14670 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Mutational Analysis of Colorectal PDX models (2016-01-06)

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2016-01-06.

  Dataset EGAD00001001872

• V4 panel bait design test (2018-03-07)

  Targeted gene screen of FFPEs, cell lines and primary CRC tumours for testing the new V4 Colorectal gene panel. . This dataset contains all the data available for this study on 2018-03-07.

  Dataset EGAD00001004001

• Persistent Mutation Burden Drives Sustained Anti-Tumor Immune Responses.

  Data includes whole exome sequenced bam files for matched tumor-normal pairs from the study.

  Dataset EGAD00001009697

• Dataset to study clonal evolution in iAMP21 patient SJBALL021901 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJBALL021901 with 71 high quality cells sequenced (67 blast and 4 normal)

  Dataset EGAD00001009755

• ESGI - Whole Genome Sequencing of samples from the Cilentogen isolates (2019-08-19)

  Deep whole genome sequencing of sampels from the Cilento isolates. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005266

• IVF Retrospective Study

  This dataset contains BAM files for 9 samples from individuals involved in a retrospective IVF trial. The BAM files were derived from whole genome sequencing. The 9 individuals consist of three trios containing mother, father and child samples.

  Dataset EGAD00001008147

• Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2026-01-19)

  Spatial transcriptome analysis of thymic cells from children with syndromic diseases such as Trisomy 21 and inflammatory/autoimmune diseases such as myasthenia gravis. . This dataset contains all the data available for this study on 2026-01-19.

  Dataset EGAD00001015798

• RaCHseq data

  Captured single-cell long-read data of a cohort of CLL patients receiving VEN treatment for resistance study

  Dataset EGAD00001008365

• HGSOC organoid sequencing study

  sWGS dataset of 18 matched PDO and ascites samples, and scDNA sequencing of three of these PDOs.

  Dataset EGAD00001010297

• WGS of HSPCs and MSCs

  Whole genome sequencing data of organoid cultures derived from human bone marrow-derived and cord blood-derived hematopoietic stem and multipotent progenitor cells to study the mutation accumulation.

  Dataset EGAD00001004451

• NiCOL Study RNA-seq dataset

  15 samples sequenced in RNA-seq. This dataset contains their raw FASTQ data and the raw count table and the TPM count table.

  Dataset EGAD00001010912

• Genomic and transcriptomic determinants of host susceptibility, protection, and viral mutation in experimental SARS CoV-2 infection: RNA (2025-08-11)

  Single-cell profiling of healthy adult volunteers that were inoculated with SARS-CoV-2. . This dataset contains all the data available for this study on 2025-08-11.

  Dataset EGAD00001015679

• Cram files for study entitled Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia

  This dataset contains three cram files for paired end sequencing of a trio, sequenced with Illumina Hiseq 2500

  Dataset EGAD00001006578

• Mutational Analysis of Colorectal PDX models (2017-05-11)

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003334

• Meso RNA-seq data (SSA cell line study)

  RNA-seq data for mesothelioma cell lines after spliceostatin (SSA) or control (DMSO) treatment.

  Dataset EGAD00001001914

• Exome sequencing of Non-syndromic Congenital Heart Defects (2019-04-24)

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD . This dataset contains all the data available for this study on 2019-04-24.

  Dataset EGAD00001004972

• Exome sequencing of Non-syndromic Congenital Heart Defects (2019-04-24)

  Exome sequencing of ~1,800 patients with non-syndromic Congenical Heart Defects (CHD) to identify genes enriched for damaging rare variants that increase risk of CHD . This dataset contains all the data available for this study on 2019-04-24.

  Dataset EGAD00001004975

• Whole genome sequence of intratumor heterogeneity study

  This dataset contains whole genome sequence data from 12 samples from 1 patient, including 8 tumor sectors and 4 normal samples. All the experiments were performed on Illumina HiSeq platform with raw reads stored in fastq format.

