-established settlements that developed from an initial group of founder settlers (~1,000) thousands of years ago. The current study has recruited 6,148 Sardinians aged 14 and older, from a cluster of four towns in the Lanusei Valley in the Ogliastra region of the province of Nuoro. This sample corresponds to approximately 62% of the population eligible in the area for recruitment. Information collected during enrollment allowed the individuals to be organized into 711 complex pedigrees, each up to five generations deep, with an average kinship coefficient of 0.1628. All volunteers have been characterized for 98 quantitative traits. Traits include anthropomorphic measures, plasma and serum markers (including cholesterol and other markers of cardiovascular disease), and personality traits (using the five-factor model). The main goal of the study is to examine phenotypic similarities between relatives that yield information on the overall contributions of genes to trait variability. Data given here provide p-values for 98 traits studied in 1,412 individuals, based on genotyping with the Affymetrix 500K chip and imputed markers using the HapMap population as a reference (N=2,259,179). Sharing this genome assessment data at high level of resolution for a variety of quantitative traits will be useful for other groups to validate newly observed associations and to investigate possible pleiotropic effects. For ulterior information, and in particular for any individual genotype information, a formal request should be addressed to the Steering Committee, c/o David Schlessinger, Chief, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd., Suite 100 Baltimore, MD 21224 USA and should include IRB approval of a detailed proposal, along with a signed statement guaranteeing that no attempt will be made to identify any individual participant.

  Study phs000338

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Coronary Artery Risk Development in Young Adults Study (CARDIA)

  Cohort Description The Coronary Artery Risk Development in Young Adults (CARDIA) study is a study examining the development and determinants of clinical and subclinical cardiovascular disease and their risk factors. It began in 1985-6 with a group of 5115 black and white men and women aged 18-30 years. The participants were selected so that there would be approximately the same number of people in subgroups of race, gender, education (high school or less and more than high school), and age (18-24 and 25-30 years) in each of 4 centers: Birmingham, AL; Chicago, IL; Minneapolis, MN; and Oakland, CA. These same participants were asked to participate in follow-up examinations during 1987-1988 (Year 2), 1990-1991 (Year 5), 1992-1993 (Year 7), 1995-1996 (Year 10), 2000-2001 (Year 15), 2005-2006 (Year 20), 2010-2011 (Year 25), 2015-2016 (Year 30), and 2021-2022 (Year 35). Data Being Submitted Wave 1 questionnaire data includes 397 variables for up to 2434 CARDIA participants in C4RWave 2 questionnaire data includes 448 variables for up to 1901 CARDIA participants in C4RDried Blood Spot/Serosurvey data includes 7 variables for up to 1332 CARDIA participants in C4RDerived data includes 43 variables for up to 2723 CARDIA participants in C4RPhenotype data includes 113 variables for up to 2723 CARDIA participants in C4R

  Study phs003045

• Array data for oesophageal and related samples - aks_paper_methyl_barretts_release

  Array data for oesophageal and related samples - aks_paper_methyl_barretts_release

  Dataset EGAD00010001972

• BMI EWAS summary stats

  Summary statistics for a multi-cohort epigenome-wide association study. This includes summary statistics (effect-size, standard error, p-value) for 470,000 methylation markers.

  Dataset EGAD00010001029

• An evaluation of different strategies for large-scale pooled sequencing study design.

  An evaluation of different strategies for large-scale pooled sequencing study design.

  Dataset EGAD00001000037

• Validation_for_human_early_embryonic_substitutions_

  PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients

  Study EGAS00001001218

• Acute myeloid leukemia sequencing data

  This study contains tumor DNA and RNA sequencing data for 1 AML patient

  Study EGAS00001006354

• Glioma sequencing data

  This study contains sequencing data for various glioma subtypes (astrocytoma, glioblastoma, diffuse midline glioma).

  Study EGAS00001006355

• Exome Sequencing

  Exome sequencing of for 10 patients: 10 tumors, 10 cell lines and 7 blood samples (for 3 patients blood was not available)

  Dataset EGAD00001002690

• Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (pacBio)

  Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (pacBio)

  Dataset EGAD00001009631

• RNA-Seq for academic use only

  RNA-Seq transcriptome data is only for academic use.

  Dataset EGAD00001009675

• Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (ONT)

  Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (ONT)

  Dataset EGAD00001009632

• Dataset for iAMP21 scRNA-seq

  10x Genomics 5' library scRNA-seq data for 4 iAMP21 patients

  Dataset EGAD00001009504

• Whole exome sequencing data for paired non-serous endometrial and ovarian carcinomas from 27 patients with concurrent tumours.

  Dataset for Synchronous Endometrial and Ovarian Cancer

  Dataset EGAD00001015680

• PACA-CA Whole Genome Sequence bam files

  Merged bam files for PACA-CA Whole Genome Sequencing, for DCC release 25

  Dataset EGAD00001003591

• DATA FILES FOR SJCPC-WGS

  DATA FILES FOR SJCPC-WGS

  Dataset EGAD00001001065

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Genetics of Pigmentation in Eastern and Southern African Populations Study

  The goal of this study was to identify genes and loci associated with pigmentation in African populations. It comprises 1,593 participants from Ethiopia, Tanzania, and Botswana. Sexes are evenly represented (768 males and 825 females) and self reported ages ranged from 18 to 103. Mean age was used for individuals without ages. For each participant, a DSM II color meter was used to measure underarm skin reflectance in triplicate. These measures averaged and converted to a melanin index (MI = 100 x log10(1/(x/255)). All individuals were included in a genome wide scan that accounted for age, sex, and genetic relatedness.

