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• BROCA cancer panel sequencing for 15 samples

  BROCA panel sequencing using the BROCA-HR v8 and BROCA-GO v1 versions of the gene panel

  Dataset EGAD50000000035

• bfast CohortD clinical data

  Clinical data for BFAST Cohort D, including time-to-event, tumor response, and baseline prognostics data.

  Dataset EGAD50000000149

• Amsterdam UMC Head and Neck Cancer Biology and Immunology

  This data access committee oversees data and assesses requests for the Head and Neck Cancer Biology and Immunology lab of Amsterdam UMC, location VUmc.

  Dac EGAC50000000350

• RCC trial WES dataset

  This dataset includes WES data for 116 runs, corresponding to 58 pairs of normal(PBMC)/tumor samples from 58 patients (116 BAM files).

  Dataset EGAD50000000953

• H3Africa KDRN Phenotype

  The phenotypic data for 6431 samples of the KDRN Study from Ghana and Nigeria.

  Dataset EGAD00001009333

• DAC "Genotyping based on SNPs covered by targeted NGS"

  DAC for the dataset from the article "Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples"

  Dac EGAC50000000358

• Dataset for desmoplastic small round cell tumor array data

  This dataset contains 24 methylation array samples of patients with desmoplastic small round cell tumor measured on Illumina 850k.

  Dataset EGAD00010002689

• Reference epigenome KNIH009 mRNA-seq data generated from KEP study

  A KNIH009 mRNA-seq paired end data for preadipocytes

  Dataset EGAD00001002175

• Reference epigenome SMC07_smRNA-Seq data generated from KEP study

  A SMC07_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003864

• Reference epigenome ADMSC02_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC02_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003855

• Reference epigenome SMC03_smRNA-Seq data generated from KEP study

  A SMC03_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003860

• Reference epigenome SMC09_smRNA-Seq data generated from KEP study

  A SMC09_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003866

• Reference epigenome SMC08_smRNA-Seq data generated from KEP study

  A SMC08_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003865

• bulkRNA

  Bulk RNA-seq for cALL patient-derived PDX samples

  Dataset EGAD00001006133

• Reference epigenome KNIH007 mRNA-seq data generated from KEP study

  A KNIH007 mRNA-seq paired end data for adipocytes

  Dataset EGAD00001002173

• Reference epigenome KNIH009 miRNA-seq data generated from KEP study

  A KNIH009 miRNA-seq single end data for preadipocytes

  Dataset EGAD00001002768

• Reference epigenome SMC01_smRNA-Seq data generated from KEP study

  A SMC01_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003858

• Whole Exome Sequencing

  Whole Exome Sequencing for a cohort of 20 B-ALL samples : 5 Down syndrome (DS), 7 Hyperdiploid (HeH), 3 iAMP21 and 5 others.

  Dataset EGAD00001005425

• Reference epigenome KNIH011 WGBS data generated from KEP study

  A KNIH011 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for podocytes

  Dataset EGAD00001002759

• Reference epigenome DB31_N_Alpha_WGBS data generated from KEP study

  A DB31_N_Alpha_WGBS paired end data for alpha cells(PSA-NCAM(-), pancreas)

  Dataset EGAD00001003472

• Fecal 16S UC metadata

  Metadata for fecal 16S-V4 rRNA gene sequence data from NCT02749630 ulcerative colitis patients.

  Dataset EGAD00001008822

• Reference epigenome ADMSC01_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC01_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003854

• Reference epigenome SMC06_smRNA-Seq data generated from KEP study

  A SMC06_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003863

• Reference epigenome SMC04_smRNA-Seq data generated from KEP study

  A SMC04_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003861

• Reference epigenome SMC05_smRNA-Seq data generated from KEP study

  A SMC05_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003862

• Sporadic multiple meningioma Genomics

  Wes for 15 multiple meningioma samples from 6 individual

  Dataset EGAD00001008710

• Reference epigenome KNIH010 WGBS data generated from KEP study

  A KNIH010 Whole-Genome Bisulfite Sequencing(WGBS) paired end data for podocytes

  Dataset EGAD00001002758

• Reference epigenome ADMSC04_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC04_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003857

