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• The Multiethnic Cohort (MEC) Study

  The Multiethnic Cohort (MEC) study of over 215,000 men and women in Hawaii and California is unique in that it is population-based and includes large representations of older adults (45-75 years at baseline) for five US racial/ethnic groups (Japanese Americans, African Americans, European Americans, Latinos and Native Hawaiians) at varying risks of chronic diseases. The MEC has established a large biorepository of mainly blood and urine collected from over 70,000 participants, linked to extensive, prospectively collected risk factors (e.g., diet, smoking, physical activity), biomarkers and clinical data for five racial/ethnic groups.

  Study phs002183

• Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

  Whole Exome Sequencing was performed in a dilution series containing known amounts of human and mouse DNA, 3x 100% human 0% mouse, 2x 90/10, 3x 50/50, 2x 25/75 and 3x 0/100. A set of breast cancer clinical samples, matched normal tissue and matched PDTXs (total number = 14) were also analysed. Paired-end 75bp sequences for the dilution series and paired-end 125bp for the clinical samples were obtained on Illumina HiSeq2500; fastq files are provided. A triplicate analysis of the transcriptome using RNA-seq was also performed for the Universal Human RNA Reference and the Universal Mouse RNA Reference samples. Paired-end 150bp fastq files obtained on Illumina HiSeq4000 are provided.

  Dataset EGAD00001003800

• Breakfast trial transcriptomic profiles

  The dataset consists in fastq files generated with RNA sequencing of 55 samples from 29 patients with stage I-III TNBC treated with anthracycline-taxane chemotherapy plus fasting-mimicking diet plus/minus metformin in the context of the BREAKFAST trial (NCT04248998). Samples are fresh-frozen tumor samples at baseline and 14-21 days after the first treament cycle sequenced to identify early predictors of treatment activity. Each sample is sequenced in multiple lanes (four or eight lanes each) and in paired ends mode (R1 and R2 fastq files). Samples were sequenced by an Illumina Nextseq500 platform.

  Dataset EGAD50000000968

• 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

• Microarray genotyping of idiopathic hypersomnia patients (11 orexin mutation-positive patients, 85 orexin mutation-negative patients)

  We performed a principal component analysis (PCA) to determine whether population stratification or differences in the genetic background are present between the orexin mutation-positive and -negative idiopathic hypersomnia groups. Genome-wide single nucleotide polymorphism (SNP) data in patients with idiopathic hypersomnia (orexin mutation-positive patients and orexin mutation-negative patients) were utilized for the PCA.

  Study JGAS000508

• TS and WGS data

  The dataset contains the targeted sequencing (TS) and the whole genome low pass (WGS) BAM files of the study. For the TS: Samples: TS_XXX There are normal and tumor DNA samples. Each DNA strand has been sequenced independently (PoolA and PoolB). A TruSeq Custom Amplicon panel of 20 genes frequently mutated in ILC and/or ER-positive BC in general was designed using DesignStudio from Illumina: AKT1, ARID1A, CDH1, ERBB2, ERBB3, ESR1, FOXA1, GATA3, IGF1R, JAK2, MAP2K4, MAP3K1, NF1, PIK3CA, PTEN, RB1, RUNX1, STAT3, TBX3, and, TP53. For the WGS: Samples: WGS_XXX There are normal and tumor DNA samples. Samples were sequenced to an average target coverage of 0.5X.

  Dataset EGAD00001006393

• Atypical teratoid/rhabdoid tumors (ATRT) are comprised of three epigenetic subgroups with distinct enhancer landscapes

  Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants and young children. Although the prognosis of ATRT patients is poor, some patients respond very well to current treatments, suggesting inter-tumor molecular heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large cohort of ATRTs (n = 170). Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location and type of SMARCB1 alterations, were identified using DNA-methylation or gene expression analyses. Whole genome DNA- and RNA-sequencing found no other recurrent mutations explaining the differences between subgroups. However, whole genome bisulfite-sequencing and H3K27Ac ChIP-sequencing of primary tumors revealed clear differences in methylation patterns and enhancer landscapes, leading to the identification of subgroup-specific regulatory networks.

  Dataset EGAD00001001444

• TTFields Glioblastoma Data Access Committee, Charité – Universitätsmedizin Berlin

  This Data Access Committee is responsible for reviewing and approving data access requests for genomic and associated clinical data from patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. The DAC ensures that any data use is consistent with the patients’ informed consent, the study’s ethical approval and applicable data protection regulations. Approved applicants may use the data only for biomedical research on brain tumours and related methods, must not attempt re-identification of participants, and may not share the data with unauthorized third parties

  Dac EGAC50000000843

• Omic Studies in Children's Respiratory and Environmental Workgroup (CREW) Cohorts

  Children's Respiratory Research Workgroup (CREW) is an NIH-funded project consisting of multiple individual U.S. cohorts and three scientific centers working together to identify phenotypes and causes of childhood asthma. CREW will include data from a large number of children and their families, with broad diversity in terms of ethnicity, family characteristics, neighborhoods and geographic locations. One of the primary goals of CREW is to put together sets of data and samples of participating cohorts to identify phenotypes of childhood asthma (i.e. specific subtypes of asthma that can be distinguished by clinical features such as natural history, triggers, exacerbation frequency, concurrent allergies, lung function, sex, etc). Omics studies will include genotyping, methylation, and RNA sequencing. By integrating the DNA genotyping with the expression, immunologic and clinical data, we will identify eQTL, inflammation QTL, and lung function QTL, as well as QTL associated with other biomarkers. Analyses will identify genetic, epigenetic, transcriptional and protein/metabolite profiles that are associated with specific exposures or phenotypes. As we obtain mechanistic insights about personal and early life risk factors, we will connect asthma phenotypes with underlying causes and pathogenic mechanisms to define endotypes of childhood asthma.

  Study phs004036

• Mutation of FOXL2 in granulosa cell tumors of the ovary

  We generated paired-end RNA-Seq data using the Illumina Genome Analyzer II platform for four adult granulosa cell tumours (GCTs) of the ovary (1 primary, 3 recurrent). We screened this data for the presence of GCT specific sequence variants and detected a non-synonymous mutation in the FOXL2 gene that was found to be recurrent in 97% of 89 additional GCTs. To measure genomic stability of the four index cases, we generated Affmetrix SNP 6.0 data and analysed these data for copy number changes. Raw sequence reads as well as Affymetrix CEL files are available to applicants.

  Study EGAS00000000040