  Study phs001396

• Estonian Biobank | Estonian Genome Center, University of Tartu

  The Estonian Biobank is the population-based biobank of the Estonian Genome Centre of University of Tartu. The biobank is conducted according to the Estonian Gene Research Act and all participants have signed broad informed consent. The cohort size is currently 51,535 people from 18 years of age and up. Metabolite concentrations (over 110; NMR and MS) are available for about 12,000 subjects; metabolic follow-up has been done for more than 2000 donors. GWAS has been performed on 20,000 subjects with different Illumina arrays and 2,500 have whole exomes and 2,400 full sequence. The data for the 2,400 fully sequenced samples is available through dbGaP.

  Study phs001230

• Study for establishment for effective screening and diagnosis of Lynch syndrome

  The purpose of this study is to establish efficient diagnostic procedure of the Lynch syndrome in Japan and to determine the MMR gene mutation spectrum and clinicopathologic characteristics.The person who is suspected Lynch Syndrome and gives informed consent for participation in this study .To carry out the project ?Construction of clinical and genetic integral information database to help Lynch syndrome management?, the following three are required. 1) screening for Lynch syndrome-suspected cases, 2) genetic testing to define Lynch syndrome, 3) integration of detailed clinical data of Lynch syndrome, and 4) The case which has not been diagnosed Lynch syndrome, is investigated causing gene.

  Study JGAS000638

• Sensitive urothelial cancer detection via high volume urine DNA analysis

  Cystoscopy and imaging are the gold standard for urothelial cancer (UC) detection and surveillance, but cystoscopy is an uncomfortable procedure associated with adverse effects and a low diagnostic yield as only 10% of hematuria patients have UC. Urine tumor DNA (utDNA) is a non-invasive UC biomarker that has suffered from poor sensitivity for Ta stage tumors (<80%). We hypothesized that high urine volume analysis with a multi-gene panel could overcome these limitations, and developed a 100 mL utDNA laboratory platform (UroScout) that analyzes 25 commonly mutated UC genes and 8 copy number-altered loci for somatic alterations to detect UC.

  Study EGAS50000000630

• Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals

  This study presents a methodology for detecting circulating tumor DNA (ctDNA) using deep whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), a less destructive alternative to bisulphite sequencing. The method enables simultaneous analysis of genomic and methylomic data for multi-cancer detection and monitoring minimal residual disease. In a diagnostic accuracy study across various cancer types, it achieved 85.3% sensitivity and 88.8% specificity, with validation done using matched tumour biopsies. Additionally, in silico validation showed strong discrimination at low ctDNA levels. The approach also successfully tracks tumour burden and ctDNA shedding from precancerous lesions post-treatment, making it ready for further clinical testing.

  Study EGAS50000000715

• Multi-omics analysis of treated cancer samples

  We treated patient-derived cell lines with effective drug inhibitors that we discovered. To understand the mechanisms behind how the inhibitor can effectively inhibit tumor growth, we performed a series of RNA-Seq, Histone ChIP-Seq, TF ChIP-Seq and ATAC-Seq profiling for samples with and without treatment with the inhibitor. There are 18 RNA-Seq, 20 ATAC-Seq and 182 ChIP-Seq experiments performed. This includes 2 biological replicates. Novaseq 6000 was used to sequence the samples. Library preparation was performed in house for ChIP-Seq and ATAC-Seq, using NEB indexes, while libraries for RNA-Seq were constructed by the sequencing company hired. Total RNA was sequenced. Sequencing parameters used are PE150, bi-directional sequencing. For ATAC-Seq, sequencing was performed up to 40M reads, for ChIP-Seq, sequencing was performed up to 20M reads and for RNA-Seq, sequencing was performed up to 20M to 40M reads. Fastq files are uploaded here.

  Dataset EGAD50000000349

• ENU_CCK_81_cetuximab_pilot_project

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC.

  Study EGAS00001001743

• CONSERTING: integrating copy number analysis with structural variation detection

  We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection to achieve high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. This study contains all data for "CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data", which was previously split between EGAS00001001202 and EGAS00001001050.

  Study EGAS00001001202

• Genome-wide genetic and epigenetic dataset of pancreatic acinar cell carcinomas

  Pancreatic acinar cell carcinoma (ACC) is an aggressive exocrine tumor with largely unknown biology. To identify potential targets for personalized treatment, integrative genome- and epigenome-wide analyses were performed. The results show frequently aberrant DNA methylation, abundant chromosomal amplifications and deletions, and mutational signatures suggesting defective DNA repair. In contrast to pancreatic ductal adenocarcinoma, no recurrent point mutations are known. The tumor suppressors ID3, ARID1A, APC, and CDKN2A are frequently impaired also on the protein level and thus potentially affect ACC tumorigenesis. Consequently, this work identifies potential novel therapeutic targets in ACC for drugs recently approved for precision cancer therapy.

  Study EGAS00001002533

• WGS___Exploration_of__mutational_processes_in_human_cancer_cell_lines

  Approximately 25 cell lines representative of 11 mutation signatures have been selected and will be grown from a single cell, referred to as parental clone, for a period of 3 months to allow accumulation of mutations. Following that period, we will obtain 2 subclones from each of the parental clone for analysis by exome-sequencing . In total we will therefore be sequencing 2 parental clones and 4 subclones per cell line for approximately 25 cell lines. Once the data has been analysed and the potential ongoing mutation processes determined, we will perform whole-genome sequencing of the parental clones and subclones of the candidate cell lines.

