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• Diabetes Multi-Omic Investigation of Drug Response (DIAMOND)

  The Diabetes Multi-omic Investigation of Drug Response (DIAMOND) cohort is a population-based cohort of individuals with type-2 diabetes (T2D) who receive their care through a large health system serving southeast Michigan and metropolitan Detroit. The cohort represents the diversity of the population from which it was created. Because of their health plan membership, participants have a rich dataset of longitudinal clinical health information related to their care. The intent of the DIAMOND study is to use genomic profiling, drug exposure information, and electronic health record (EHR) derived outcome data to identify genetic predictors of treatment response. Genome-wide genotyping was performed using the AxiomTM Precision Medicine Research Array (ThermoFisher Scientific Inc.).

  Study phs003350

• Genome-wide evaluation of the maturation of the immune response to the tuberculin skin test from day 2 to day 7

  The tuberculin skin test (TST) is a standardised human challenge model to evaluate the immune response to Mycobacterium tuberculosis (Mtb) antigens in vivo. To study the temporal evolution of the TST, we recruited healthy volunteers with evidence of peripheral blood Mtb reactive T cells, to undergo a TST in each arm that was sampled on day 2 at one site and on day 7 at the contralateral site on day 7. Genome-wide TST transcriptomes at day 2 and day 7 were defined by differential gene expression compared to transcriptomes from the site of control saline injections performed in a separate subset of volunteers.

  Study EGAS50000000822

• Targeted Myeloid DNA-Panelsequencing, MLL

  Sequencing data from a targeted myeloid DNA-Panelsequnencing at the MLL Dx, Munich lab. Targeted sequencing was performed using the Nextera DNA Flex library preparation kit, starting with 100ng of genomic DNA (Illumina, San Diego, CA, USA). The target regions were enriched by a custom xGen Lockdown panel using a hybridization capture workflow (IDT Integrated DNA Technologies, Coralville, IA, USA). All libraries were sequenced with 100bp paired-end reads on a NovaSeq6000 (Illumina) with a mean coverage of 3206x. Somatic variant calling was performed with Pisces and a sensitivity cut off of 2%. Large deletions and medium-sized insertions, as they are for example found in CALR and FLT3, were called with Pindel. Variant annotation considered the publicly available data bases Cosmic (v91), ClinVar (2020-03), gnomAd (non-cancer, v2.1.1), dbNSFP (v3.5) and UMD TP53 (2017_R2). Variants that are described as somatic, protein truncating or affecting splice sites were considered as mutations while variants with no or discrepant data base information were considered as variant of uncertain significance.

  Dataset EGAD00001008485

• An exome sequencing study of the HIV elite-long term non progressors and rapid progressors (CASCADE cohorts)

  Background: A rare subgroup of HIV infected individuals naturally controls infection without treatment. These ?elite controllers? constitute an important model for the natural control of HIV infection. Indeed, the study of these individuals may provide insights into strategies for the development of HIV vaccines. Although several HLA and chemokine alleles are known to be over-represented in elite controllers, only a small portion of HIV phenotypic variation is explained by known genetic variants. The elite controller phenotype is rare and distinct, representing the extreme of an infectious disease trait. As such, this phenotype may be partly explained by variation in host immune control, which may be characterized by differences in rare functional genetic variants. Genomic regions underlying elite control can be potentially identified by comparing the presence or frequency of variants in this group to that representing the opposite extreme. In this context, ?rapid progressors? is a group defined by its rapid immunological and clinical disease progression. Aim: To extend an existing study, in order to identify DNA sequence variants involved in the control of HIV infection with greater statistical resolution. Specifically, we aim to sequence up to 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (a collaboration of 25 HIV seroconversion cohort studies across Europe).

