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• HipSci HumanExome BeadChip analysis - Kabuki syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome.

  Study EGAS00001002007

• HipSci HumanExome BeadChip analysis-Healthy volunteers

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000866

• HipSci HumanExome BeadChip analysis-Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001272

• HipSci HumanExome BeadChip analysis - Primary immune deficiency

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Primary immune deficiency.

  Study EGAS00001002012

• HipSci HumanExome BeadChip analysis - Hereditary Spastic Paraplegia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002006

• HipSci HumanExome BeadChip analysis - Congenital Hyperinsulinia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Congenital Hyperinsulinia.

  Study EGAS00001002010

• HipSci HumanExome BeadChip analysis - Hypertrophic Cardiomyopathy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002011

• HipSci HumanExome BeadChip analysis - Battens disease

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002016

• HipSci HumanHT 12 Expression BeadChip analysis - Alport syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport syndrome.

  Study EGAS00001002024

• HipSci HumanHT 12 Expression BeadChip analysis - Hypertrophic Cardiomyopathy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002026

• HipSci HumanHT 12 Expression BeadChip analysis - Macular Dystrophy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular Dystrophy.

  Study EGAS00001002029

• HipSci HumanHT 12 Expression BeadChip analysis - Battens disease

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002031

• Wnt Activity Reveals Context-Dependent Genetic Effects on Gene Regulation in Neural Progenitors

  In this study we aimed to identify context-dependent regulatory functions of common genetic variation after stimulation of the canonical Wnt pathway. Fetal cortical tissue between 14 and 21 gestation weeks was subjected to RNA-Sequencing (242 samples) and ATAC-Sequencing (222 samples) to profile expression and chromatin accessibility, respectively. Considering donor genotypes, we were able to identify eQTLs, caQTLs, as well as response QTLs of both categories. The dataset provided here includes 242 RNA-sequencing files in bam format and 222 ATAC-sequencing files in bam format. We also provide 83 donor genotypes in VCF format (hg38).

  Study phs003642

• Genetic landscape of pediatric Infant Acute Lymphoblastic leukemia

  We performed whole genome sequencing of tumor and normal DNA samples obtained from 22 infant ALL cases with MLL rearrangements. In addition, we sequenced 2 paired diagnostic-relapse samples. Using complementary pipelines, somatically acquired genetic changes were analyzed, including single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes. In addition, exome sequencing was performed on paired diagnostic and normal DNA samples obtained from 20 cases of non-infant MLL rearranged leukemias and somatic mutations in the coding regions were identified.

  Study EGAS00001000246

• The multifaceted genomic history of Ashaninka from Amazonian Peru

  Genome-wide profiles of Ashaninkas from Peruvian Amazonia reveal two genetic subgroups. Ashaninka ancestors derived from a south-north migration from southeastern South America. The Ashaninka1 subgroup testifies to an Arawakan-Caribbean genetic link in the Early Ceramic Age. The Ashaninka2 subgroup had recent interactions with Andean and Pacific Indigenous populations.

  Study EGAS00001006958

• Whole Exome Sequencing of Bipolar cases and controls on a cohort from Umea, Sweden

  Whole Exome Sequencing of 924 Bipolar cases and matched controls performed at the Broad Institute on a cohort from Umea, Sweden. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000470

• Gene expression by RNAseq in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential expression in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using RNAseq.

  Study EGAS00001003735

• DNA methylation in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential methylation in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using Illumina 450k arrays.

  Study EGAS00001003739

• Sequencing-based counting and size profiling of plasma Epstein-Barr virus DNA enhance population screening of nasopharyngeal carcinoma.

  We used targeted sequencing to capture and measure the abundance as well as the size profiles of EBV DNA in plasma of subjects with and without NPC

  Dataset EGAD00001004204

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

  This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

  Dataset EGAD00001010036

• Prevalence of rare pathogenic variants in cancer-predisposing genes among Japanese advanced prostate cancer patients.

  The prevalence of rare pathogenic variants in cancer-predisposing genes including those associated with DNA repair remains unknown among Japanese patients with advanced prostate cancer. This study was designed to elucidate the prevalence of pathogenic variants in 27 known cancer-predisposing genes and to explore the prognostic significance of the variants identified.

  Study JGAS000509

• Immune Landscape of Cervical Lymph Nodes in Multiple Sclerosis

  This study aimed to investigate the cellular compartment of deep cervical lymph nodes (dcLNs) during early MS before the influence of immunosuppressive treatments. We used ultrasound-guided FNAs followed by scRNA-seq,CITE-seq, TCR and BCR seq to characterize the immune landscape in MS patients compared to controls within the dcLNs.

  Study EGAS50000000843

• Whole exome DNA sequence profiling of spatial biopsies of high grade serous epithelial ovarian cancer

  The study aims at dissecting the heterogeneity across multiple biopsies of high grade serous epithelial ovarian cancer (HGS-EOC) through a comprehensive characterization of variants and structural changes at the whole exome level. To this aim, the study uses samples from multiple bioptic sites taken from eight HGS-EOC patients.

  Study EGAS00001003048

• Impact of cryopreservation on transcriptome analysis of peripheral blood mononuclear cells

  To investigate the effect of cryopreservation on PBMCs, we conducted an experiment using samples from three healthy donors under four conditions: fresh PBMCs, PBMCs subjected to a single freeze–thaw cycle, PBMCs refrozen in freezing mix, and PBMCs refrozen in TRIzol. This resulted in a total of 12 samples (three replicates per condition). RNA was extracted from all PBMC samples using the Qiagen miRNeasy Mini Kit, followed by polyA RNA sequencing on the Illumina NovaSeq 6000 platform. Blood was collected from one male and two female adult donors. Sequencing yielded high-quality data, with an average of 27.8 million reads per sample and over 94% of bases exceeding a Q30 quality score.

  Study EGAS50000001196