  Study EGAS00001002680

• ENU_NCI_H508_cetuximab_fixed_concentration_project

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Study EGAS00001001744

• ENU_NCI_H508_Cetuximab_SecondRound

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Study EGAS00001001745

• Enhanced cortical neural stem cell identity through SMAD/WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells

  For scRNA-Seq, single live cells were suspended in 0.4% BSA in DPBS buffer (1000 cells/µL) and subjected for GEM generation and barcoding. Library preparation was performed according to the recommended procedures of the manufacture Chromium Single Cell 3’ reagent Kit V3.1 chemistry. 10,000 cells were targeted for capturing and 9 cycles were used for cDNA amplification, while 12 cycles were performed for library formation, and sequencing was performed on an Illumina NovaSeq 6000 sequencer. For bulk RNA-Seq, RNA was purified using the miRNeasy™ RNA MiniPrep (Qiagene) and RNA-seq libraries were generated either using the Illumina TruSeq RNA Library Preparation Kits and sequenced on the Illumina HiSeq 2500 sequencer as 76 bp paired-end reads, or using the NEBnext UltraDirectional RNA Library Preparation Kits after rRNA depletion using the NEBNext rRNA depletion kit and sequenced on an Illumina HiSeq 2500 sequencer using 50 cycles of single-end sequencing.

  Dataset EGAD00001008609

• GAW16 Framingham and Simulated Data

  Important links to apply for individual-level data Genetic Analysis Workshop Instructions to Request Authorized Access Data Use Certification Requirements (DUC) Apply here for controlled access to individual level data Research Use Statement Questions regarding GAW16 should be directed to Vanessa Olmo at vanessa@business-endeavors.com. Problem 2: Description of the Framingham Heart Study In GAW16, we use data drawn from the Framingham Heart Study. The Framingham Heart Study &#8212; under the direction of National Heart, Lung, and Blood Institute; NHLBI &#8212; began in 1948 with the recruitment of adults from the town of Framingham, Massachusetts. At the time, little was known about the general causes of heart disease and stroke, but the death rates for cardiovascular disease (CVD) had been increasing steadily since the beginning of the 20th century and had become an American epidemic. The Framingham Heart Study is now conducted in collaboration with Boston University. The objective of the Framingham Heart Study was to identify the common factors or characteristics that contribute to CVD by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms of CVD or suffered a heart attack or stroke. Between 1948 and 1953 the researchers recruited 5,209 subjects (2,336 men and 2,873 women) between the ages of 29 and 62 from the town of Framingham, Massachusetts and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Subjects were recruited from lists of addresses recorded for the town. Two out of every three households were approached for participation in the study. While there was no intention to recruit families for family studies, the plan was to recruit all household members in the ages 30-60 within each house that was selected for study. Hence, many biologically related individuals were recruited, including 1644 spouse pairs. Since 1948, these participants have returned to the study every two years for a detailed medical history, physical examination, and laboratory tests. Now in 2008 at 60 years of follow up, there remain about 500 participants from this cohort. Between 1971 and 1975 the study enrolled a second-generation group &#8212; 5,124 of the original participants&#39; children and the spouses of these children &#8212; to participate in similar examinations. 2,616 subjects are offspring of the original spouse pairs and 34 are stepchildren. A total of 898 offspring are children of cohort members where only one parent was a study participant and 1,576 are spouses of the offspring. The Offspring Cohort has been followed every four years through 2001 (except between Exams 1 and 2 with an intervening 8 years) using protocols similar to those used for study of the Original Cohort. Between 2002 and 2005 the study enrolled the third generation (Gen3) of the Framingham Heart Study - 4095 offspring of the second generation. None of their spouses were recruited. An additional 103 parents of this third generation, who were not recruited between 1971 and 1975, were also recruited at this time. The latter group is not included in the GAW16 data. With the recruitment of this third generation, the study has increasingly focused on genetic factors associated with the development of cardiovascular disease and its associated risk factors. To date, there is only one examination of this generation of participants. A description of the recruitment of this third generation and comparison with the earlier generations at their initial recruitment is presented in Splansky GL et al., 2007. Further information on the Study can be found at http://www.nhlbi.nih.gov/about/framingham/index.html. Genome-wide Dense SNP Scan in Framingham Heart Study Genetic studies did not begin in the FHS until the 1990s. In the late 1980s and through the 1990s DNA was extracted from blood samples of surviving FHS participants. In 2007, the FHS entered a new phase with the conduct of genotyping for the FHS SHARe (SNP Health Association Resource) project, for which dense SNP genotyping was performed using approximately 550,000 SNPs (GeneChip&#174; Human Mapping 500K Array Set and the 50K Human Gene Focused Panel) in 10,775 samples (some duplicates) from the three generations of subjects (including over 900 pedigrees). Affymetrix conducted all genotyping for the FHS SHARe project, using the 250K Sty, 250K Nsp, and the supplemental 50K platforms. Eighty-nine percent of the DNA samples were collected during the 1990s. To maximize the power of the study, we also extracted DNA from 1133 blood samples, drawn from subjects who had no DNA, to include in the SHARe project. These samples had been sitting in our refrigerators for some time, a few as far back as the 1970s. We refer to these DNA samples as the legacy samples. These samples had a higher failure rate in the genotyping process (40%) than the other eighty-nine percent (3%). Affymetrix invoked its own criteria for a sample to succeed in genotyping. All non-legacy samples must succeed on all three platforms, while legacy samples needed to pass on at least one platform. When a sample failed, additional attempts were made. Samples that repeatedly failed 2-4 times were called failures. Other samples failed due to issues of genotyped sex identification not matching our records or low SNP concordance among SNPs common across arrays or contamination. Eighty-nine percent of the legacy samples for which genotyping results are available passed all three platforms. The genotyping data from the 10,043 samples from 9354 subjects that passed the Affymetrix criteria were additionally checked for gender consistency and consistency with family structure, resulting in genotyping data for 9,274 participants in FHS SHARe. Genotype calls were made with the BRLMM algorithm. The SHARe database is housed at the National Center for Biotechnology Information database of genotypes and phenotypes (NCBI dbGaP) and contains all ~550,000 SNPs. This genome-wide dense SNP scan and a subset of phenotypes from the Framingham Heart Study are the focus of the Genetic Analysis Workshop 16. Further information on the specific variables in the Problem 2 dataset can be found by clicking on the Documents tab at the top of the page. Problem 3: Description of the Simulated Data Set The focus of this simulation is gene discovery in genome-wide association scans (GWAS). The Framingham Heart Study data set (distributed as "Problem 2") is the basis for the FHS* simulated data. The pedigree structures are derived from the data distributed for Problem 2, and we distribute an accompanying triplet file (triplet_sim) containing person ID, father ID, mother ID, to ensure the identical subjects, pedigrees, and singletons are used in the simulated data analysis. Consistent with standard practice, founders and singletons are designated as subjects with both fshare and mshare equal to zero (missing). The simulated data includes a total of 6,479 subjects with both phenotype and genotype data, in 942 pedigrees distributed among 3 generations and 188 singletons. Data inclusion is consistent with the subjects&#39; consent for use by both for-profit and not-for-profit researchers. The genotypes for all Problem 3 replicates are fixed as measured and distributed for Problem 2 for both the genomewide scan and the additional candidate gene SNPs, for a total of approximately 550,000 SNPs (GeneChip&#174; Human Mapping 500K Array Set and the 50K Human Gene Focused Panel). Thus, to analyze the Problem 3 simulated data you also will need to download the Problem 2 genotypes. Note that there are slight discrepancies in counts between Problems 2 and 3 due to a change in consents between the two datasets. Several phenotypes that contribute to coronary heart disease (CHD) were simulated for all individuals with genotypes across three different time points, 10 years apart. All genotyped individuals have complete data; the effects of missing values can be investigated by user-specified missing value patterns. There are 200 longitudinal datasets created, based on the generating model, and each replication is found in a separate dataset. We suggest that if only one replication is to be analyzed, that it be replication 1 to enable more precise comparisons among analytical approaches. The &#39;shareid&#39; will allow you to merge the simulated phenotype data with the Problem 2 genotype data, and reconstruction of the pedigrees using the distributed &#39;triplet_sim&#39; file or for larger families&#39; relationships with the triplet distributed with the Problem 2. The simulated data problem is further described in the associated readme file, and a data dictionary is provided defining all the variables. For disclosure of the generating model for these data, please contact Jean MacCluer at jean@sfbrgenetics.org.