• PDX WES

  2 patient-derived xenograph tumours, and associated normal blood samples. Duplicated samples for each gave 8 pairs of fastq files

  Dataset EGAD00001009657

• WES data for HCC patients from Y90+Nivolumab trial

  This dataset includes WES fastq files of pre-treatment and on-treatment samples from 29 patients

  Dataset EGAD00001010133

• DLP+ Single Cell Genomic Library A98193

  DLP+ Single Cell Genomic Library A98193 for Follicular lymphoma patient sample TFRI_Pair_6_FL

  Dataset EGAD00001010241

• DLP+ Single Cell Genomic Library A98205

  DLP+ Single Cell Genomic Library A98205 for Follicular lymphoma patient sample TFRIPAIR9_FL

  Dataset EGAD00001010243

• Reference epigenome SMC02_smRNA-Seq data generated from KEP study

  A SMC02_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003859

• DLP+ Single Cell Genomic Library A98297

  DLP+ Single Cell Genomic Library A98297 for Follicular lymphoma patient sample TFRIPAIR3_FL

  Dataset EGAD00001010248

• Reference epigenome KNIH008 mRNA-seq data generated from KEP study

  A KNIH008 mRNA-seq paired end data for adipocytes

  Dataset EGAD00001002174

• Reference epigenome ADMSC03_ChIP-Seq(H3K27me3) data generated from KEP study

  A ADMSC03_ChIP-Seq(H3K27me3) paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003856

• Reference epigenome ADMSC01_WGBS data generated from KEP study

  A ADMSC01_WGBS paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003878

• Reference epigenome ADMSC02_WGBS data generated from KEP study

  A ADMSC02_WGBS paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003879

• Reference epigenome ADMSC03_WGBS data generated from KEP study

  A ADMSC03_WGBS paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003880

• Reference epigenome ADMSC04_WGBS data generated from KEP study

  A ADMSC04_WGBS paired end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003881

• CRISPR screen M14, NCI-H3122

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung

  Dataset EGAD00001001389

• Reference epigenome KNIH007 miRNA-seq data generated from KEP study

  A KNIH007 miRNA-seq single end data for adipocytes

  Dataset EGAD00001002766

• Reference epigenome KNIH008 miRNA-seq data generated from KEP study

  A KNIH008 miRNA-seq single end data for adipocytes

  Dataset EGAD00001002767

• Dataset for the study of ulcerative colitis

  Whole exome sequencing and RNAseq data.

  Dataset EGAD00001005237

• Res1_H23_exp2_MC_13.07.22

  8 samples are cell pellets for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Dataset EGAD00001012234

• Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

  We tested the efficiency and reproducibility of 10 RNA isolation methods on 5 different biofluids. Pooled human plasma and serum, bile and urine were used along with cell culture supernatants from human embryonic stem cells (hESC), primary neonatal rat ventricular myocytes (NRVM) and human cholangiocarcinoma cells (KMBC). 4 RNA isolation methods designed to isolate total RNA from bio fluids without enrichment of exRNA carriers were used. 6 methods that preferentially enriched for exRNA carriers were also compared. Small RNA libraries were constructed using the NEBNext small-RNA library prep. The efficiency and reproducibility of the different RNA isolation methods was compared using small-RNA seq.

  Study phs002143

• Sequencing data of multiple sarcoma samples for personalized medicine and endotype identification

  Sequencing data derived from multiple patient samples was used to guide multiple patient-specific experiments and identify potential therapeutic options. These diseases are rare and high-risk (undifferentiated pleomorphic sarcoma, rhabdomyosarcoma) and thus have few available validated clinical options. This leaves the population of patients with few options if, and when, standard therapy fails to cure or control disease. An aspect of the personalize therapy design included the identification of broader disease endotypes (a combination of genetic and clinical data describing patient status) to identify subgroups of the individual disease that could better define treatments and could segment patient populations for deeper preclinical research.

