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• Genomic Evolution of Breast Cancer Metastasis and Relapse

  Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

  Dataset EGAD00001002698

• Head and neck tumor organoid biobank for modelling individual responses to radiation therapy according to the TP53/ HPV status

  Head and neck cancers (HNC) represent an extremely heterogeneous group of diseases with a poorly predictable therapy outcome. Here, we have established a comprehensive molecularly and functionally characterized head and neck organoid biobank recapitulating the clinically relevant subtypes of TP53 mutant and human papillomavirus type 16 (HPV 16) infection-driven HNC. Organoids were exposed to radiotherapy and genetically engineered normal and tumor organoids were used for testing the direct functional consequences of TP53-loss and HPV infection. We identified subtype-associated transcriptomic signatures and pathological features, including sensitivity to TP53 stabilization by the MDM2 inhibitor Nutlin-3. TP53 loss-of-function alone was insufficient to promote radiation resistance, whereas HPV 16 oncogenes E6/E7 mediated radiosensitivity via induction of cell cycle arrest.

  Study EGAS50000001219

• National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) Consortium Glaucoma Genome-Wide Association Study

  This is a case-control study of primary open angle glaucoma (POAG). POAG is an intraocular pressure (IOP) related progressive optic neuropathy that ultimately leads to blindness. For this study we have formed a collaborative consortium contributing 2170 POAG cases and 2347 controls with a unified definition of POAG (the NEIGHBOR consortium: NEI Glaucoma Human genetic collaBORation). The case definition has also been harmonized with an additional 976 cases and 1140 controls from the NHGRI supported GENEVA (gene-environment) study of glaucoma (GLAUGEN) (NIH/NHGRI U01HG004728, Pasquale PI). Cases and controls were recruited from ophthalmology clinics and were examined by ophthalmologists. For cases, the clinical exam included intraocular pressure measurements, optic nerve assessment and visual field evaluation. Controls had no family history of glaucoma, normal intraocular pressure and normal optic nerves. Cases and controls were also drawn from two clinical trial populations: Advanced Glaucoma Intervention Study (AGIS, NEI U10EY006827, D. Gaasterland PI) and Collaborative Initial Glaucoma Treatment Study (CIGTS, NEI U10 EY009149, P. Lichter PI). The NEIGHBOR consortium has two Co-Principal Investigators: J. Wiggs (Harvard, MEEI), and M. Hauser (Duke). The consortium includes eleven different centers where data collection and analysis take place. The eleven sites and investigators are: Harvard Medical School (Massachusetts Eye and Ear Infirmary) (J. Wiggs, L. Pasquale); Duke University Medical Center (M. Hauser, E. Hauser, R. Allingham, S. Schmidt); University of Michigan (J. Richards, S. Moroi, P. Lichter); University of Miami (M. Pericak-Vance, R. Lee, D. Budenz); Vanderbilt University (J. Haines); University of California San Diego (K. Zhang, R. Weinreb; T. Gaasterland); University of Pittsburgh (J. Schuman, G. Wollstein); University of West Virginia (A. Realini, J. Charlton, S. Zareparsi); Johns Hopkins University (D. Friedman, D. Zack); Stanford University (D. Vollrath, K. Singh), Eye Doctors of Washington (D. Gaasterland). Hemin Chin serves as the NEI Staff Collaborator. This national collaborative study is supported by multiple NIH grants: NEI R01 EY015543 (Allingham); NEI U10 EY006827 (D. Gaasterland); NHLBI R01 HL073389 (E. Hauser); NEI R01 EY13315 (M. Hauser); NEI U10 EY009149 (Lichter); NEI R01 EY015473 (Pasquale); NEI U10 EY012118 (Pericak-Vance); NEI R03 EY015682 (Realini); NEI R01 EY011671 (Richards); NEI R01 EY09580 (Richards); NEI R01 EY013178 (Schuman); NEI R01 EY015872 (Wiggs); NEI R01 EY009847 (Wiggs); NEI R01 EY010886 (Wiggs); NEI R01 EY144428 (Zhang); NEI R01 EY144448 (Zhang); NEI R01 EY18660 (Zhang). Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited Disease Research, was provided by the National Eye Institute (X01HG005259).

