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• Juntendo Muscle Study (JMS)

  Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor intensive and costly methodology that limited these studies. This data was used to present a new method based on muscle tissue RNA sequencing data to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested in a cost and labor efficient way. Muscle biopsies were taken from the vastus lateralis muscle of 23 human subjects from Japan. Samples were sequenced on the NextSeq® 500/550 (Illumina).

  Study EGAS00001006362

• Muscle SATellite cell study (MSAT)

  Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. This data was used to present a new method based on muscle tissue RNA sequencing data to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested in a cost and labor efficient way. Muscle biopsies were taken from the vastus lateralis muscle of 39 Swedish male subjects. Samples were sequenced on the NextSeq® 500/550 (Illumina).

  Study EGAS00001006363

• Center for Common Disease Genomics (CCDG) - Cardiovascular: Harvard Gene-Diet Interaction in a Costa Rican Cohort

  The National Human Genome Research Institute (NHGRI) has funded the Centers for Common Disease Genomics (CCDG), a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to multiple common disease phenotypes and to better understand the general principles of genomic architecture underlying common, complex inherited diseases. This study contains whole genome sequence data and associated variant calls of more than 4200 participants in a cohort collected by the Harvard School of Public Health. The cohort includes subjects from thirty-four countries in the Central Valley of Costa Rica covering a full range of socioeconomic levels, as well as urban, peri-urban and rural lifestyle

  Study phs002282

• Osteosarcoma Genomics

  In this study we attempt to elucidate the genomic characteristics of osteosarcoma. Clinical characteristics 58 tumor / normal pairs from 58 patients were included in the study. Median age at diagnosis was 12 years. 49% of the patients were male and 47% had metastases at diagnosis. 5 year overall survival was 49% for the entire population, 33% for patients with metastatic disease and 64% for patients with localized disease. Patients with metastatic disease at diagnosis had a significantly worse overall survival. All cases except 2 were sporadic and no patients had stigmata of Rothmund-Thomson, Bloom's or Werner's syndromes or Paget's disease. Two familial cases were affected siblings from a family in which there were 2 unaffected parents and 2 unaffected siblings. None of the patients had known Li Fraumeni or hereditary retinoblastoma. Sample Selection and Clinical Data Samples were contributed by hospitals in Brazil, Spain, Mexico and the United States. All patients had histopathology confirmed to be osteosarcoma by a pathologist at the local institution. All but 5 tumor specimens sequenced were obtained pre-chemotherapy from the primary tumor at the time of diagnosis. 2 tumor specimens were obtained pre-chemotherapy from a metastatic tumor at the time of diagnosis. 3 tumor specimens were obtained post-chemotherapy from a metastatic tumor.

  Study phs000699

• Comprehensive survey for the construction of an integrated database of food, gut microbiome, and health information (the "Sukoyaka Health Survey"). A study on the relationship between food and health and genetic background.

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 50 healthy Japanese. We analyzed some participants living in Miyazaki. The SNP array (Japonica Array v2) was used for genotyping. Shotgun metagenomic sequencing of fecal microbiome and metabolome of feces and blood were analyzed.

  Study JGAS000679

• Developing somatic copy number and mutation calling tools for a bespoke sequencing platform

  We previously developed a linked-read sequencing platform (DigiPico) for analysing whole cancer genomes from picogram quantities of tumour DNA. The aim of this study was to develop and evaluate the specialised computational approaches required to obtain clinically useful results from the raw data. To this end, we performed matched DigiPico, bulk tumour and germline WGS on samples from four patients.

  Study EGAS00001007195

• Dac for "Combined single-cell transcriptomics and T-cell receptor sequencing reveal heterogeneity of mycosis fungoides between and within patients and identify a CD4+ cytotoxic subtype"

  Dac for "Combined single-cell transcriptomics and T-cell receptor sequencing reveal heterogeneity of mycosis fungoides between and within patients and identify a CD4+ cytotoxic subtype" with Name: Menghong Yin Email address: menghong.yin@dkfz-heidelberg.de Associated affiliation: Translational Skin Cancer Research Lab (DKFZ)

  Dac EGAC50000000168

• SALTO: chromosomal copy number alterations to predict response to bevacizumab

  Study of the correlation between vessel formation and or CMS subtypes in relation to a predictive copy number marker for bevacizumab. Shallow Whole Genome Sequencing of 92 mCRC samples.