  Study EGAS00001003981

• Genetic analysis of Hirschsprung disease

  Hirschsprung disease (HSCR) is a birth defect resulting from the absence of nerve (ganglion) cells in the gastrointestinal tract. Hirschsprung disease has a population incidence of 1/5,000 live births and most often occurs as an isolated condition. However, approximately 30% of HSCR cases are associated with other birth defects such as Down syndrome, deafness, hypopigmentation, and Congenital Central Hypoventilation syndrome (CCHS). Hirschsprung disease is a genetic condition with autosomal dominant, autosomal recessive, and multigenic patterns of inheritance described. The goal of the research study is to identify genes harboring causative HSCR mutations and to better understand the complex inheritance of HSCR in families using whole genome mapping and sequencing studies with functional follow-up of candidate genes and variants. We intend to ascertain the frequency with which mutations in any human gene lead to familial and isolated forms of HSCR. Clinical information is collected to allow investigation of possible genotype - phenotype correlations. The subject population consists of individuals diagnosed with HSCR and their unaffected relatives. Individuals/families are ascertained through support groups, web-based listings of research studies and genetic testing services, an educational study website, and referrals from genetic counselors and physicians. Blood, or tissue, samples are requested from affected individuals and their unaffected relatives.

  Study phs000497

• Whole genome sequencing of core-binding factor leukemia

  Pediatric de novo acute myeloid leukemia (AML) is a heterogeneous disease that can be divided into clinically distinct subtypes based on the presence of specific chromosomal abnormalities or gene alterations. One of the best characterized subtypes of AML involves leukemias with alterations of the core-binding factor (CBF)-complex, which comprises the FAB subtypes M2 and M4Eo and associates with a favorable outcome. Patients with the AML M2 subtype harbor a translocation between chromosomes 8 and 21 [t(8;21)] that yields the chimeric fusion gene RUNX1(AML1)-RUNX1T1(ETO), while patients with AML M4Eo express the chimeric fusion gene CBFβ-SMMHC(MYH11) as a result of an inversion/translocation event of chromosome 16 [inv(16)/t(16;16)]. In an effort to define the total complement of genetic changes in CBF-leukemia, we performed paired-end whole genome sequencing (WGS) on diagnostic leukemia blasts and matched germ line samples from 17 pediatric CBF-leukemia patients using the Illumina platform. Somatic alterations, including single nucleotide variations (SNVs) and structural variations (SVs), including insertions, deletions, inversions, and inter- and intra-chromosomal rearrangements, were detected using complementary analysis pipelines (Bambino, CREST and CONSERTING). Recurrent screening of identified mutations will be performed in a cohort of approximately 94 cases of CBF-leukemias.

  Study phs000414

• Targeted MitoExome Sequencing of Mitochondrial OXPHOS Diseases (Massachusetts General Hospital)

  Human disorders of mitochondrial oxidative phosphorylation (OXPHOS) represent a devastating collection of inherited diseases. These disorders impact at least 1:5000 live births, and are characterized by multi-organ system involvement. They are characterized by remarkable locus heterogeneity, with mutations in the mtDNA as well as in over 77 nuclear genes identified to date. It is estimated that additional genes may be mutated in these disorders. To discover the genetic causes of mitochondrial OXPHOS diseases, we performed targeted, deep sequencing of the entire mitochondrial genome (mtDNA) and the coding exons of over 1000 nuclear genes encoding the mitochondrial proteome. We applied this 'MitoExome' sequencing to 124 unrelated patients with a wide range of OXPHOS disease presentations from the Massachusetts General Hospital Mitochondrial Disorders Clinic. The 2.3Mb targeted region was captured by hybrid selection and Illumina sequenced with paired 76bp reads. The total set of 1605 targeted nuclear genes included 1013 genes with strong evidence of mitochondrial localization from the MitoCarta database, 377 genes with weaker evidence of mitochondrial localization from the MitoP2 database and other sources, and 215 genes known to cause other inborn errors of metabolism. Approximately 88% of targeted bases were well-covered (>20X), with mean 200X coverage per targeted base.

