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• Developmental Mechanisms of Human Congenital Heart Disease in Subjects with 22q11.2 Deletion Syndrome (DiGeorge Syndrome/Velocardiofacial Syndrome)

  The study is designed to identify genetic modifiers of cardiovascular defects in subjects with 22q11.2 deletion syndrome (22q11.2DS), also known as DiGeorge syndrome or velo-cardio-facial syndrome. Affymetrix 6.0 arrays were processed on 1,480 subjects with known cardiovascular anomalies or with normal structures, all with 22q11.2DS. One sample is a duplicate so it was removed. There are 1,472 samples total of unrelated, de-identified, probands. Over 90% have the same sized 3 million base pair deletion flanked by low copy repeats (LCR22) A and D, while approximately 6% have nested A to B deletions. The rest have other nested deletions, that include a deletion in the vicinity of TBX1 (between LCR22 A and B). A subset of the data was used to identify copy number variations serving as modifiers. Some data were previously published by Dr. Emanuel's team at Children's Hospital of Philadelphia in PA, USA (PMID:26742502; PMID:4896312; PMID:25892112; PMID:4570279). The de-identified DNA data from unrelated subjects come from multiple research sites in the US and Europe as part of the International 22q11.2 Consortium and the International 22q11.2 Brain and Behavior Consortium.

  Study phs001339

• HIPO016 - glioblastoma tumour methylation microarray profiling

  Methylation microarray profiling (Illumina Human Methylation 450k and EPIC platforms) of 60 adult glioblastomas. Tumours were subtyped using the approach from Sturm et al. (https://doi.org/10.1016/j.ccr.2012.08.024): 12 IDH, 18 MES, 12 RTK I, 18 RTK II. DNA was prepared, assayed on the microarrays, and raw data computationally processed as described in Capper et al., "DNA methylation-based classification of central nervous system tumours": https://www.nature.com/articles/nature26000

  Dataset EGAD00010001797

• Large B cell lymphomas with CCND1 rearrangement have different immunoglobulin gene breakpoints and genomic profile than mantle cell lymphoma

  Next-generation sequencig data including whole-genome sequencing, whole-exome sequencing, and capture-based gene panels of large B cell lymphomas with CCND1 rearrangementas described in Özoğul,Montaner, Pol et al 2024.

  Study EGAS50000000564

• Analysis for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA analysis)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. Single cell metadata and analysis 38 Barrett's and normals

  Dataset EGAD00001005455

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. scRNAseq (BAM files) 38 Barrett's and normal samples

  Dataset EGAD00001005438

• He et al. WES data

  This dataset are the bam files of WES data from the paper by He et al.

  Dataset EGAD00001007134

• Dataset-linking-WGS-samples-in-ega-box-81-via-README-for-study-EGAS00001002923

  This dataset contains 318 Tumor and Control WGS files submitted in another EGA box for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007861

• SJCRH Patient-derived orthotopic xenografts of pediatric brain tumors

  Primary patient pediatric brain tumors from patients treated at SJCRH were implanted and amplified only in the brain of immunocompromised mice without tissue culture steps and referred as patient-derived orthotopic xenografts (Smith et al, Acta Neuropathologica, 2020).

  Study EGAS00001005533

• Sequencing data for oesophageal and related samples - Linossi et al

  Data supporting: "Utility of ctDNA assessment after six weeks of immunotherapy to predict radiological response in advanced oesophageal cancer" Linossi et al

  Dataset EGAD00001015434

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074