  Dataset EGAD00001005452

• Cam_121 RNA-Seq data

  This dataset contains RNA-Seq data from 204 primary melanomas and 177 regional lymph nodes. More details can be found in the manuscript: "Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study"

  Dataset EGAD00001006401

• The Dutch Microbiome Project Batch 1

  The Dutch Microbiome Project (DMP) data includes shotgun metagenomic sequencing of faecal samples 8,208 Dutch individuals. Paired-end sequencing was performed using Illumina HiSeq 2000 platform. Data is archived in two batches to facilitate easier data access and upload to EGA. Batch 1 of DMP includes 4396 samples.

  Dataset EGAD00001007027

• NCI Expanded Genome-Wide Association Study of Renal Cell Carcinoma

  The National Cancer Institute (NCI) expanded genome-wide association study (GWAS) of renal cell carcinoma (RCC) was a 2nd GWAS of this cancer performed by NCI to further investigate common genetic variants associated with RCC risk. The GWAS includes 2,781 cases and 2,940 controls of European background from 13 studies conducted in the US and Finland (10 cohorts, 2 case series, 1 hospital biorepository), scanned using the Illumina OmniExpress and Omni2.5 SNP arrays. SNP-level results from this GWAS were combined by meta-analysis with results from the earlier NCI RCC GWAS (phs000351.v1.p1; 1,311 cases and 3,424 controls) and others conducted by the International Agency for Research on Cancer (scan 1: 2,438 cases and 5,071 controls; scan 2: 2,781 cases and 2,940 controls), The University of Texas MD Anderson Cancer Center (893 cases and 556 controls) and the Institute for Cancer Research, UK (944 cases and 4,024 controls). Only data from the second NCI scan are included in this dbGaP submission. Data from 239 cases and 229 controls from this scan will be deposited in dbGaP separately under the Women's Health Initiative (phs000200).

  Study phs001736

• Cohort-Based Genome-Wide Association Study of Glioma (GliomaScan)

  We conducted a new independent GWAS of adult glioma using 1,856 cases and 4,955 controls from 14 cohort studies belonging to the Cohort Consortium, 3 case-control studies, and 1 population-based case only study. Cases were newly diagnosed glioma [ICDO-3 codes 9380-9480 or equivalent], and controls were cancer-free at the time of glioma diagnosis. We found evidence of strong replication for three of the seven previously reported associations at 20q13.33 (RTEL), 5p15.33 (TERT), and 9p21.3 (CDKN2BAS), and consistent association signals for the remaining four at 7p11.2 (EGFR both loci), 8q24.21 (CCDC26) and 11q23.3 (PHLDB1). The direction and magnitude of the signal were consistent for samples from cohort and case-control studies, but the strength of the association was more pronounced for loci rs6010620 (20q,13.33; RTEL) and rs2736100 (5p15.33, TERT) in cohort studies despite the smaller number of cases in this group, likely due to higher grade tumors being captured in the cohort studies. Our findings suggest that larger studies focusing on novel approaches as well as specific tumor subtypes or subgroups will be required to identify additional common susceptibility loci for glioma risk.

  Study phs000652

• Whole Genome Association Study of Systemic Lupus Erythematosus

  The goal of this collaborative study was to identify new genetic risk factors for Systemic Lupus Erythematosus (SLE). To do this we conducted a genome-wide scan by combining the resources and expertise from a number of SLE researchers to establish a large sample set comprising 1311 SLE cases and 3340 controls. The SLE case samples were genotyped from the following collections: 338 subjects from the Autoimmune Biomarkers Collaborative Network (ABCoN), an NIH/NIAMS funded repository, 141 subjects from the Multiple Autoimmune Disease Genetics Consortium (MADGC), 613 subjects from the University of California San Francisco (UCSF) Lupus Genetics, and 335 subjects from the University of Pittsburgh Medical Center (UPMC), plus 8 samples collected at The Feinstein Institute for Medical Research. A total of 3583 control samples were examined in the association analyses. As part of this project, 1861 control samples were selected and then genotyped from the New York Cancer Project (NYCP), based on self-described ethnicity, gender and age. In addition, genotype data from 1722 control samples (all self-described North Americans of European descent) were obtained from the publicly available iControlDB database (http://www.illumina.com/pages.ilmn?ID=231).