  Study phs000339

• snRNA: A Cultured Leukemia Stem Cell Model Enables Validation of CDK6 as a Stemness Target Against Acute Myeloid Leukemia

  Acute myeloid leukemia (AML) represents a group of aggressive hematological malignancies, the clinical management of which is made challenging due to the persistence of rare and therapy resistant leukemia stem cells (LSCs) which serve as a source of disease relapse and poor outcomes. There are currently a paucity of methods to reliably enrich and study LSCs, hindering the development of therapies that specifically target LSCs. In this study, we deeply characterize the OCI-AML8227 culture model, which maintains a functional stemness hierarchy originating from its highly primitive CD34⁺CD38⁻ cells, to elucidate LSC biology and uncover LSC-specific therapeutic vulnerabilities. We analyzed both bulk and single-cell proteomics, transcriptomics, and epigenomics to generate a LSC protein-protein interaction network, which was then integrated with an LSC-focused small molecule screen using this model. From these findings, CDK6 was discovered as a therapeutic vulnerability specific to LSCs, which was validated in findings from the BEAT-AML cohort and a patient-derived xenograft (PDX) panel of AML samples through palbociclib treatment. Taken together, our studies validate CDK6 as a druggable vulnerability in LSCs, and authenticate OCI-AML8227 cells as a LSC target discovery engine.

  Study EGAS50000000786

• bulk ATACseq: A Cultured Leukemia Stem Cell Model Enables Validation of CDK6 as a Stemness Target Against Acute Myeloid Leukemia

  Acute myeloid leukemia (AML) represents a group of aggressive hematological malignancies, the clinical management of which is made challenging due to the persistence of rare and therapy resistant leukemia stem cells (LSCs) which serve as a source of disease relapse and poor outcomes. There are currently a paucity of methods to reliably enrich and study LSCs, hindering the development of therapies that specifically target LSCs. In this study, we deeply characterize the OCI-AML8227 culture model, which maintains a functional stemness hierarchy originating from its highly primitive CD34⁺CD38⁻ cells, to elucidate LSC biology and uncover LSC-specific therapeutic vulnerabilities. We analyzed both bulk and single-cell proteomics, transcriptomics, and epigenomics to generate a LSC protein-protein interaction network, which was then integrated with an LSC-focused small molecule screen using this model. From these findings, CDK6 was discovered as a therapeutic vulnerability specific to LSCs, which was validated in findings from the BEAT-AML cohort and a patient-derived xenograft (PDX) panel of AML samples through palbociclib treatment. Taken together, our studies validate CDK6 as a druggable vulnerability in LSCs, and authenticate OCI-AML8227 cells as a LSC target discovery engine.

  Study EGAS50000000787

• scATAC: A Cultured Leukemia Stem Cell Model Enables Validation of CDK6 as a Stemness Target Against Acute Myeloid Leukemia

  Acute myeloid leukemia (AML) represents a group of aggressive hematological malignancies, the clinical management of which is made challenging due to the persistence of rare and therapy resistant leukemia stem cells (LSCs) which serve as a source of disease relapse and poor outcomes. There are currently a paucity of methods to reliably enrich and study LSCs, hindering the development of therapies that specifically target LSCs. In this study, we deeply characterize the OCI-AML8227 culture model, which maintains a functional stemness hierarchy originating from its highly primitive CD34⁺CD38⁻ cells, to elucidate LSC biology and uncover LSC-specific therapeutic vulnerabilities. We analyzed both bulk and single-cell proteomics, transcriptomics, and epigenomics to generate a LSC protein-protein interaction network, which was then integrated with an LSC-focused small molecule screen using this model. From these findings, CDK6 was discovered as a therapeutic vulnerability specific to LSCs, which was validated in findings from the BEAT-AML cohort and a patient-derived xenograft (PDX) panel of AML samples through palbociclib treatment. Taken together, our studies validate CDK6 as a druggable vulnerability in LSCs, and authenticate OCI-AML8227 cells as a LSC target discovery engine.