  Study phs000238

• Access to public datasets in the EGA

  Dac EGAC00001000514

• Genomic alterations in MM - CEL

  RNA from the same tumor sample (n=98) was also processed using the 3' IVT kit (Affymetrix) and hybridized to U133 Plus 2.0 arrays (Affymetrix).

  Dataset EGAD00010001577

• MalariaGEN-MassArray_b37

  EGAS00001001311: Genome-wide study of resistance to severe malaria in eleven worldwide populations: Sequenom MassArray genotypes

  Dataset EGAD00010001799

• methylation_mifepristone_set

  Raw methylation from breast biopsies in BRCA mutation carriers or controls before and after 3 months of preventive mifepristone treatment.

  Dataset EGAD00010002073

• B and T Cell Determinants of Influenza Vaccine Responses in the Elderly

  The study sequenced antibody heavy chain gene rearrangements from human subjects receiving influenza vaccination.

  Study phs000666

• Raw NGS data of primary AML samples

  Raw NGS data of primary Acute Myeloid Leukemia samples. The libraries were obtained with Sophia Genetics Myeloid Solution kit, targeting 30 genes involved in AML.

  Dataset EGAD50000000506

• WGS

  Our cohort represents infants with ALL in whom KMT2Ar was not detected by FISH or by standard cytogenetics. Whole-genome sequencing (WGS) was performed using Illumina’s HiSeqX to a depth of >30X.

  Dataset EGAD50000000594

• Variants Derived From CONCOR Biobank TOF Probands (Netherlands)

  Short variants identified in 125 TOF probands enrolled through the CONCOR Biobank (Netherlands).

  Dataset EGAD50000000837

• RODAM cohort: 16S gut microbiome data

  16S rRNA sequencing data of fecal samples of 1211 RODAM cohort participants in three research sites: rural Ghana, urban Ghana and Amsterdam, the Netherlands.

  Dataset EGAD50000001182

• WES bam files associated with HNSCC patients in the LIONESS study

  This dataset contains 85 WES bam/bai files of HNSCC cancer patients as part of with the LIONESS study

  Dataset EGAD50000001487

• Methylation profiling of CDS and ES tumor samples

  Methylation profiling of 9 CDS and ES tumor samples, using the approach described in "Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target

  Dataset EGAD00010002760

• WGS sequencing of an ES tumor sample

  This Datasets contains whole genome sequencing data of one ES tumor sample. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was paired in bulk.

  Dataset EGAD00001015607

• scRNAseq: Human periportal liver assembloids recapitulate periportal liver tissue in vitro

  Sample number: 8 Sample details: Total 8 samples, including Homeostatic-like assembloids (4 samples), Fibrotic-like assembloids (4 samples).

  Dataset EGAD50000001453

• Germline variants in patients diagnosed with both uveal and cutaneous melanoma

  We sequenced the constitutional DNA from patients affected by both uveal and cutaneous melanoma.

  Study EGAS00001007584

• subset of MASTER-Cohort, as used in EGAS00001004157

  linking MASTER H021-Cohort to EGAS0001004157

  Dataset EGAD00001006184

• Cell line sequencing data

  SmMIP libraries using bulk cell line DNA and DNA mixes were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)

  Dataset EGAD00001007790

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• CHEWIE ctDNA in Rhabdomyosarcoma

  Targeted DNA based panel of multiple ctDNA samples from 10 patients througout clinical care to assess treatment response. The panel is custom-designed and property of UGS, IC.

  Dataset EGAD00001011127

• Targeted deep mtDNA amplicon sequencing MS discordant twins

  Single-end BAM files of the targeted deep sequencing analysis of several mtDNA candidate regions in blood and buccal-derived DNA of the corresponding twin pairs.

  Dataset EGAD00001002190

• Neoadjuvant Breast Cancer Validations

  This study aims to re-sequence findings from whole genome studies using a bespoke pulldown method to validate mutations in those genomes sequenced.

  Dataset EGAD00001000663

• Angiosarcoma follow-up 2 validation study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Dataset EGAD00001000679

• DNMT3A MOPD patient ChIP-seq data

  ChIP-seq data from controls and patients with de novo DNMT3A mutations resulting in microcephalic primordial dwarfism.

  Dataset EGAD00001004473