  Dataset EGAD00001002179

• Star2xml: metadata converter into XML

  Star2xml: metadata converter into XML Welcome to the landing page for star2xml - a tool developed by the European Genome-phenome Archive (EGA) that enables users to convert metadata into XML format that is compliant with EGA's programmatic submission system. For starters, if you are not sure what metadata is in this context, you may want to explore our brief metadata introduction. . Star2xml is useful for users who have already submitted their data to the EGA and want to also submit their metadata programmatically without having to create the XML files manually. The need for these XMLs containing metadata is explained in the EGA's metadata schemas and programmatic submission guidelines. In summary, star2xml allows for users to deposit metadata in a tabular format (e.g. excel spreadsheet) and transform it into a compliant XML format. This saves time in large submissions, where the sheer size of metadata makes it difficult to manage. For smaller submissions, it is recommended to use EGA's Submitter Portal (SP) instead. The installation of the tool is straightforward, and it contains detailed documentation on how to use it in its GitHub repository . While star2xml can help users convert metadata formats, it does not validate the resulting metadata against EGA's schemas. Therefore, after creating your XMLs, you should still validate your metadata before submitting it to EGA, as described in the documentation for programmatic metadata validation.

  Documentation tools/star2xml

• Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

  Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de-novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondaryrearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

  Study EGAS00001000659

• BLUEPRINT Gene expression analysis during human B-cell differentiation using the Affymetrix Human Genome U219 Array

  We performed gene expression analysis using the Affymetrix Human Genome U219 Array of 9 subpopulations covering the complete B-cell maturation program: hematopoietic progenitor cells (HPC); pre-B-I cells (preB1C); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); naive B cells from tonsil (t-naiBC); germinal center B cells (gcBC); plasma cells from tonsil (t-PC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). All the samples were isolated from healthy donors and, with the exception of bm-PC (only 1 replicate), we used 3 to 11 biological replicates of each subtype.

  Study EGAS00001001197

• Comprehensive analysis of the (epi)genome of pediatric atypical teratoid/rhabdoid tumours (AT/RTs)

  Whole exome sequencing of atypical teratoid /rhabdoid tumors (AT/RTs) revealed recurrent mutations only in SMARCB1, a gene involved in chromatin remodeling. However, preliminary data from our lab using gene expression and DNA methylation arrays shows that there are three distinct molecular subgroups of AT/RTs, suggesting that other molecular alterations underlying the development of these aggressive pediatric brain tumors must be found outside the coding genome or at the epigenomic level. Identification of these (epi)genomic alterations, which we intend to address in this project, may lead to novel treatment strategies for these tumors and reveal options for meaningful patient stratification.

  Study EGAS00001001297

• CRC Promoter capture Hi-C

  Genome organisation determines chromosome interactions between regulatory elements, such as promoters and enhancers, influencing gene expression. Despite the fact that it is possible to assess whether a gene is actively transcribed, it has been challenging to point out the genomic regions that are involved in the regulation of a particular gene. We are interested in better understanding the interactions between promoters and their regulatory elements in colorectal cancer in order to unveil novel non-coding regions which might have a role in tumour development. To do so, we utilise the HiC method complemented with promoter capture in combination with NGS to map promoter interactions in two CRC cell lines, representing two distinct CRC subtypes.

  Study EGAS00001001946

• Lebanon_HighCov_seq

  We propose to investigate the genomics of a Lebanese sample. we plan (1) genotyping (2.5M) of 120 Lebanese individuals, choosing this platform to allow comparison with the 1000 Genomes and African Genome Variation project populations, (2) 8x sequencing of 100 individuals to provide unbiased population-level sequence information including allele frequencies, and (3) 30x sequencing of four individuals to allow inferences such as from PSMC/MSMC to be obtained. The current form is for the high-coverage sequencing. 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 EGAS00001002085

• Samples from the Greek island of Crete, MANOLIS cohort

  Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on isolated populations from Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.

  Study EGAS00001000067

• Genomic profiling of ovarian adult type granulosa cell tumors

  To investigate the genomic landscape of primary and recurrent ovarian adult type granulosa cell tumors, we first identified an exploratory cohort comprised of cryopreserved surgical biopsies from 24 patients (primary, n = 8; recurrent, n = 16) with 20 having matched normal tissue or peripheral blood samples. We performed whole exome sequencing (WES) on these tumor samples at 200X target coverage (mean 226; range 165-296) and also performed WES on the available normal samples. In addition, we performed cancer gene panel sequencing using the T200.1 hybrid capture platform on FFPE tissue from 55 additional patients (primary, n = 27; recurrent, n = 28), of which we sequenced matched normal tissue for a total of 44.