  Study EGAS50000000788

• bulk RNA-seq: A Cultured Leukemia Stem Cell Model Enables Validation of CDK6 as a Stemness Target Against Acute Myeloid Leukemia

  Acute myeloid leukemia (AML) represents a group of aggressive hematological malignancies, the clinical management of which is made challenging due to the persistence of rare and therapy resistant leukemia stem cells (LSCs) which serve as a source of disease relapse and poor outcomes. There are currently a paucity of methods to reliably enrich and study LSCs, hindering the development of therapies that specifically target LSCs. In this study, we deeply characterize the OCI-AML8227 culture model, which maintains a functional stemness hierarchy originating from its highly primitive CD34⁺CD38⁻ cells, to elucidate LSC biology and uncover LSC-specific therapeutic vulnerabilities. We analyzed both bulk and single-cell proteomics, transcriptomics, and epigenomics to generate a LSC protein-protein interaction network, which was then integrated with an LSC-focused small molecule screen using this model. From these findings, CDK6 was discovered as a therapeutic vulnerability specific to LSCs, which was validated in findings from the BEAT-AML cohort and a patient-derived xenograft (PDX) panel of AML samples through palbociclib treatment. Taken together, our studies validate CDK6 as a druggable vulnerability in LSCs, and authenticate OCI-AML8227 cells as a LSC target discovery engine.

  Study EGAS50000000789

• Phylogenetic analysis of paired breast carcinomas identifies genetic events associated with clonal recurrence and invasive progression

  Development of ipsilateral breast carcinoma following diagnosis of breast ductal carcinoma in situ (DCIS) has been assumed to represent recurrence of the primary tumour. However, this may not be the case and it is important to know how often recurrences are new tumours. Ipsilateral primary-recurrence pairs (n=78) were sequenced to test their clonal relatedness. Shared genetic events were identified from whole exome sequencing (n=54 pairs) using haplotype-specific copy number and phylogenetic analysis. The remaining pairs were sequenced by a targeted panel or low-coverage whole genome sequencing. We included 32 non-recurrent DCIS to compare recurrent and non-recurrent disease. We found that 7% of DCIS recurrences were non-clonal by whole exome sequencing, indicative of a new breast carcinoma. Lower resolution methods detected a higher non-clonality rate (29%). Comparing primary DCIS with their recurrences found that evolution of DCIS to invasive disease was associated with increased ploidy and copy number events. TP53 mutations were enriched in DCIS with clonal recurrence compared with non-recurrent DCIS. Our results verify that de novo “recurrent tumours” of independent origin occur in patients who may be at high risk. (https://www.biorxiv.org/content/10.1101/2024.05.19.594731v2.full)

  Study EGAS50000001298

• Ethiopia_Genome_Project__high_coverage_

  The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

  Study EGAS00001000237

• The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias

  Pediatric de novo acute myeloid leukemia (AML) is a heterogeneous disease that can be divided into clinically distinct subtypes based on the presence of specific chromosomal abnormalities or gene alterations. One of the best characterized subtypes of AML involves leukemias with alterations of the core-binding factor (CBF)-complex, which comprises the FAB subtypes M2 and M4Eo and associates with a favorable outcome. Patients with the AML M2 subtype harbor a translocation between chromosomes 8 and 21 [t(8;21)] that yields the chimeric fusion gene RUNX1(AML1)-RUNX1T1(ETO), while patients with AML M4Eo express the chimeric fusion gene CBFβ-SMMHC(MYH11) as a result of an inversion/translocation event of chromosome 16 [inv(16)/t(16;16)]. In an effort to define the total complement of genetic changes in CBF-leukemia, we performed paired-end whole genome sequencing (WGS) on diagnostic leukemia blasts and matched germ line samples from 17 pediatric CBF-leukemia patients using the Illumina platform. Somatic alterations, including single nucleotide variations (SNVs) and structural variations (SVs), including insertions, deletions, inversions, and inter- and intra-chromosomal rearrangements, were detected using complementary analysis pipelines (Bambino, CREST and CONSERTING). Recurrent screening of identified mutations will be performed in a cohort of approximately 94 cases of CBF-leukemias.

