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• Susceptibility to Respiratory Infections Due to Autosomal Recessive IFIH1 Mutations

  We studied a child with life-threatening and recurrent respiratory tract infections, caused by multiple viruses including rhinovirus, influenza virus, and respiratory syncytial virus (RSV). We identified in her a homozygous missense mutation in IFIH1 that encodes MDA5 by Whole Exome Sequencing. MDA5-deficiency is a novel inborn error of innate immunity that results in impaired dsRNA-sensing, reduced IFN induction, and susceptibility to the common cold virus.

  Study phs001235

• Integrated Genetic and Pharmacologic Interrogation of Rare Cancers

  Due to the paucity of patient derived models in rare cancers, identification of therapeutic targets remains challenging. We developed a patient derived model, CLF-PED-015-T, from a patient with an undifferentiated sarcoma. From this model, we performed pooled RNAi and CRISPR-Cas9 negative selection screens and integrated that with a small molecule screen. Integration of these data identified CDK4 and XPO1 as potential therapeutic targets.

  Study phs001121

• NHLBI TOPMed - NHGRI CCDG: Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

  This study contains whole genome sequence data. A case-control sample of individuals from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a multicenter prospective cohort study of 16,415 persons of Cuban, Dominican, Mexican, Puerto Rican, Central American, and South American background (phs000810), was selected for whole genome sequencing, including participants with a history of physician-diagnosed asthma and asthma-free participants.

  Study phs001395

• Genotype data from Nagahama cohort project

  Genotype data with basic phenotypes (age and gender) for 3693 samples from Nagahama Cohort project are provided. Genotyping are performed by A)Human610-Quad?B)HumanOmni2.5-4?C)HumanOmni2.5-8?D)HumanOmni2.5S?E)HumanCoreExome?F)HumanExome BeadChip from Illumina Inc. 1708, 1017, 185, 112, 479 and 192 samples are genotyped by A only, B only, C only, A+B+E, B+D+F and C+D+F respectively.

  Study JGAS000012

• Whole genome sequencing of AML with FUS-ERG

  FUS-ERG is a chimeric gene with a poor prognosis, found in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). We investigated whether azacitidine (Aza) are effective in AML with FUS-ERG and how FUS-ERG induces chemoresistance. In a clinical case of AML with FUS-ERG, we compared whole-genome alterations between the initial diagnosis of MDS and the recurrence of AML after Aza treatment.

  Study JGAS000587

• Molecular Characterization of Large Cell Neuroendocrine Carcinoma of the Lung by Multilayered Omics Analysis

  Large cell neuroendocrine carcinoma (LCNEC) is a rare lung cancer type with a very poor prognosis. The underlying molecular features remain unclear. Here, we conducted a multi-omics analysis of 27 LCNEC cases along with 7 small cell lung carcinoma and aimed to propose new classification by extracting genomic and transcriptomic features in LCNEC, leading to the elucidation of the therapeutic approaches.

  Study JGAS000832

• Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP)

  The Post-Transfusion Pupura (PTP) syndrome although rare has severe side effects for 5-10 cases per annum in the UK as a result of transfusion. High quality DNA has been isolated from either whole blood or from cryopreserved mononuclear cells of 4 patients in order to study our postulation that the condition is caused by a loss-of-function mutation in a specific gene.

  Study EGAS00001000053

• RNA004 DRS METTL5 variant

  RNA004 is a method for direct RNA sequencing (DRS) that holds promise to enhance the detection of modopathies. To this end, we provide DRS data for a patient sample harboring heterozygous inactivating SNPs for the methyltransferase METTL5, which modifies m6A on 18S rRNA. Companion datasets are 1) EGAS50000001201 for DRS of a healthy control with intact METTL5 and 2) PRJEB74238 for IVT 18S rRNA vector data as unmodified control.

  Study EGAS50000001321

• SLC9A3R1 variant associated with age-related hearing loss

  Age-related hearing loss (ARHL) is the most common sensory impairment in the elderly affecting millions of people worldwide. To shed light on the genetics of ARHL, a large cohort of 464 Italian patients has been deeply analyzed at clinical and molecular level. A missense variant in SLC9A3R1 has been identified in two unrelated ARHL patients. A knock-in zebrafish model confirmed the pathogenic effect of the variant.

  Study EGAS00001003072

• Complement C1s deficiency in a male Caucasian patient with systemic lupus erythematosus: A case report

  This study involves whole genome sequencing of a 34-year-old male with a rare deficiency in complement component C1s, linked to systemic lupus erythematosus (SLE). Genomic analysis revealed two novel mutations in the C1S gene, resulting in absent C1s protein and impaired classical complement pathway function. The goal was to confirm the C1s deficiency and identify the specific mutations causing this condition.

  Study EGAS50000000707

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• Analysis of tumor periphery and center-specific mutations in renal cell carcinoma

  Renal cell carcinoma (RCC) is a genomically heterogeneous tumor. In the present project, the question whether intratumoral heterogeneity follows a zonal pattern indicating spatial niches was addressed. Whole exome sequencing of 16 paired samples from tumor periphery and center revealed a number of region-specific functional SNVs and Indels. Therefore, RCCs are not composed of evenly admixed tumor cells but show topological differences in their clonal composition.