  Study phs000128

• NHLBI TOPMed: MESA and MESA Family AA-CAC

  The Multi-Ethnic Study of Atherosclerosis (MESA) is a study of the characteristics of subclinical cardiovascular disease (disease detected non-invasively before it has produced clinical signs and symptoms) and the risk factors that predict progression to clinically overt cardiovascular disease or progression of the subclinical disease. MESA researchers study a diverse, population-based sample of 6,814 asymptomatic men and women aged 45-84. Thirty-eight percent of the recruited participants are white, 28 percent African-American, 22 percent Hispanic, and 12 percent Asian, predominantly of Chinese descent. Comprehensive phenotypic and pedigree data for MESA study participants are available through dbGaP entry phs000209. MESA Participants were recruited from six field centers across the United States: Wake Forest University, Columbia University, Johns Hopkins University, University of Minnesota, Northwestern University and University of California - Los Angeles. Each participant received an extensive physical exam and determination of coronary calcification, ventricular mass and function, flow-mediated endothelial vasodilation, carotid intimal-medial wall thickness and presence of echogenic lucencies in the carotid artery, lower extremity vascular insufficiency, arterial wave forms, electrocardiographic (ECG) measures, standard coronary risk factors, sociodemographic factors, lifestyle factors, and psychosocial factors. Selected repetition of subclinical disease measures and risk factors at follow-up visits allows study of the progression of disease. Blood samples have been assayed for putative biochemical risk factors and stored for case-control studies. DNA has been extracted and lymphocytes cryopreserved (for possible immortalization) for study of candidate genes and possibly, genome-wide scanning, expression, and other genetic techniques. Participants are being followed for identification and characterization of cardiovascular disease events, including acute myocardial infarction and other forms of coronary heart disease (CHD), stroke, and congestive heart failure; for cardiovascular disease interventions; and for mortality. In addition to the six Field Centers, MESA involves a Coordinating Center, a Central Laboratory, and Central Reading Centers for Computed Tomography (CT), Magnetic Resonance Imaging (MRI), Ultrasound, and Electrocardiography (ECG). Protocol development, staff training, and pilot testing were performed in the first 18 months of the study. The first examination took place over two years, from July 2000 - July 2002. It was followed by five examination periods that were 17-20 months in length. Participants have been contacted every 9 to 12 months throughout the study to assess clinical morbidity and mortality. MESA Family The general goal of the MESA Family Study, an ancillary study to MESA funded by a grant from NHLBI, is to apply modern genetic analysis and genotyping methodologies to delineate the genetic determinants of early atherosclerosis. This is being accomplished by utilizing all the current organizational structures of the Multi-Ethnic Study of Atherosclerosis (MESA) and Genetic Centers at Cedars-Sinai Medical Center and University of Virginia. In the MESA Family Study, the goal is to locate and identify genes contributing to the genetic risk for cardiovascular disease (CVD), by looking at the early changes of atherosclerosis within families (mainly siblings). 2128 individuals from 594 families, yielding 3,026 sibpairs divided between African Americans and Hispanic-Americans, were recruited by utilizing the existing framework of MESA. MESA Family studied siblings of index subjects from the MESA study and from new sibpair families (with the same demographic characteristics) and is determining the extent of genetic contribution to the variation in coronary calcium (obtained via CT Scan) and carotid artery wall thickness (B-mode ultrasound) in the two largest non-majority U.S. populations. In a small proportion of subjects, parents of MESA index subjects participating in MESA Family were studied but only to have blood drawn for genotyping. The MESA Family cohort was recruited from the six MESA Field Centers. MESA Family participants underwent the same examination as MESA participants during May 2004 - May 2007. DNA was extracted and lymphocytes immortalized for study of candidate genes, genome-wide linkage scanning, and analyzed for linkage with these subclinical cardiovascular traits. While linkage analysis is the primary approach being used, an additional aspect of the MESA Family Study takes advantage of the existing MESA study population for testing a variety of candidate genes for association with the same subclinical traits. Genotyping and data analysis will occur throughout the study.

