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• HLA-A*3101 and Carbamazepine-Induced Hypersensitivity Reactions in Europeans

  Based on the prior knowledge of involvement of the human leukocyte antigen locus in Han Chinese patients with carbamazepine-induced Stevens-Johnson syndrome, we imputed the HLA types for each case and control subject from the array of SNPs in the Human610-Quad GWAS platform (NCBI Build 36.1). We then performed a genome-wide association test which included the imputed HLA alleles as markers.

  Study EGAS00000000036

• Identification of Recurrent SMO and BRAF Mutations in Ameloblastomas

  RNA-seq data from two cases of ameloblastoma was analyzed for candidate gene fusions and point mutations. Recurrent point mutations identified in the RNA-seq data, as well as mutations identified with limited panel targeted deep sequencing, were validated as somatic. Expanding to a larger cohort of 28, one of two activating mutations was found in 80% of cases. No recurrent gene fusions events were identified.

  Study phs000739

• Identification of ALS Associated Genes Using Whole Genome Sequencing

  The overall aim of this study is to discover of novel genetic elements associated with amyotrophic lateral sclerosis (ALS). Towards this goal, we have performed exome and whole genome sequencing for over 2000 samples. This data will be process and harmonized to yield high quality variant calling. These variants will be combined with control cohorts to identify novel genetic elements associated with ALS through case: control analyses.

  Study phs001585

• Interruption of BTK Inhibitor Improves Response to SARS-CoV-2 Booster Vaccination in Patients with Chronic Lymphocytic Leukemia

  This study investigates the effect of booster SARS-CoV-2 vaccination and Bruton tyrosine kinase inhibitor (BTKi) interruption on antibody response to vaccination. Patients with chronic lymphocytic leukemia (CLL) are immunocompromised, at increased risk of infection, and have historically poor response to immunization. BTKi therapy is a standard treatment for CLL in frontline and salvage settings and further suppresses antibody vaccine responses.

  Study phs003319

• Genomic sequencing of Ewing's Sarcoma

  The Ewing sarcoma family of tumors (EFT) is a group of malignant small round blue cell tumors that arise in bone or soft tissue. Ewing sarcoma (ES) is the second most common type of primary bone tumor to affect children and adolescents and accounts for 2.9% of all childhood cancers. This data set reports whole-genome sequencing of 6 primary Ewing's Sarcoma samples and matching germline samples.

  Study phs000768

• Epigenetic Mechanisms of Inflammation and Fatigue in Head and Neck Cancer

  This was a longitudinal observational study to examine the association between fatigue and DNA methylation as well as gene expression among patients with head and neck cancer. Demographic and clinical variables were collected before chemoradiotherapy and/or at follow-up visits as appropriate. Fatigue was assessed and biosamples (for DNA methylation and gene expression) were collected before, immediately after, and at six- and twelve-months post-chemoradiotherapy.

  Study phs002106

• Cellular Origins and Genetic Landscape of Cutaneous GD T Cell Lymphoma

  Cutaneous gamma-delta T cell lymphomas are a rare and aggressive subtype of cutaneous lymphoma. In the present study, we analyzed these cancers by DNA and RNA sequencing in order to illuminate the genetic landscape for this rare disease. We obtained tumor samples from multiple institutions, including Northwestern University (Chicago, IL), University of Chicago (Chicago, IL), University of Virginia (Charlottesville, VA), and Massachusetts General Hospital (Boston, MA).

  Study phs001969

• A Genome-Wide Association Study of CALGB 90401: Randomized, Double-Blind, Placebo-Controlled Phase III Trial Comparing Docetaxel and Prednisone with or without Bevacizumab in Men with Metastatic Castration-Resistant Prostate Cancer

  The Cancer and Leukemia Group B (CALGB) 90401 trial compared docetaxel and prednisone with or without bevacizumab in men with metastatic castration-resistant prostate cancer. A genome-wide association study using clinical outcomes and toxicities was conducted on the basis of data from CALGB patients who provided consent for pharmacogenomic studies and usable DNA

  Study phs001002

• Acral melanoma targeted exome sequencing study (UCSF)

  Acral melanoma affects world populations irrespective of skin color. It has comparatively few single nucleotide mutations, but exhibits genomic instability characterized by structural rearrangements and amplifications. As acral melanoma harbors BRAF (GeneID:673) mutations at low frequencies, we searched for alternative therapeutic targets. We performed targeted deep sequencing of cancer-related genes on 37 acral melanomas and identified point mutations, structural rearrangements and copy number alterations.

  Study phs001596

• Collaborative Association Study of Psoriasis

  The goal of this collaborative study is to combine the resources and expertise of three groups with long-standing studies of psoriasis genetics in order to identify new genetic susceptibility factors for psoriasis, a common inflammatory skin disease that affects over 4 million Americans. Consent groups and participant set General research use (GRU): 1677 (950 cases, 692 controls, 35 others) Autoimmune disease (AD): 1198 (449 cases, 734 controls, 15 others)

  Study phs000019

• Clinical and Genetic Analysis of Retinopathy of Prematurity (ROP)

  Retinopathy of prematurity (ROP) is a leading cause of childhood blindness worldwide and is treated based on the presence of symptoms of "plus disease", a dilation and tortuosity of retinal vessels. This project aims to identify the genetic and clinical underpinnings of the disease by comparing the germline variants of ~1,400 premature babies. 100 samples have been selected for WES and all have been genotyped.