  Study EGAS50000000711

• Data Access Committee for the DNA sequencing data included in the study "A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes”

  Dac EGAC00001003111

• Sequencing data for oesophageal and related samples - ICGC DCC release 27 earmarked (WGS)

  WGS sequencing for 63 cases (126 samples) from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are earmarked for inclusion in ICGC release 27 (deferred to release 28)

  Dataset EGAD00001004028

• 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.

  Dataset EGAD00001000598

• Next Generation Mendelian Genetics: Auriculocondylar syndrome (ACS)

  This project is part of an ongoing project to identify the molecular genetic basis of rare craniofacial disorders. This specific project involved the collection of DNA samples from four probands with severe manifestations of auriculocondylar syndrome and their parents. Detailed clinical phenotypic data is available on each proband. The sole purpose of this research is to identify the molecular cause(s) of auriculochondylar syndrome.

  Study phs000437

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples (n=374) for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs (n=96) for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).

  Dataset EGAD50000000942

• Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML

  Our aim was to identify regulators of the EVI1/MECOM gene, which is the most lethal oncogenic TF and is highly expressed in AML with chromosome 3q26 abnormalities.

  Study EGAS50000000347

• Mesothelioma_Whole_Genomes

  Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project.

  Study EGAS00001000830

• Control human putamen and Substantia Nigra

  The study is affiliated to the UKBEC sample of healthy human putamen and substantia nigra phenotype. The gender is from both male and female samples of the the phenotype.

  Study EGAS00001003065

• Exome sequencing for LySeqST

  Exome sequencing of 120 lymphoma samples and 13 normal samples for LySeqST: A targeted sequencing assay for robust genomic classification of diffuse large B-cell lymphoma.

  Dataset EGAD50000002289

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015376

• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015377

• Changes in AXL and/or MITF melanoma subpopulations in patients receiving immunotherapy

  Our data demonstrate large interpatient variability and variable therapy-induced changes independent of the type of therapy. We identify the presence of previously described AXL+ and MITF+ subpopulations in metastatic tissues both at the mRNA level and in situ at the protein level, and demonstrate that MITF+ melanoma cells are significantly decreased upon immunotherapy, while AXL+ melanoma cell numbers are stable. MITF+ tumor cells showed the most significant inverse correlation with CD8+ T cells. Our patient cohort also shows that immunotherapy-induced changes in the abundance of AXL+ or MITF+ tumor cells did not correlate with improved survival.

  Study EGAS50000001080

• Long-read and short-read RNA sequencing of human normal liver organoid with or without SF3B4 overexpression

  There are 2 matched short and long read RNA sequencing samples. The project aims to find alternative splicing events and resulting transcript isoforms modulated by SF3B4

  Study EGAS50000001131

• Growth Hormone (GH) -secreting Pituitary Adenoma

  Data from 12 fresh-frozen somatotropinomas and their corresponding blood samples. Details are given in Valimaki et al. Whole-genome sequencing of Growth Hormone (GH) -secreting Pituitary Adenoma. Provisionally accepted, 2015.

  Study EGAS00001001293

• IMSGC and MultipleMS project MS patients from Germany, Mainz

  Genotype and phenotype data on 301 MS patients from Germany, Mainz. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002484

• IMSGC and MultipleMS project MS patients from Italy, Piedmont

  Genotype and phenotype data on 1067 MS patients from Italy, Piedmont. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002490

• IMSGC and MultipleMS project MS patients from Germany, TUM

  Genotype and phenotype data on 683 MS patients from Germany, TUM. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002489