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• The analysis of gene mutations in Hematology malignancy

  We analysed the mutations of target genes regarding malignant lymphoma and myeloma to investigate the relationships between clonal evoutions and disease status. The gene mutation analyses using NGS at the point of diagnosis and relapse or proceeding disease.

  Study JGAS000232

• Dataset of the sequenced and imputed genotypes

  Samples from 149 trios from the Saguenay-Lac-Saint-Jean asthma familial cohort were all sequenced using a custom capture panel developed by our group, followed by next-generation sequencing. This custom capture panel covers around 3% of the genome, including coding and non-coding immune regulatory regions. We inferred the sequence in the non-sequenced siblings who were part of the same families as the trios and we imputed the sequence using IMPUTE2 in the whole cohort.

  Dataset EGAD00001004268

• Refractory Cancer (RC) Program

  The Refractory Cancer (RC) Program will investigate the underlying genomic hallmarks involved in the observed inferior response to treatment of certain tumor types. Comprehensive genomic characterization will be performed utilizing the NCI CCG Genome Characterization Pipeline. Subsequent genomic data will be hosted at the NCI Genomic Data Commons (GDC) (https://portal.gdc.cancer.gov/).

  Study phs002097

• Genome-wide gene expression analysis following CRISPRi of transposable elements

  human induced pluripotent stem cells constitutely expressing the CRISPRi machinery were transduced with gRNAs targeting genomic regions of transposable elements (TEs), and differentiated to neural progenitor cells. The aim of the study was to annotate the function of these TEs in the context of early neurodevelopmental processes.

  Study EGAS00001008265

• 300-Obese: clinical cohort of obese individuals, Nijmegen, the Netherlands

  300-Obese cohort was recruited at the Radboud University Medical Center (RUMC), Nijmegen, the Netherlands. The cohort comprises 377 participants included by the following criteria: age>55 years, BMI>27 kg/m2. The cohort data includes gut microbiome, NMR serum metabolomics, deep cardiovascular phenotyping and broad range of phenotypic information.

  Study EGAS00001003508

• 112 "KOREAN" never-smoker female adenocarcinoma exome-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). 1 ug of genomic DNA was sheared to an average size of 150 bp by using the Covaris System. The libraries were prepared by using TruSeq DNA Sample Prep Kit (Illumina). The purified DNA library was hybridized with the SureSelect Human All Exon V3 probe set (Agilent Technologies) to capture 50 Mb of targeted exons following the manufacturer’s instructions. Exome capture was carried out using the Agilent SureSelect Human All Exon 50Mb Kit. The captured exome libraries were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols.

  Dataset EGAD00001005126

• Indonesian sea-nomads genomic history

  This study observes the origin of the last living sea nomad group in Indonesia using genome-wide SNP data, and tracks their dispersal in the archipelago. This study involves new samples on not only the sea nomad group, but also surrounding populations where the sea nomad settled. We revealed the scenario of their origin and unique admixture patterns during their dispersal and re-settlement.

  Study EGAS00001002246

• Platinum-based chemotherapy induces opposing effects on immunotherapy response-related spatial and stromal biomarkers in the bladder cancer microenvironment

  The goal of the current project was to investigate the modulation of the tumor-immune microenvironment (TME) by neo-adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer. Furthermore, we aimed to focus on how this modulation affects biomarkers of response to immune checkpoint inhibitors. Additionally, we aimed to explore the differences between MVAC and gemcitabine-containing platinum-based regimens regarding their effects on the bladder TME.

  Study EGAS50000000309

• Detection of maternal DNA contamination in the placenta

  We use whole-genome sequencing of monozygotic (and dizygotic) twins to detect somatic mutations to infer the cellular history of the twinning event. We recruited monozygotic twins with varying degrees of fetal membranes to compare the twinning events between theses subsets. We used blood, buccal epithelial cell, placenta, and umbilical cord to trace the embryonic somatic mutations. Using the somatic mutations from various tissues we infer the approximate timing of twinning in each monozygotic twin subtypes.

  Study EGAS00001006155

• Targeted exome sequencing identify compound heterozygous TYK2 mutations in patients with primary immunodeficiency who developed EBV-associated lymphoma

  In this study, we evaluated 2 siblings with primary immunodeficiency who developed EBV-associated lymphoma. Immunophenotyping of PBMCs revealed that both patients had significant T cell lymphopenia characterized by low na?ve CD4+ T cell counts. To identify the causative genetic mutations in the patients, we performed targeted exome sequencing using the Illumina MiSeq on the patients and their parents. The results showed a novel compound heterozygous mutations in the gene encoding tyrosine kinase 2 (TYK2) in the patients.

  Study JGAS000098