  Study phs000122

• Study on the proliferation history of colorectal adenomas

  Mismatch repair (MMR) deficient colorectal adenomas are composed of transformed cells that descend from a common founder and progressively accumulate genomic alterations but their proliferation history is still largely unknown. Here we rebuilt the proliferation history of four MMR deficient colorectal adenomas from male individuals by deep sequencing the X chromosome and mapping the somatic mutations that were progressively acquired during tumor growth. We developed a novel method to call high and low frequency mutations, to cluster them according to their frequencies and rebuild the proliferation trees directly from these mutation clusters using a recursive algorithm. The trees of all four lesions were formed of a dominant subclone that coexisted with other genetically heterogeneous subpopulations of cells. Despite this similar hierarchical organization, however, the growth dynamics varied among and within tumors, likely depending on a combination of tumor-specific genetic and environmental factors. Our study provides insights into the biological properties of individual MMR deficient colorectal adenomas that may influence their growth and also the response to therapy. Extended to other solid tumors, our approach could inform on the mechanisms of cancer progression, thus providing insight into the best choice of cancer treatment methods.

  Study EGAS00001000883

• Understanding the genetic risk underlying racial disparities in uterine fibroids

  Fibroids affect 77% of women by onset of menopause in the U.S. and account for $2.1 billion in healthcare costs each year. Fibroids negatively impact reproductive health causing heavy and painful menses, pelvic pain and pressure, pregnancy complications, and interventions including myomectomy and hysterectomy. Until recently, tumor tissue and cell culture studies investigating fibroid growth have been the primary sources for understanding fibroid pathophysiology. Genetic analysis can provide a powerful and cost effective tool to identify etiological and causal factors, especially since a genetic predisposition to fibroids has already been documented from twin studies. As much as 69% of risk is explained by genetic factors. Racial disparities also support a role for genetics with fibroid risk. African American women have earlier age of onset, more numerous and larger fibroids with a greater lifetime incidence compared to Caucasians. We propose to identify genetic markers for risk of fibroids through a genome-wide association study (GWAS) of African American and Caucasian participants, leveraging ancestral differences to narrow down genomic regions for targeted follow- up analyses. To accomplish this we will take advantage of a unique Vanderbilt resource, the BioVU DNA databank. BioVU currently has over 122,470 adults linked to electronic medical records. From BioVU we have already identified 2,902 African American and Caucasian subjects who meet our stringent inclusion criteria to conduct a GWAS of fibroids, including pelvic imaging. Available imaging is critical, because many women with fibroids are asymptomatic and without imaging, studies may misclassify as many as 51% of women. We have also defined definitive controls who reached menopause without fibroids. We have a strong group of nationally known fibroid researchers who will provide over 10,000 samples for replication. Our first Specific Aim is to conduct a GWAS for association between common single nucleotide polymorphisms (SNPs) and fibroid risk. Using a case-control design we will perform a GWAS in 2,902 (1,451 fibroid cases and 1,451 controls) women from BioVU stratified by African American and Caucasian race. Secondary admixture mapping (AM) analyses will also be performed to identify chromosomal regions of interest to prioritize for replication. Our second Aim is to resequence chromosome regions identified from GWAS and AM to discover rare variants. Finally, in Aim 3 we will replicate SNPs selected from Aim 1 and 2 in independent samples of at least 3,230 fibroid cases and 7,097 controls. We propose an efficient and cost-effective approach to identify genetic risk factors for fibroids, by taking advantage of imaging information and DNA available through BioVU. This study represents the largest GWAS of uterine fibroids and the first among African Americans leveraging emerging technologies and new statistical approaches to conduct this study. Our proposed study will fundamentally change knowledge about fibroids and lay the ground work for breakthroughs in understanding mechanisms of fibroid formation and in identifying novel therapeutic approaches.

  Study phs001409