  Study EGAS00001001784

• Molecular characterization of hepatocellular carcinoma in patients with non-alcoholic steatohepatitis

  Patients with hepatocellular carcinoma (HCC) associated to non-alcoholic steatohepatitis (NASH) are increasing globally, but their molecular traits are not well characterized. Our molecular characterization revealed higher rates of ACVR2A mutations (10%) – a potential tumour suppressor, presence of a novel mutational signature (MutSig-NASH-HCC), a more relevant role of Wnt/TGF-β proliferation subclass in tumours (42%) and immunosuppressive traits in the adjacent non-tumoral tissue.

  Study EGAS00001005222

• Discriminating Th17.1 cell driven sarcoidosis-like inflammation from relapse after anti-BCMA CAR T cells in multiple myeloma

  We present a case study on sarcoidosis-like flare-up after Idecabtagen Vicleucel (Ide-cel), a BCMA targeting CAR T cell therapy, and identified a Th17.1 driven autoimmune mechanism as the biological underpinning of this phenomenon using single-cell RNA-seq analysis. Furthermore, single-cell RNA-seq allowed to discriminate between immune-mediated changes and true relapse after CAR T cell treatment.

  Study EGAS00001006133

• Study the genetic susceptibility of esophagus squamous cell carcinomas (ESCC) in high-risk area Henan Chinese

  This study utilized a genetically-enriched cohort of patients with familial ESCC from the high-risk Henan region, located near the Tai-Hang Mountain region in Northern China, to identify high penetrance ESCC predisposition genes using a comprehensive unbiased whole-exome sequencing (WES) strategy. Subsequent validate the prevalence of rare damage variants by targeted gene sequencing in a large sample size.

  Study EGAS00001003423

• Vitamin C boosts DNA demethylation in TET2 germline mutation carriers

  We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte predominant Hodgkin lymphoma. In a clinical trial of one year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members.

  Study EGAS00001006916

• Segmental_cherry_angioma_case

  Cherry angiomas are common benign blood vessel growths on the skin. In this study we characterise mutational profile of a cherry angioma and adjacent skin biopsied from a patient with multiple lesions with segmental presentation.

  Study EGAS00001008212

• Whole_Exome_sequencing_in_a_large_IBD_pedigree

  We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.

  Study EGAS00001000240

• Response_SLE

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  Study EGAS00001007963

• A Phase I/II Trial of T Cell Receptor Gene Therapy Targeting HPV-16 E7 for HPV-Associated Cancers

  This is a phase I clinical trial testing the safety and efficacy of gene-engineered T cells expressing a T-cell receptor targeting an HLA-A*02:01-restricted epitope of HPV-16 E7 (E7 TCR T cells) in patients with metastatic HPV-16+ epithelial cancers. A total of 12 patients were treated. The maximum tested dose was tolerated. Side effects were most consistent with the expected toxicities of the lymphocyte-depleting conditioning regimen and high-dose aldesleukin. Six of the 12 patients demonstrated objective clinical responses. Translational studies of the infused T cell characteristics did not correlate strongly with clinical response. Genomic defects in the targeted peptide-HLA complex did demonstrate definitive mechanisms of resistance in some patients.

  Study phs002286

• Effect of 28-day administration of Urolithin A to sedentary elderly on muscle gene expression

  Urolithin A (UA) is a natural dietary, microflora derived, metabolite shown to stimulate mitophagy and improve muscle health in old animals and pre-clinical models of aging. UA was administered for 28-day in a first-in-human clinical trial to sedentary elderly subjects. Muscle biopsies were collected before the first dosing, and at the end of the 28-day period, under fasted conditions. Gene expression was measured by microarray. Gene-set enrichment analysis of the gene expression data showed that UA increased the transcription of mitochondrial related genesets. These observed effects on mitochondrial biomarkers show that UA induces a molecular signature of improved mitochondrial and cellular health following regular oral consumption in humans.

  Study EGAS00001003638

• Hereditary Cancer Diagnostics with I2HCP gene panel

  Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.

  Dataset EGAD00001006171

• Single-Cell DNA Methylation Profiling via scTAMseq

  This dataset comprises single-cell DNA methylation and nuclear genotyping profiles of 7 total bone marrow aspirates (donors A.1-A.7) and 5 CD34+-enriched bone marrow samples (donors B.1-B.5) generated using the scTAMseq protocol. Sequencing was performed on the Mission Bio Tapestri platform, targeting a panel of 448 CpGs to assess epigenetic patterns and We also included 147 genomic regions commonly mutated in clonal hematopoiesis and 20 regions targeting chromosome Y. Samples B.1 & B.5, B.2 & B.4 and A.2 & A.5 were, in pairs, multiplexed into single tapestri lanes.

  Dataset EGAD00001015498

• Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

  In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. We provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

  Study phs000525

• STAMPEED: Myocardial Infarction Genetics Consortium (MIGen)

  Myocardial infarction (MI) is a common complex disease and the leading cause of death and disability worldwide. The genetic basis of this disease is largely unknown. It has been thought that early-onset MI events would have a substantially greater heritability, thus making DNA collections with younger individuals desirable. More recently, genome-wide association studies have become feasible through the development of whole genome arrays and a large catalogue of common variants reported in the International HapMap database. This study aims to use Affymetrix genotyping platform to do a whole genome scan in 3000 early-onset MI cases and 3000 matched controls from 6 study collection sites.

  Study phs000294