  Study EGAS00001002833

• Guardians_of_the_genome__protecting_DNA_from_endogenous_sources_of_damage_

  Analysis of mutational signatures caused by DNA repair defects in human induced pluripotent stem (iPS) cells. A reference human iPS cell line will be used for genetic manipulation to introduce homozygous knockouts of 100 genes known to be involved in or connected to DNA repair or DNA editing. Following a defined period of growth after homozygous knockout of each gene, sub clones will be generated and sequenced. The progenitor “parental” IPS cell line will be used to generate reference sequence data, in order to determine the mutational signature acquired due to the gene knockout. This is a pilot study to investigate the effects of oxygen conditions and growth period on mutations acquired

  Study EGAS00001000874

• Lebanon_LowCov_seq

  we propose to investigate the genomics of a Lebanese sample. we plan (1) genotyping (2.5M) of 120 Lebanese individuals, choosing this platform to allow comparison with the 1000 Genomes and African Genome Variation project populations, (2) 8x sequencing of 100 individuals to provide unbiased population-level sequence information including allele frequencies, and (3) 30x sequencing of four individuals to allow inferences such as from PSMC/MSMC to be obtained. The current form is for the low-coverage sequencing. 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 EGAS00001002084

• EPIC arrays data for chemotherapy response project

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). DNA methylation analysis was performed using DNA from 72 patients. We used 500 ng genomic DNA for bisulfite conversion followed by whole-genome amplification prior to hybridization to EPIC BeadChip (Illumina, San Diego, CA) overnight as described by the manufacturer and then scanned with the Illumina iSCAN system. Data provided here consist of 144 idat files.

  Study EGAS00001004515

• T cell reactivity of MHC epitopes

  By using >36,000 immunogenicity assay results, we developed a method to identify peptide-MHC complexes whose structural alignment facilitates T cell reaction. Our method accurately predicted neoepitopes for MHC II as well as MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types and on-therapy melanoma samples. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naïve tumors in association with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure particularly with high TCR clonality and MHC II expression.

  Study EGAS00001006445

• Genetic Basis of Breast Cancer Resistance in BRCA1 Mutation Carrier

  Our study addressed a specific question in NCI RFA-CA-12-022: "What underlying causal events - e.g., genetic, epigenetic, biologic, behavioral, or environmental - allow certain individuals to survive beyond the expected limits of otherwise highly lethal cancers?". A germline mutation in BRCA1 (BRCA1+) is the most penetrant genetic predisposition for breast cancer. Nevertheless, a portion of BRCA1+ carriers does not develop breast cancer in their lifetime, suggesting that the genetic predisposition can be antagonized by resistant factors. BRCA1+ was inherited from an ancestor of the carrier family thousand years ago. We hypothesize that evolution could select certain genetic components to suppress oncogenesis caused by the predisposition. We compared germline variants in all genes in 27 pairs of breast cancer-unaffected and -affected BRCA1+ carriers, each pair inherited the same BRCA1+. We identified 12 deleterious variants enriched in breast cancer-unaffected carriers, all are common variants. A variant rs3735400 is located in ANLN, a cytokinesis-essential gene. Overexpression of variant-containing ANLN and suppressed expression of endogenous ANLN decrease ANLN nuclear localization and delay cell growth. Our findings suggest that common variants can be selected to resist oncogenesis imposed by BRCA1+.

  Study phs001243

• Whole Exome Sequencing in Alopecia Areata Identifies Rare Mutations in KRT82

  Alopecia areata (AA) is an autoimmune disorder, in which the body's own immune cells attack hair follicels resulting in hair loss. It is a complex genetic disease with 14 associated loci previously identified in our genome-wide association study (GWAS). In the study, we performed the whole-exome sequencing (WES) on 849 AA patients with the aim to identify the novel rare variants in genes contributing to AA susceptibility. We performed gene-collapsing analyses and identified keratin 82 (KRT82 Gene ID: 3888) as the highest associated AA gene in the three rare damaging collapsing models with p<6.7E-07 in one of the models. The KRT82 gene is a hair-specific type II keratin expressed in the hair shaft cuticle during the anagen phase of the hair cycle. We reported the lower expression of KRT82 in AA hair follicles, compared to controls, and the KRT82 expression is absent from the bulb region, the site of AA immune attack. This study emphasizes the significance of using WES and gene collapsing analyses to identify rare variation in a functionally relevant risk gene using a moderate sample size.  