  Study phs001416

• Mechanisms of Risk for Sulfonamide Hypersensitivity

  Hypersensitivity (HS) reactions to sulfonamide antibiotics occur uncommonly, but with potentially severe clinical manifestations. A familial predisposition to sulfonamide HS is suspected, but robust predictive genetic risk factors have yet to be identified. Strongly linked genetic polymorphisms have been used clinically as screening tests for other HS reactions prior to administration of high-risk drugs. The purpose of this study was to evaluate for genetic risk of sulfonamide HS in the immunocompetent population using genome-wide association. Ninety-one patients with symptoms after trimethoprim-sulfamethoxazole (TMP-SMX) attributable to "probable" drug HS based on medical record review and the Naranjo Adverse Drug Reaction Probability Scale, and 184 age- and sex-matched patients who tolerated a therapeutic course of TMP-SMX, were included in a genome-wide association study using both common and rare variant techniques. Additionally, two subgroups of HS patients with a more refined clinical phenotype (fever and rash; or fever, rash and eosinophilia) were evaluated separately. For the full dataset, no single nucleotide polymorphisms were suggestive of or reached genome-wide significance in the common variant analysis, nor was any genetic locus significant in the rare variant analysis. A single, possible gene locus association (COL12A1) was identified in the rare variant analysis for patients with both fever and rash, but the sample size was very small in this subgroup (n=16), and this may be a false positive finding. No other significant associations were found for the subgroups. No convincing genetic risk factors for sulfonamide HS were identified in this population. These negative findings may be due to challenges in accurately confirming the phenotype in exanthematous drug eruptions, or to unidentified gene-environment interactions influencing sulfonamide HS. Reprinted under PLOS ONE&#39;s open access license, CC-BY (http://www.plos.org/open-access).

  Study phs001124

• RNA-seq as a tool for evaluating human embryo competence

  The majority of embryos that are created through IVF do not implant. One possibility for this inefficiency is an incomplete understanding of the molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer utilizes an ad-hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing of embryos could yield highly dimensional data, which may provide additional insight and illuminate the discrepancies among current selection criteria. Indeed, recent advances enabling the production of RNA-sequencing (RNA-seq) libraries from single cells have facilitated the application of this technique to the study of some transcriptional events in early human development. However, these studies have not assessed the quality of their constituent embryos relative to commonly used embryological criteria. Here, we perform proof-of-principle advancement to clinical selection procedures by generating high quality RNA-seq libraries from a trophectoderm biopsy as well as the remaining whole embryo. We combine state-of-the-art embryological methods with low-input RNA-seq to develop the first transcriptome-wide approach for use in future predictive embryology studies. Specifically, we demonstrate the capacity of RNA-seq as a promising tool in preimplantation screening by showing that biopsies of an embryo can capture valuable information content available in the whole embryo from which they are derived. Furthermore, we show that this technique can be used to generate a RNA-based digital karyotype, and to develop a foundational dataset for identifying candidate competence-associated genes. Together, these data establish the foundation for a future RNA-based diagnostic in IVF.

  Study EGAS00001003667

• A benchmarking resource for NGS testing of cancer predisposition genes

  A benchmarking resource of 639 individuals, to assess the analytical sensitivity of cancer predisposition gene (CPG) testing.The dataset includes sequencing data generated using the TruSight Cancer Panel (TSCP) a targeted NGS assay for analysis of CPGs and orthogonally generated data supporting at least one pathogenic variant in a CPG for a total of 645 pathogenic CPG variants.The set of pathogenic CPG variants includes strong representation of some of the most challenging types of pathogenic variants, with 339 indels, including 16 complex indels and 24 insertions or deletions with length greater than 5bp, and 74 exon CNVs, including 23 single exon CNVs. There are 502 pathogenic variants in BRCA1 or BRCA2, making this an important first-line validation dataset for laboratories performing NGS testing of BRCA1 and BRCA2.