  Study EGAS00001000349

• Whole-exome and targeted sequencing of pediatric hyperdiploid B-cell precursor acute lymphoblastic leukemia

  High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion of relapses. The cause and origin of these relapses remains obscure. We therefore explored the mutational landscape in high hyperdiploid (HD) ALL with whole-exome (n=19) and subsequent targeted deep sequencing of 60 genes in 100 relapsing and 51 non-relapsing cases. We identified multiple clones at diagnosis that were primarily defined by a variety of mutations in receptor tyrosine kinase (RTK)/Ras pathway and chromatin-modifying genes. The relapse clones consisted of reappearing as well as new mutations, and overall contained more mutations. Although RTK/Ras pathway mutations were similarly frequent between diagnosis and relapse, both intergenic and intragenic heterogeneity was essentially lost at relapse. CREBBP mutations, however, increased from initially 18-30% at relapse, then commonly co-occurred with KRAS mutations (P<0.001) and these relapses appeared primarily early (P=0.012). Our results confirm the exceptional susceptibility of HD ALL to RTK/Ras pathway and CREBBP mutations, but, more importantly, suggest that mutant KRAS and CREBBP might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone.

  Study EGAS00001001113

• Whole genome, whole exome, and targeted sequencing of high-grade meningioma tumor samples.

  High-grade meningiomas frequently recur and are associated with high rates of morbidity and mortality. To determine the factors that promote the development and evolution of these tumors, we analyzed the genomes of 274 high-grade meningiomas and compared this information with data from 456 low-grade meningiomas. High-grade meningiomas had a higher mutation burden than low-grade meningiomas but did not harbor any statistically significant mutated genes aside from NF2. High-grade meningiomas also possessed significantly elevated rates of chromosomal gains and losses, especially among tumors with monosomy 22. Meningiomas previously treated with adjuvant radiation had significantly more copy number alterations than radiation-induced or radiation-naïve meningiomas. Across serial recurrences, genomic disruption preceded the emergence of nearly all mutations, remained largely uniform across time, and when present in low-grade meningiomas, correlated with subsequent progression to a higher grade. In contrast to the largely stable copy number alterations, mutations were strikingly heterogeneous across tumor recurrences, likely due to extensive geographic heterogeneity in the primary tumor. While high-grade meningiomas harbored significantly fewer overtly targetable alterations than low-grade meningiomas, they contained numerous mutations that are predicted to be neoantigens, suggesting that immunologic targeting may be of therapeutic value.

  Study EGAS00001002294

• Ethiopia_Genome_Project__low_coverage_

  The Ethiopian area stands among the most ancient ones ever occupied by human populations and their ancestors. Particularly, according to archaeological evidences, it is possible to trace back the presence of Hominids up to at least 3 million years ago. Furthermore, the present day human populations show a great cultural, linguistic and historic diversity which makes them essential candidate to investigate a considerable part of the African variability. Following the typing of 300 Ethiopian samples on Illumina Omni 1M (see Human Variability in Ethiopia project, previously approved by the Genotyping committee) we now have a clearer idea on which populations living in the area include the most of the diversity.This project therefore aims to sequence the whole genome of 300 individuals at low (4-8x) depth belonging to the six most representative populations of the Ethiopian area to produce a unique catalogue of variants peculiar of the North East Africa. Furthermore 6 samples (one from each population) will also be sequenced at high (30x) depth to ensure full coverage of the diversity spectrum.The retrieved variants will be of great help in evaluating the demographic dynamics of those populations as well as shedding light on the migrations out of Africa.

  Study EGAS00001000238

• Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients

  Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease. We performed deep sequencing of viral samples from patients chronically infected with HBV to investigate the association between viral genome variation and patients’ clinical characteristics. We discovered novel viral variants strongly associated with viral load and HBeAg status. Patients with viral variants C1817T and A1838G had viral loads nearly three orders of magnitude lower than patients without those variants. These patients consequently experienced earlier viral suppression while on treatment. Furthermore, we identified novel variants that either independently or in combination with precore mutation G1896A were associated with the transition from HBeAg positive to negative phase of infection. These observations are consistent with the hypothesis that mutation of the HBeAg open reading frame is an important factor driving CHB patient’s HBeAg status. This analysis provides a detailed picture of HBV genetic variation in the largest patient cohort to date and highlights the diversity of plausible molecular mechanisms through which viral variation affects clinical phenotype.