  Study phs002632

• Human Pilocytic Astrocytoma Single Cell RNA Sequencing

  Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement. Here, we perform scRNAseq in six PAs using methods that enabled detection of the rearrangement. When compared to higher-grade gliomas, a strikingly higher proportion of the PA cancer cells exhibit a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibit a progenitor-like phenotype with evidence of proliferation. These express a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Immune cells, especially microglia, comprise 40% of all cells in the PAs and account for differences in bulk expression profiles between tumor locations and subtypes. These data indicate that MAPK signaling is restricted to relatively undifferentiated cancer cells in PA, with implications for investigational therapies directed at this pathway. Note that 931 out of 1234 samples in the Sequence Read Archive (SRA) passed QC and have transcript count data available from the Broad Institute Single Cell Portal. The transcript count data can be found at https://singlecell.broadinstitute.org/single_cell/study/SCP271/pilocytic-astrocytoma-single-cell-rna-seq#study-download

  Study phs001854

• Extracorporeal Life Support Survival in a Pediatric Hematopoietic Cellular Transplant Recipient with Presumed Graft Versus Host Disease-Related Fulminant Myocarditis

  We report the case of a 15-year-old female with hypodiploid pre-B acute lymphoblastic leukemia status post allogeneic hematopoietic stem cell transplantation (HCT) from a matched unrelated male donor who presented on transplant day +75 with cardiac arrest due to ventricular fibrillation associated with fulminant myocarditis. Using conventional diagnostics, an exhaustive search for microbial pathogens in the heart biopsy as well as nasopharynx, blood, urine, and endotracheal aspirate was performed but did not uncover a candidate pathogen. The family consented to a research study for the use of unbiased next-generation genomic sequencing for pathogen identification in the myocardial biopsy. DNA sequencing was performed on 1.5 x 108 sequencing pairs and no microbial pathogens were identified. Interestingly, a significant component of Y-chromosomal human DNA was identified, suggesting infiltration of at least 10 donor leukocytes per host cell. This finding is grossly consistent with the lymphocyte:myocyte ratio in the biopsy according to visual inspection at 40x magnification. This case merits discussion due to (1) her survival after 17 days of veno-arterial extracorporeal life support (ECLS) and (2) the possibility of cardiotropic graft versus host disease (GVHD).

  Study phs001336

• CSER: Evaluating Utility and Improving Implementation of Genomic Sequencing for Pediatric Cancer Patients in the Diverse Population and Healthcare Settings of Texas: The KidsCanSeq Study

  Through this Clinical Sequencing Evidence-Generating Research (CSER) with Enhanced Diversity project we are completing a clinical study (The Texas KidsCanSeq Study) comparing the results of targeted cancer panel sequencing versus genome-scale testing in pediatric cancer patients across diverse clinical settings. We will compare the targeted pediatric cancer panel to germline whole exome sequencing (WES) of unselected childhood cancer patients. We will also compare an RNA/DNA targeted pediatric cancer panel versus WES, transcriptome sequencing and copy number array of FFPE tumor samples for the subset of patients with high-risk tumors. Exome sequencing is performed from a blood or saliva sample of the pediatric age (0-18) patient. We are building on our success completing the CSER program BASIC3 exome sequencing trial (which included 60% Hispanic and African-American patients from a single large academic center) in this large multi-institutional study of an even more diverse patient population from six pediatric oncology healthcare settings across Texas. Data from the Texas KidsCanSeq study will be submitted through the CSER Data Coordinating Center for access in NIH-supported databases.

  Study phs002378

• Vaccine-Expanded Plasmablast-like B Cells Are Associated with Response to Dendritic Cell Therapy in Metastatic Melanoma

  Dendritic cells (DCs), either monocyte-derived (moDCs) or naturally circulating, have been employed in cancer treatment across both metastatic and adjuvant settings. DC vaccines (DC Vax) are capable of inducing tumor-specific immune responses, yet clinical outcomes have thus far fallen short of expectations. Here, we performed a multi-omics analysis of the apheresis product, including CD14⁺ monocytes, and the final DCVax formulation. Among all the components analyzed, the most striking finding was the unexpected presence of CD19⁺ B cells within the DC Vax formulation, which distinguished Responders from Non-Responders to moDC vaccination in metastatic melanoma. The abundance of B cells in DC Vax correlated with their peripheral frequency; however, within the vaccine, these cells acquired a CD20lowCD27hiCD38hi plasmablast-like phenotype, distinct from their autologous circulating B-cell precursors. Notably, a parallel observation was made in Responders, whose pre-treatment lesions were enriched in B cells organized as Tertiary Lymphoid Structures. These results underscore the importance of B cells in both baseline immunity and DCVax formulation, hinting at unexplored mechanisms by which they may influence vaccine effectiveness.