  Study EGAS00001002993

• PASCAL-MID Data Access Committee

  DAC for the center of Personalized Approach to Genome Editing of Stem Cells for Autotransplantation of Monogenic Immunodeficiencies (PASCAL-MID) at Aarhus University and Aarhus University Hospital

  Dac EGAC50000000680

• DATA FILES FOR SJPHALL

  DATA FILES FOR SJPHALL

  Dataset EGAD00001000163

• V4_Colorectal_panel_test

  Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel.

  Study EGAS00001001807

• KiCS cancer panel academic only data

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009733

• Dataset for B-ALL scRNA-seq

  10x Genomics 5' library scRNA-seq data for 85 B-ALL patients with different subtypes

  Dataset EGAD00001011327

• DATA FILES FOR GRUBER SJAMLM7 EXOME

  DATA FILES FOR GRUBER SJAMLM7 EXOME

  Dataset EGAD00001003134

• PACA-CA RNASeq fastq files

  Fastq files for PACA-CA RNA Seq analysis, for DCC release 27

  Dataset EGAD00001003972

• DATA FILES FOR BALL-PAX5

  DATA FILES FOR BALL-PAX5

  Dataset EGAD00001000654

• DATA FILES FOR SJMEL-WGS

  DATA FILES FOR SJMEL-WGS

  Dataset EGAD00001001032

• DATA FILES FOR SJTALL

  DATA FILES FOR SJTALL

  Dataset EGAD00001001052

• Analysis of genes related to the oncogenesis, progression or effectiveness of drug therapies of urological tumors .

  To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.

  Study JGAS000737

• Analysis of genes related to the oncogenesis, progression or effectiveness of drug therapies of urological tumors .

  To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.

  Study JGAS000303

• Analysis of genes related to the oncogenesis, progression or effectiveness of drug therapies of urological tumors .

  To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.

  Study JGAS000564

• SECRETO Oral metagenome study

  The main goal of the project is to study the associations between the oral metagenome and young-onset cryptogenic ischemic stroke (CIS). The dataset includes information for n=329 participants who underwent saliva sampling. Participants for the SECRETO Oral study were enrolled between December 2013 and November 2019. Shotgun metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform.

  Study EGAS00001007505

• Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue

  The dataset "Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue" includes CRAM and CRAI files derived from WGS of 555x plasma cfDNA, 209x white blood cells (normal DNA) and 209x FFPE tumor tissue (tumor DNA) samples for 209 stage III colorectal cancer patients. WGS (150bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 80x for tumor DNA, 40x for normal DNA and 30x for cfDNA. Reads were aligned to GRCh37 (plasma cfDNA) or GRCh38 (tumor/normal DNA).

  Dataset EGAD50000001180

• Population_sequencing_phasing

  Whole-genome sequencing of human individuals from Polynesian and Native American populations, as well as 10x Genomics Chromium data from Polynesian, Native American and Aboriginal Australian populations, allowing for experimental phasing of haplotypes. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001852

• Ultra-fast multiplex small DNA sequencing on the MinION nanopore sequencing platform

  Here, we developed an ultra-rapid multiplexed library preparation and sequencing method for the MinION and applied this method to accurately test euploid and aneuploid genomic DNA samples in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  Study EGAS00001002650

• Functional_characterisation_of_CpG_islands_in_human_and_mouse_tissues

  Tissue-specific methylation patterns suggest a role for CpG island (CGI) methylation in differentiation and cell-type-specific gene regulation. We have applied CXXC affinity purification (CAP), MBD affinity purification (MAP) and chromatin immunoprecipitation (ChIP) in combination with solexa sequencing to investigate the extent and functional significance of CGI methylation in sperm, blood, cerebellum and ES cells for both human and mouse.

  Study EGAS00001000075

• Genomic landscape of signals of positive natural selection in North Eurasia

  We searched for the genomic signatures of positive selection in the genome-wide data of 432 people from eight different northern Russian populations (Russians from the Archangelsky and Vologdsky regions, Izhemski Komi, Priluzski Komi, Veps, Khanty, Mansi and Nenets) who were genotyped using microarrays for 700,000 SNPs (InfiniumOmniExpress-24v1-2_A1) through testing the extended haplotype homozigosity (EHH).

  Study EGAS00001003955

• Whole genome sequencing of adult glioblastoma nuclei

  Nuclei were extracted from three primary adult glioblastoma samples and processed for scATAC-seq, and residual nuclei left over from these same samples were used to extract DNA and processed and sequenced for WGS. This WGS data was then used to cross-validate assessment of large-scale copy number alterations with scATAC-seq using the Copy-scAT tool.

  Study EGAS00001005256

• Sequencing of cancer autopsies and ctDNA

  Tumor heterogeneity is a major obstacle for precision oncology strategies. To characterize inter-lesion heterogeneity in pre-treated cancers, we performed genetic and transcriptomic profiling of synchronous lesions from ten rapid autopsies comprising six cases of breast cancer, three of cholangiocarcinoma and one lung cancer case. For nine patients, we studied mutation representation in circulating cell-free DNA (cfDNA).

  Study EGAS00001005109

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  COG-N-519 primary neuroblastoma cells were innoculated by subcutaneous injection into NSG mice. When tumours reached a size of 100-200mm3 miRNAs conjugated to nanoparticles were injected intratumourally every 2 days for 1 week. 24 hr after the last injection, snap frozen tumour tissue was harvested for RNA extraction and RNA-seq analysis.