  Study phs002047

• Sensitive circulating tumor DNA based residual disease detection in epithelial ovarian cancer

  In this study we implemented a circulating tumor DNA (ctDNA) based blood test for more accurate post-operative surveillance of this disease. We analyzed 264 plasma samples collected between June 2016 and September 2021 from 63 epithelial ovarian cancer patients using tumor-guided plasma cell-free DNA analysis to detect residual disease after treatment. Assay specificity was verified using cross-patient analysis of 1195 control samples.

  Study EGAS50000000245

• Brazilian Thyroid WES

  Medullary thyroid cancer (MTC) is a rare malignant tumor that arises from parafollicular cells. Approximately 8% of thyroid cancer cases are MTC, and about 25% of these have a hereditary component. Incorporating molecular parameters into tumor classification is important. Besides, the presence of pathogenic germline variants can impact directly on cancer prevention. Thus, the aim of this study was to perform whole exome sequencing (WES) on a consecutive series of hereditary RET wild-type MTC patients to identify genetic variants that may be involved in the carcinogenesis of this tumor. WES was performed on 28 patients negative for germline RET pathogenic variants using the NovaSeq 6000 platform. Variant classification followed American College of Medical Genetics and Genomics guidelines.Our study represents a significant advancement in gene discovery for MTC genetics.

  Dataset EGAD50000000086

• DAC for a single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Dac EGAC50000000226

• Mate-pair sequencing of 12q-amplified osteosarcomas

  Mate-pair sequencing of 12q-amplified osteosarcomas for the detection of structural variants. This was carried out in order to study the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification. Mate-pair data was also used to verify gene fusions detected with RNA-seq.

  Study EGAS50000000493

• RNA sequencing data from 10 patient derived colorectal cancer organoids

  This dataset comprises RNA-sequencing data from ten colorectal cancer (CRC) organoids, derived from histologically verified primary tumor tissues of patients undergoing surgical resection. Paired-end sequencing produced 20 FASTQ.gz files. The organoids were cultured in Geltrex-based droplets using PDO culture medium and harvested for RNA extraction. Total RNA was isolated and subjected to full-length mRNA sequencing, producing high-quality RNA-seq data. The dataset includes transcriptomic profiles of seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors, providing a valuable resource for the analysis of non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline. This dataset aids in uncovering potential immunotherapy targets in CRC, particularly in hard-to-treat low-TMB MSS cases.

  Dataset EGAD50000000962

• RNASeq from PPGL-derived PC12 cell lines cultivated in normoxia and hypoxia conditions.

  PC12 cells derived from rat PPGL were then either continued cultivated in the same normoxia condition (37˚C, 5% CO2 and 21% O2 balanced with N2) or were placed in a hypoxic incubator, that maintained a constant hypoxic environment (37˚C, 5% CO2 and 1% O2 balanced with N2), for different short (12h, 24h, and 48h) or prolonged time (36 days, approximately 860h).

  Study EGAS50000000814

• 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

• Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  This study aims to evaluate the efficacy of the combination of olaparib, durvalumab, and fulvestrant for the treatment of patients with ER-positive, HER2-negative, locally advanced or metastatic breast cancer with BRCA gene alterations or alterations of genes involved in HRR or MSI status, in terms of the progression-free survival rate (PFSR) at 24 weeks.

  Study EGAS50000001166

• 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

• Analysis of Large Cell Neuroendocrine Carcinoma Expressing HNF4alpha Using WGS

  Lung LCNEC (Large Cell Neuroendocrine Carcinoma) has a poor prognosis, and no effective treatment has yet been established. We have found that the gastrointestinal marker HNF4alpha is specifically expressed in some LCNEC cases. By performing Whole Genome Sequencing (WGS) on samples from 10 LCNEC patients, we aim to identify changes characteristic of LCNEC expressing HNF4alpha and explore new classifications and treatment options for LCNEC.

  Study JGAS000732

• Molecular Correlatives from SU2C-SARC032

  SU2C-SARC032 was a phase II international, randomized trial for patients with localized, high-risk undifferentiated pleomorphic sarcoma or dedifferentiated or pleomorphic liposarcoma of the extremity and limb girdle. On the trial, the addition of perioperative pembrolizumab to preoperative radiotherapy and surgery improved disease-free survival compared to preoperative radiotherapy and surgery alone. Bulk RNA-sequencing was performed on pre-treatment and surgically resected tumor specimens.

  Study phs003921

• Molecular profiles in early onset prostate cancer

  Paired germline (blood) and tumour samples were collected from prostate cancer cases <65 years at diagnosis to identify genetic changes in early onset prostate cancer.  Whole exome sequencing was performed on these samples. The aim was to determine if these changes are associated with more aggressive disease and to identify targets for treatment and screening by identifying associations with family history, DNA repair germline mutations, and clinical features.

  Study EGAS50000001467

• Shotgun metagenome sequencing of saliva samples using PromethION

  Using PromethION, we conduct shotgun metagenome sequencing of human saliva, where both bacteria and bacteriophages are densely living, to study both microbiome and virome. We aim to explore, for example, relative abundance of bacteira and bacteriophages, distribution of contig lengh. types of phages and prophages, frequency of novel phages revealed by the long-reads and their taxonomic classification, and characteristics of genes encoded by the phages.

  Study JGAS000186

• 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