  Study EGAS50000001177

• An_exome_sequencing_study_of_the_HIV_elite_long_term_non_progressors_and_rapid_progressors__CASCADE_cohorts_

  Background: A rare subgroup of HIV infected individuals naturally controls infection withouttreatment. These ?elite controllers? constitute an important model for the natural control ofHIV infection. Indeed, the study of these individuals may provide insights into strategies forthe development of HIV vaccines. Although several HLA and chemokine alleles are knownto be over-represented in elite controllers, only a small portion of HIV phenotypic variation isexplained by known genetic variants. The elite controller phenotype is rare and distinct,representing the extreme of an infectious disease trait. As such, this phenotype may be partlyexplained by variation in host immune control, which may be characterized by differences inrare functional genetic variants. Genomic regions underlying elite control can be potentiallyidentified by comparing the presence or frequency of variants in this group to thatrepresenting the opposite extreme. In this context, ?rapid progressors? is a group defined byits rapid immunological and clinical disease progression.Aim: To extend an existing study, in order to identify DNA sequence variants involved in thecontrol of HIV infection with greater statistical resolution. Specifically, we aim to sequence upto 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (acollaboration of 25 HIV seroconversion cohort studies across Europe).

  Study EGAS00001000522

• Defective T-cell expansion in RASGRP1 deficiency

  Inherited CTPS1- CD27- and CD70-deficiencies in humans have revealed key factors of T-lymphocyte expansion, that is a prerequisite for an efficient immunity to Epstein-Barr virus (EBV) infection. RASGRP1 is a T-lymphocyte specific nucleotide exchange factor known to activate the MAP kinases pathway. A deleterious homozygous mutation in RASGRP1 leading to the loss RASGRP1 expression was identified in two siblings who both developed a persistent EBV infection leading to Hodgkin lymphoma. RASGRP1-deficient T cells exhibited defective MAPK activation and impaired proliferation that was restored by expression of wild-type RASGRP1. Similar defects were observed in T cells from healthy individuals when RASGRP1 was downregulated. RASGRP1-deficient T cells also exhibited decreased CD27-dependent proliferation toward CD70-expressing EBV-transformed B cells, a crucial pathway required for expansion of antigen-specific T cells in anti-EBV immunity. Furthermore, RASGRP1-deficient T cells failed to upregulate CTPS1, an important enzyme required for DNA synthesis. These results show that RASGRP1 deficiency leads to susceptibility to EBV infection, and demonstrate the key role of RASGRP1 at the crossroad of pathways required for the expansion of activated T lymphocytes.

  Study EGAS00001002753

• Genomic Profiling of Thyroid Cancer Reveals a Role for Thyroglobulin in Metastasis -Part II

  Papillary thyroid carcinoma (PTC) has a wide geographic variation in incidence, being highest in Saudi Arabia where it is only second to breast cancer as the most common cancer among females. Genomic profiling of PTC from Saudi Arabia has not been attempted previously. We performed whole-exome sequencing of 101 PTC samples and the corresponding genomic DNA to identify genes with recurrent somatic mutations, followed by sequencing of these genes using a next-generation gene panel approach in further 785 samples. In addition to BRAF, N-RAS and H-RAS, which have previously been shown to be recurrently mutated in PTC, our analysis highlights additional genes, including thyroglobulin (TG), which harbored somatic mutations in 3% of the entire cohort. Surprisingly, although TG mutations were not exclusive to mutations in the RAS-MAP kinase pathway, their presence was associated with a significantly worse clinical outcome, which suggests a pathogenic role beyond driving initial oncogenesis. Analysis of metastatic PTC tissue revealed significant enrichment for TG mutations (p<0.001), including events of apparent clonal expansion. Our results suggest a previously unknown role of TG somatic mutations in the pathogenesis of PTC and its malignant evolution.

  Study EGAS00001003357