  Study EGAS00001005581

• DNA methylation of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  Genomic DNA (~ 1 μg) from LFS patients was treated using sodium bisulfite (Qiagen) converting unmethylated cytosine to uracil but leaving methylated cytosine intact. These samples were then hybridized to the HumanMethylation450 BeadChip or HumanMethylationEPIC BeadChip from Illumina at the Centre for Applied Genomics (TCAG) at the Hospital for Sick Children using the manufacturer’s recommended protocol.

  Study EGAS00001007075

• March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001959

• March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001958

• March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001957

• March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001987

• Capturing the Genetic Diversity of the Himba Population

  The Himba people are a semi-nomadic, Bantu-speaking pastoralist group from the northwestern Kunene region of Namibia. Because of their limited population size, restricted geographic distribution, and endogamy, founder populations represent an ideal system for genetic analyses due to reduction of the confounding environmental and cultural variables. The original study used genotype data and demographic interview data to understand family dynamics and ancestry in a population of Himba pastoralists. HLA allele calls and genome-wide methylation array data were later generated for a subset of the initial dataset for 2 additional studies. These 3 molecular datasets, available through dbGaP, are relevant to broader studies of ancestry, allele frequencies and the relationship of Himba to other ethnic groups in sub-Saharan Africa. The Himba population provides a unique opportunity to study questions regarding extra-pair paternity and mate selection because Himba culture allows both men and women, married and not, to take multiple partners. Previous estimates of extra-pair paternity rates in human populations have been very low, but these estimates lack global and cultural diversity in population representation. Thus, investigating the rate of extra-pair paternity in the Himba greatly aids in understanding the global variation in non-paternity rates among human populations. Saliva samples were collected from parents and children, and were genotyped on Illumina SNP array platforms (MEGAex and H3Africa). In total, 678 individuals' genotype array data are deposited. Paternity results were de-identified and protected by a double blind protocol (no researcher has full knowledge of individual paternity results). Due to the sensitive nature of this study, paternity assertions are not available for access. For a subset of 360 individuals, HLA class 1 (A, B, C) and class 2 (DPA1, DPB1, DQA1, DQB1, DRB1) genes were targeted for DNA sequencing using a probe-based capture method. HLA alleles at the four field resolution were determined from the sequence capture using the consensus calls obtained from two algorithms: NGSengine&#174; 2.10.0 (GenDX, Utrecht, the Netherlands) and HLA Explore&#8482; (Omixon Biocomputing Ltd. Budapest, Hungary). These data were used to investigate evidence for mate selection based on HLA dissimilarity in the Himba. Himba cultural norms permit concurrent arranged marriages and chosen sexual partnerships allowing us to directly test for evidence of disassortative mate selection based on HLA genotype. Due to the sensitive nature of this study, partnership data are not available for access.For a subset of 51 Himba individuals methylation array data was generated from the saliva-derived DNA. These data were generated in order to investigate the accuracy of epigenetic age predictors in this population and to construct population-specific epigenetic age predictors in a subsequent publication. Chronological ages are available for these 51 individuals.

  Study phs001995

• Natural Killer Cell Therapies for Hematologic Malignancies

  The "Natural Killer Cell Therapies for Hematologic Malignancies" study is an umbrella repository for data pertaining to multiple related clinical trials that aim to assess NK cell therapies as part of treatment strategies for a range of hematologic malignancies. Here, data from two trials, NCT03068819 and NCT02782546, are presented.Cytokine Induced Memory-like NK Cell Adoptive Therapy for Relapsed AML after Allogeneic Hematopoietic Cell Transplant in Children and Adults (NCT03068819)Pediatric and young adult (YA) patients with acute myeloid leukemia (AML) who relapse after allogeneic hematopoietic cell transplantation (HCT) have extremely poor prognosis. Standard salvage chemotherapy and donor lymphocyte infusions (DLI) have little curative potential. Previous studies showed that natural killer (NK) cells can be stimulated ex vivo with interleukin-12 (IL-12), IL-15, and IL-18 to generate memory-like (ML) NK cells with enhanced anti-leukemia responses. We treated nine pediatric/YA patients with post-HCT relapsed AML with donor ML NK cells on a phase I trial. Patients received fludarabine, cytarabine, and filgrastim followed two weeks later by infusion of DLI and ML NK cells from the original HCT donor. ML NK cells were successfully generated from haploidentical, matched-related and matched-unrelated donors. Following infusion, donor-derived ML NK cells expanded and maintained ML multidimensional mass cytometry phenotype for over 3 months. Furthermore, ML NK cells exhibited persistent functional responses as evidenced by leukemia-triggered IFN-gamma production. Following DLI and ML NK cell adoptive transfer, 4 of 8 evaluable patients achieved complete remission at day 28. Two patients maintained a durable remission for over 3 months with one patient in remission for greater than two years. No significant toxicity was experienced. This study demonstrates that in a compatible immune environment post-HCT, donor ML NK cells robustly expand and persist with potent anti-leukemic activity in the absence of exogenous cytokines. ML NK cells in combination with DLI present a novel immunotherapy platform for AML that has relapsed after allogeneic HCT. This trial was registered at https://www.clinicaltrials.gov/study/NCT03068819.A Phase II Study of Cytokine Induced Memory-like NK Cell Adoptive Therapy after Haploidentical Donor Hematopoietic Cell Transplantation (NCT02782546)Natural killer (NK) cells are innate lymphoid cells that eliminate cancer cells, produce cytokines, and are being investigated as a nascent cellular immunotherapy. Impaired NK cell function, expansion, and persistence remain key challenges for optimal clinical translation. One promising strategy to overcome these challenges is cytokine-induced memory-like (ML) differentiation, whereby NK cells acquire enhanced anti-tumor function following stimulation with IL-12, IL-15, and IL-18. Here, reduced-intensity conditioning (RIC) for HLA-haploidentical hematopoietic cell transplantation (HCT) was augmented with same-donor ML NK cells on Day 7 and 3 weeks of N-803 (IL-15 superagonist) to treat patients with relapsed/refractory acute myeloid leukemia (AML) in the clinical trial (NCT02782546). In 15 patients, donor ML NK cells were well-tolerated and 87% of patients achieved a composite complete response at Day 28, which corresponded with clearing high-risk mutations, including TP53 variants. NK cells were the major blood lymphocytes for two months post-HCT with prolific expansion (1104-fold) over 1-2 weeks. Multidimensional mass cytometry and CITE-seq identified donor ML NK cells as distinct from conventional NK cells and persisting for over two months. ML NK cells expressed CD16, CD57, and high granzyme B and perforin, along with a unique transcription factor profile. ML NK cells differentiated in patients had enhanced ex vivo function compared to conventional NK cells from both patient and healthy donors. Overall, same-donor ML NK cell therapy with 3 weeks of N-803 support safely augmented RIC haplo-HCT for AML, with ML NK cells demonstrating enhanced in vivo persistence and functionality, overcoming barriers in the field.

