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• CRISPR_Screening_of_Brazilian_Acral_Melanoma_Cell_Lines

  Perform CRISPR Screening in acral melanoma cell lines, using a genome-wide gRNA library, aiming to identify genes essential for their survival and proliferation. The results will aid the identification of key genes and pathways implicated in acral melanoma progression, paving the way to understand the disease and offer potential targets for precision therapies to this subtype of melanoma.

  Study EGAS00001008230

• Y_phylogeny_haplogroupDE

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. 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 EGAS00001002674

• Mutator phenotype and specific mutational signature explain an increased risk of hematological malignancies in patients with Xeroderma Pigmentosum

  In this study we report for the first time the unique collection of 6 leukemias and two sarcomas from XP-C. Comprehensive WGS-based mutational analysis provides genetic explanation for the increased incidence of leukemia in XP-C and describes an unique mutational process in internal tumors associated with NER deficiency.

  Study EGAS00001004511

• Mutation tracking in single cell RNA-Seq reveals consequences of subclonal evolution in acute myeloid leukemia

  Total bone marrow from AML patients was FACS index sorted with staining for Lineage markers (Lin), CD33, CD34, CD38, CD45RA, CD90, CD99, Tim3 and GPR56, and enrichment for Lin- and Lin-CD34+ cells. Single cells were subjected to a modified smart-seq2 protocol with targeting of mutant sites of interest ("MutaSeq”).

  Study EGAS00001003414

• Exome sequencing of patients with rare neurological disorders

  Exome sequencing of patients and their families with diverse rare neurological disorders. Some families have prior linkage data identifying a specific chromosomal interval or interest, other families do not have linkage data available. Many of these families come from special populations whose demography or preference for consanguineous marriages make them particularly tractable for genetic studies.

  Study EGAS00001000159

• A somatic reference standard for cancer genome sequencing.

  Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

  Dataset EGAD00001002142

• Study of Environment, Lifestyle and Fibroids SNP Data

  Uterine fibroids are hormonally-dependent benign tumors of the uterine muscle that develop in premenopausal women. Currently, the primary symptoms (pain and bleeding) are treated, but when those treatments fail, major procedures to remove or shrink the fibroids are frequently the only options for women. Fibroids are the leading indication for hysterectomy in the United States. African-American women develop fibroids an average of 10 years earlier than white women in the U.S., and they are approximately three times more likely to have a hysterectomy for fibroids. The known risk factors for fibroids do not explain this disparity.The goal of the Study of Environment, Lifestyle & Fibroids (SELF) is to identify risk factors for uterine fibroid development. It is the first study to identify incident cases based on ultrasound screening. We enrolled a cohort of 1693 women who self-identified as Black or African American, ages 23-35, from the Detroit, Michigan area. Women with a prior diagnosis of fibroids were not eligible. Participants were screened for fibroids with ultrasound at enrollment, and follow-up ultrasounds occurred approximately every 20 months to identify new fibroids. Fibroids that were detected at enrollment and those that arose during follow up were monitored at subsequent visits for fibroid growth. We collected risk factor and symptom data, physical measurements, as well as blood, urine, and vaginal swab specimens at enrollment and follow-up visits.The study was designed to test three primary hypotheses:Vitamin D deficiency is a risk factor for fibroid incidence and/or growth.Reproductive tract infections can increase risk of fibroid development.Genotypic variation in African ancestry may influence fibroid development directly, or through interaction with life-course risk factors.In addition, we collected extensive information to examine other exposures of interest, and our extra specimens can be used to test new hypotheses in the future.With this first prospective study of fibroid development, we aim to identify new preventative factors that could directly benefit women. We anticipate that the detailed data on fibroid development can be used to help design new interval treatment strategies to limit fibroid growth and thus reduce the need for the invasive treatments that remain the standard of care when first-line treatments fail.

  Study phs002513

• Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Framingham Heart Study (FHS)

  Cohort DescriptionIn 1948, the researchers recruited 5,209 men and women between the ages of 30 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. Since 1948, the subjects have returned to the study every two years for an examination consisting of a detailed medical history, physical examination, and laboratory tests, and in 1971, the study enrolled a second-generation cohort -- 5,124 of the original participants' adult children and their spouses -- to participate in similar examinations. The second examination of the Offspring cohort occurred eight years after the first examination, and subsequent examinations have occurred approximately every four years thereafter. In 1994, the need to establish a new study reflecting a more diverse community of Framingham was recognized, and the first Omni cohort of the Framingham Heart Study, consisting of 506 participants, was enrolled. In April 2002 4095 third generation of participants, the grandchildren of the original cohort, were added. In 2003, 103 spouses of the offspring Cohort (NOS), and a second group of 410 Omni participants were enrolled. Through 2019, the original cohort has completed a total of 32 exams, the Offspring cohort 9 exams, the OMNI1 cohort 4 exams, and GEN3, NOS and OMNI2 cohorts each have completed 3 exams. The FHS is a joint project of the National Heart, Lung and Blood Institute and Boston University.Data Being Submitted Wave 1 questionnaire data includes 3967 variables for up to 3112 FHS participants in C4R.Wave 2 questionnaire data includes 448 variables for up to 2337 FHS participants in C4R.Dried Blood Spot/Serosurvey data includes 7 variables for up to 2189 FHS participants in C4R.Derived data includes 43 variables for up to 3151 FHS participants in C4R.Phenotype data includes 113 variables for up to 3151 FHS participants in C4R.