  Study EGAS00001003689

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities WGS

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006865

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities RNA-Seq

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006866

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities DNA-Methylation

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006881

• The Nordic Centre of Excellence Programme in Molecular Medicine Data Access Committee

  Dac EGAC00000000006

• Expression-Based Subtypes Define Pathologic Response to Neoadjuvant Immune-Checkpoint Inhibitors in Muscle-Invasive Bladder Cancer

  Dac EGAC00001002276

• EGAD00010000724

  Pilot experiment on functional genomics in osteoarthritis (methyl)

  Dataset EGAD00010000724

• EGAD00010000474

  blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 2 (CC2)

  Dataset EGAD00010000474

• EGAD00010000476

  blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 1 (CC1)

  Dataset EGAD00010000476

• EGAD00010000478

  blood-based gene expression from breast cancer cases and age-matched controls in case-control serie 3 (CC3)

  Dataset EGAD00010000478

• Methylation differences in trisomy 21 using monozygotic twins - RRBS dataset

  Dataset EGAD00001001272

• Identification of molecular subgroups in multiple myeloma by whole exome sequencing.

  Dataset EGAD00001004408

• RHD_NC_OMNI_Cases

  Rheumatic heart disease cases recruited in New Caledonia with higher density genotyping

  Dataset EGAD00010000956

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Study EGAS00001005346

• Somatic mutations in healthy and leukemic blood progenitors reveal evolutionary mechanisms underlying childhood leukemia and differential patient outcome

  Study EGAS00001004593

• Novel de novo pathogenic variant in the GNAI1 as a cause of severe disorders of intellectual development with autistic features

  Study EGAS00001005355

• RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Study EGAS00001007618

• Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens

  Study EGAS00001007404

• Single cell RNA sequencing reveals induced bifurcated differentiation after RUNX1::RUNX1T1 depletion in patient-derived leukemic blasts

  Study EGAS00001008050

• Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

  Study EGAS00001006137

• Clonal evolution study of Intrahepatic cholangiocarcinoma in Zhongshan Hospital

  Clonal evolution study of Intrahepatic cholangiocarcinoma

  Study EGAS00001002625

• Cetuximab treatment of metastasis-derived organoids (LMO)

  Cetuximab treatment in organoids

  Dataset EGAD00001009404

• Whole Exome Sequencing in resected HCC

  35 paired samples ressected HCC

  Dataset EGAD00001006073

• NPC genome-wide human SNP array data for HongKong population

  nasopharyngeal carcinoma genome-wide human SNP array data for 423 NPC cases and 573 controls

  Dataset EGAD00010002298

• Geisinger Health System - MyCode, eMERGE III Exome Chip

  DNA samples were obtained from participants of the Geisinger MyCode biobank. Phenotype data to determine case or control status for abdominal aortic aneurysm or extreme obesity were derived from Geisinger electronic medical record data through an enterprise data warehouse. Samples were genotyped using the Illumina Human CoreExome-12 v1.0 Array. Genotype data were filtered using standard quality control measures.

  Study phs000957

• Kids First: Pediatric Research Project on Adolescent Idiopathic Scoliosis

  Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. For the current study, families with inherited adolescent idiopathic scoliosis were included. Both affected and unaffected family members were included.

  Study phs001410

• The Genomic Complexity of Primary Human Prostate Cancer

  Seven primary prostate cancers and their paired normal counterparts were DNA-sequenced on a massively parallel sequencing platform. This approach was taken to investigate the genomes for mutations and genomic alterations that would be undetectable by lower-resolution methods. As result, tumors containing chains of balanced rearrangements that occurred within or adjacent to known cancer genes were discovered.

  Study phs000330

• Oncogenic FOXL2C134W has gain-of-function chromatin remodeling activity that reprograms glucocorticoid receptor occupancy to promote ovarian granulosa cell tumor growth

  This dataset contains bam files from the whole exome sequencing performed on granulosa cell tumors and 7 sequencing experiments performed on human-derived KGN granulosa cell tumor cells and isogenic cell lines. The latter include transcription factor ChIP-seq for Foxl2 as well as transcription factor ChIP-seq for Foxl2 and GR under dexamethasone treatment and untreated conditions, two ATAC-seq data sets, two RNA-seq data sets, and Histone marks ChIP-seq.