  Study phs002681

• Molecular Analysis of Short- Versus Long-Term Survivors of High-Grade Serous Ovarian Carcinoma

  The underlying determinants for long-term survival (LTS, &#8805;10 years) versus short-term survival (STS, &lt;3 years) of patients diagnosed with high-grade serous ovarian carcinoma (HGSC) are largely unknown. The present study sought to identify molecular predictors of LTS for women with HGSC. A cohort of 24 frozen HGSC samples (12 LTS and 12 STS) were collected and analyzed at DNA and RNA levels. Copy number variation and mutation did not indicate large differences between LTS and STS. From RNA-Seq analysis, 11 genes were found to be differentially expressed between the STS and LTS groups (fold change &gt;2; false discovery rate &lt;0.01). In the validation cohort, transmembrane protein 62 (TMEM62) was found to be related to LTS. Our in vitro and in vivo studies demonstrate that restoring TMEM62 may be a novel approach for treatment of HGSC. These findings may have implications for biomarker and intervention strategies to help improve patient outcomes.

  Study phs003020

• Genetic Effects on Gene Expression and Splicing during Human Neurogenesis

  Interpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing quantitative trait locus (e/sQTL) analyses is generally performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements active during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs, and allele-specific expression in cultured cells representing two major developmental stages, primary human neural progenitors (n=85) and their sorted neuronal progeny (n=74), identifying numerous loci not detected in either bulk developing cortical wall or adult cortex. Using colocalization and genetic imputation via transcriptome-wide association, we uncover cell-type specific regulatory mechanisms underlying risk for brain-relevant traits that are active during neocortical differentiation. Specifically, we identified a progenitor-specific eQTL for CENPW co-localized with common variant associations for cortical surface area and educational attainment.

  Study phs002493

• NIDCD Otitis Media Genetic Susceptibility and Middle Ear Microbial Shifts

  The study funded by R01 DC015004 aims to: (1) Identify rare OM susceptibility variants within families and in probands; and (2) Identify differences in the middle ear microbiome due to OM susceptibility variants. This study will also elucidate mechanisms responsible for the formation and growth of cholesteatoma, and bony erosion and complications due to cholesteatoma e.g. intracranial, hearing/vestibular loss, facial nerve palsy. A better understanding of cholesteatoma pathogenesis will potentially reveal novel drug targets, which can lead to new non-surgical therapies for cholesteatomatous OM. Our specific aims for this administrative supplement are: Aim 1 -- Perform RNA-sequencing using cholesteatoma samples collected from Filipino and Colorado patients who will be screened for FUT2, SPINK5 and A2ML1 variants; and Aim 2 -- Using network analysis, identify bone-expressed proteins potentially interacting with FUT2, SPINK5 or A2ML1, then test protein expression in archival human temporal bone in direct contact with cholesteatoma.

  Study phs001941

• Characterizing Individual Cells Obtained from Bone Marrow Biopsies of MPN Patients

  We profiled the transcriptomes of individual cells obtained from bone marrow aspirates of 7 treatment-na&#239;ve newly diagnosed JAK2-mutant myeloproliferative neoplasm (MPN) patients (3 polycythemia vera and 4 essential thrombocythemia patients), and 2 healthy controls. The submitted data corresponds to sequencing reads mapped to the human reference genome GhRC38 build using CellRanger for a total of 9 samples (one per patient). In addition, to reconstruct the lineage histories of single cells in MPN patients, we performed whole-genome sequencing of single-cell-derived colonies of hematopoietic stem and progenitor cells from 2 essential thrombocythemia (ET) patients: 22 JAK2-mutant colonies and 20 WT colonies for patient ET 1; and 13 JAK2-mutant colonies and 21 WT colonies for patient ET 2. The submitted data consists of sequencing reads aligned to the human reference genome GhRC38 build using bwa-mem. Each file corresponds to the whole-genome sequencing data for one colony.

  Study phs002308