  Study phs002911

• After the completion of CINECA, EUCANCan, and euCanSHare. What's next?

  CINECA, EUCANCan, and euCanSHare were part of the EUCAN Cluster, made up of six projects that received funding under the same Horizon 2020 call. All EUCAN projects (CINECA, EUCANCan, EUCAN-Connect, euCanSHare, Receptor Plus, and ReCoDID) were aimed at facilitating data reuse and knowledge discovery by enhancing data exchange and long-term collaboration in the health field. Here are some highlights about EGA’s contribution to these projects. CINECA: advances in Federated discovery and infrastructure for cohorts CINECA (Common Infrastructure for National Cohorts in Europe, Canada, and Africa) developed a federated cloud-based infrastructure for making genomic and biomolecular data accessible. The project has assembled a virtual cohort of 1.4 million individuals from sources such as the EGA, CanDIG and H3Africa. The EGA–CRG co-leaded a work package Work Package 1 on Federated Data Discovery and Querying. Beacon v2, championed by Jordi Rambla and Lauren Fromont, has been one of the central elements for the discovery of human genetic and phenotypic data. The EGA-CRG contributed to the development of a model for cohort discovery inside the Beacon v2 model. The team also delivered a Discovery Portal was implemented to explore cohorts and individuals of synthetic data. It is a UI that gathers a network of Beacons, a service for query expansion, and a visualisation tool. Have a look at the Discovery Portal UI, gathering a network of Beacons. You will find entities such as the Barcelona Supercomputing Center (BSC), BioData.pt and the European Genomic Data Infrastructure (GDI), among others. euCanSHare: facilitation of data access management This joint EU-Canada project aimed to build a European and Canadian FAIR platform for cardiovascular data sharing and analysis. The EGA’s tasks contributed to the development of the data management plan and data flows, main web-portal and interoperability protocols. An important part of the EuCanShare platform is the data access manager, a tool for the data owners to control the access to their sensitive datasets. We built a user-friendly interface for data access committees (data owners) to easily manage their data requests and access credentials. The data access portal facilitates the creation and internal organization of the data access committees as well as the linkage of data usage conditions to specific datasets. The interface includes filters for browsing requests and page to visualize the request history helping with the handling of data access requests. EUCANCan: toward a federation of clinical institutions in oncology The EUropean-CAnadian CANcer Network worked towards building a federated network to advance personalized medicine in oncology, by promoting the standard analysis, management and sharing of harmonized genomic and phenotypic data. The EGA led tasks on defining data flows and preparing an adapted infrastructure for long-term data storage and sharing. One of the key contributions was the conception of the EGA communities, offering standard and interoperable solutions for data discovery, processing, and sharing to projects and institutions that would like to manage and share data in the context of the EGA ecosystem. What's Next? The participation in projects such as CINECA, EUCANCan, and euCanSHare provide us with experience for future projects. We are happy to enhance data sharing and reuse, vital for advancing clinical and genomic research. The Discovery Portal is a wonderful proof of concept for the Beacon network. Next, we will finalise both the network and the user interface, and make sure it can be applied to more clinically-centred settings like hospitals. Most data hosted at the EGA are about cancer research. Currently, we contribute to building tools and infrastructure to empower oncology research in several European projects such as EUCAIM, EUCANIMAGE and EOSC4Cancer. We also do not lose sight of initiatives in the field such as the International Cancer Genome Consortium (ICGC) with the project ARGO, whose data model was adopted in EUCanCan.

  Blog cineca-eucancan-and-eucanshare-were-concluded-in-june

• Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

  Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies (ONT) PromethION platform is a now a viable solution for WGS. New bioinformatic methods have been developed to take advantage of this long read data, however much of the validation of these tools has focussed on calling germline variants (both SNVs and structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated due to their frequency varying depending on tumour purity/subclonality. Here, we evaluate the extent to which Nanopore WGS enables genome-wide detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma. We examine the capability of currently available tools for calling somatic variants in ONT data by comparing the data with results from 150bp short-read sequencing of the same samples. We then conduct a detailed analysis of the performance of multiple long-read mappers and structural variant callers for calling large, somatic structural variants (SVs) in ONT data. Our protocol achieved yields of up to 96 mapped Gb per PromethION flow cell with average read lengths of ~5kb. Calling germline SNVs from these data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialized joint calling algorithms. Our analysis of structural variants shows that the comparative performance of different tools varies significantly between SV types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants by using the ONT data to confirm that a somatic 1.6Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.

  Study EGAS00001004266