  Dataset EGAD50000000880

• Paired-end RNA-Seq Dataset of 72 Brain Organoid Samples: Sequencing and Gene Expression Analysis

  72 fastq sequencing files of 72 brain-organoid paired-end sequenced samples (R1/R2). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (New England Biolabs, USA). mRNAs were first enriched with Oligo(dT) beads. The samples were sequenced using a 2x150 Pair-End configuration (ver. 1.5) on an Illumina NovaSeq 6000 The raw sequence reads were aligned to the human reference genome GRCh38 using the STAR aligner (Dobin et al., 2013). Gene expression levels were quantified using the FeatureCounts tool (Liao et al., 2014) (file: "All_Counts_final.xlsx") For more information, see "Study Description"

  Dataset EGAD50000000935

• Genotyping Data From Subjects With Brain Lesions

  These data are from subjects with adult diffuse glioma (IDH wildtype, IDH mutant/1p19q intact, and IDH mutant/1p19q co-deleted), brain lesions, tumefactive multiple sclerosis, brain metastases, central nervous system lymphoma and controls genotyped on the Affymetrix Axiom Precision Medicine array. Data from this study were used for case/control association studies and developing polygenic risk scores.

  Study phs003806

• Targeted pancancer RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoeitic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood.The data is used for tumour driver identification. SNVs, indels and fusion detection.

  Study EGAS50000000700

• Genetic and Microenvironmental Analysis of Peripheral T-cell Lymphoma

  This study enrolled 129 patients diagnosed with PTCL, comprising 94 cases of nTFHL and 35 cases of PTCL-NOS. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) were performed using DNA and RNA of sufficient quality extracted from their tumor specimens. WES was conducted for all 129 cases, while RNA-seq was performed on 57 tumor samples.

  Study EGAS50000001258

• ICARUS-LUNG01-GEOMx

  A GeoMx spatial transcriptomic study using 7 patients from the ICARUS LUNG01 trial focusing on tumour and immune cell compartments. We selected 7 paired baseline and on-treatment patient samples for analysis. We selected up to 4 regions of interest (ROI) per sample tissue. We identified tumour and immune cell areas of illumination (AOI) using CK and CD45 antibodies respectively

  Study EGAS50000001679

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• ICGC_Benchmarking_Exercise

  The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.

  Study EGAS00001000433

• Prostate_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331

  Study EGAS00001000427

• Whole Exome Sequencing of High grade T1 non-muscle invasive bladder cancer

  High-grade T1 (HGT1) bladder cancer (BC) is the highest risk subtype of non-muscle-invasive BC with unpredictable outcome and poorly understood risk factors. Here we performed whole exome sequencing across 61 HGT1 samples to identify genomic predictors of good outcome, recurrence or progression. This study includes somatic mutation calls and clinical data for 61 HGT1 tumors.

  Study EGAS00001004603

• Gene_Characterization_in_Carbohydrate_metabolic_alterations__neonatel_diabetes___congenital_hyperinsulinemic__in_early_childhood

  Whole Exome Sequencing of trios (proband + parents) or probands only with Neonatal Diabetes Mellitus (NDM) or Congenital Hyperinsulinism of Infancy (CHI) of unknown genetic origin. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002074

• Amplified EPOR/JAK2 genes define a unique subtype of acute erythroid leukemia

  Acute erythroid leukemia (AEL) is a unique subtype of acute myeloid leukemia characterized by prominent erythroid proliferation, whose molecular basis is poorly understood. To elucidate the underlying mechanism of erythroid proliferation, we performed comprehensive genomic study. The aim of this study is to unveil genotype phenotype correlations and the feasible molecular targets for therapy of AEL.

  Study EGAS00001005810

• Single cell RNA sequencing of bone marrow mononuclear cells

  Bone marrow aspirates were obtained from patients with relapsed/refractory large B cell lymphoma (rrLBCL), mononuclear cells isolated by ficoll density-gradient centrifugation, and loaded onto a 10X Chromium for single cell RNA-sequencing using 5’ chemistry without prior cryopreservation. Healthy donor bone marrow mononuclear cells were obtained from healthy allogeneic stem cell transplant donors and analyzed following viable cryopreservation.

  Study EGAS00001006836