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• Research for genetic causes and mechanisms of Hirschsprung's or Hirschsprung's related diseases

  Hirschsprung's disease (HD) is an abdomen disorder which is caused by absence of enteric neurons. HD is a complex genetic disorder and several causing gene mutations have been identified including the receptor tyrosine kinase gene. However, the whole mechanism of HD remains unknown and additional genetic causalities are implicated. To further investigate the genetic causalities of HD, we conducted whole-exome sequencing of patients with HD and unaffected patient's families.

  Study JGAS000007

• Susceptibility loci for tanning ability in Japanese population identified by genome-wide association study

  We performed genome-wide association studies of Japanese Skin Type for Japanese individuals from a cohort study by the Tohoku Medical Megabank Project in order to identify variants related to tanning ability and skin pigmentation. We used imputed genotype data of 9,187 Japanese individuals, of which 4,475 individuals are from Miyagi prefecture and 4,712 individuals are from Iwate prefecture. Skin Type information was obtained from the questionnaire for cohort participants.

  Study JGAS000160

• OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients.

  The OTOF gene, encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing (MPS) to reveal the frequency and clinical characteristics of OTOF-related hearing loss in a large hearing loss population.

  Study JGAS000166

• TMM whole genome analysis of 4566 Japanese individuals

  Tohoku University Tohoku Medical Megabank Organization (ToMMo) and Iwate Tohoku Medical Megabank Organization (IMM) were founded to establish an advanced medical system to foster the reconstruction from the Great East Japan Earthquake. These organizations are developing a biobank that includes medical and genome information for supporting health and welfare in the Tohoku area. In the first stage, the part of our mission was to sequence the 4,000 individuals to construct Japanese whole-genome reference panel.

  Study JGAS000239

• Comprehensive biomarker analysis from phase II study of nivolumab in patients with thymic carcinoma

  In a phase II trial of nivolumab in advanced thymic carcinoma (UMIN000022007), long SD (SD for more than 24 weeks) was seen in three patients and irAE (Gr2 or higher) was seen in four patients among 15 patients. We conducted preplanned comprehensive biomarker analyses. We obtained whole blood for Immuno Pharmacogenomic analysis using PBMC DNA. Immuno-PGx analysis showed non-synonymous SNVs in ITGAX and PDCD1 had some correlation with PFS.

  Study JGAS000588

• An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

  We investigated the effects of different incubation temperatures and duration, and formalin scavenger (Tris) concentrations on the recovery of DNA from FFPE tissue sections. We optimized the conditions for preserving the integrity and maximizing the yield of DNA from FFPE tissue sections. Furthermore, DNA obtained using the optimized procedure was compared with that obtained using a commonly used extraction procedure with regard to their performance in whole-genome and targeted gene panel sequencing.

  Study JGAS000520

• Discovery of genetic factors associated with thiopurine-induced severe adverse events

  Despite NUDT15 variants showing significant association with thiopurine-induced adverse events (AEs) in Asians, it remains unclear whether additional genetic variants should be tested to predict AEs. To clarify it, we performed a genome-wide association study to discover additional variants associated with thiopurine-induced severe AEs, alopecia and leukopenia. GWASs of these AEs were performed with 1221 Japanese patients with inflammatory bowel disease using population-optimized genotyping array and imputation.

  Study JGAS000661

• Whole-exome sequencing of MDS and related myeloid neoplasms

  Myelodysplastic syndromes(MDS) and related myeloid neoplasms (myelodysplasia) are heterogenous group of myeloid neoplasms characterized by deregulated blood cell production with evidence of myeloid dysplasia. Previously, frequent mutations in genes on RNA splicing machinery and DNA methylation pathway have been identified. However, comprehensive analysis of genetic alterations have not performed on a large cohort of these diseases. Therefore, in this study, we performed whole-exome sequencing of MDS and related myeloid neoplasms.

  Study JGAS000023

• Genomic profiling identified ERCC2 helicase domain mutations respond to platinum-based neoadjuvant therapy in urothelial bladder cancer

  Genomic profiling of tumours enables therapeutic decisions, and identifying drug-matched mutations will prolong survival and prognosis. Here, we generated a custom panel for detecting genetic alterations in 19 patients with urothelial bladder cancer. This panel targeted 71 genes associated with urological cancer. Targeted sequencing was performed on formalin-fixed paraffin-embedded tumour tissues. In this study, we revealed genome profiles and actionable mutations in patients with urothelial bladder cancer.

  Study JGAS000241

• Predicting resistance to chemotherapy using chromosomal instability signatures

  The aim of this study is to assess whether three chromosomal instability signature biomarkers are capable of predicting resistance to standard chemotherapies, namely platins, taxanes and anthracyclines. As part of this study we compiled a proof of principle cohort of ovarian cancers treated with these therapies, profiled using the Illumina TSO500 panel. Analysis of these data demonstrated that accurate biomarker calling can be computed from these gene panel data.

  Study EGAS50000000992

• Integrated targeted deep sequencing reveals unique tissue-of-origin and donor cell-free DNA signatures in transplant recipients

  We have developed a targeted deep methylation sequencing assay that integrates cell-free DNA (cfDNA) tissue-of-origin analysis with donor-derived cfDNA quantification to non-invasively monitor transplant health. In this study, liver and kidney transplant recipients were assessed in conjunction with healthy controls to characterize the dynamic patterns of cfDNA release and clearance, and to identify distinct tissue injury signatures throughout the transplant journey.

  Study EGAS50000000987

• ResolveCRPS study - RNA-fragment sequencing from snap-frozen skin biopsies

  Complex Regional Pain Syndrome (CRPS) is a disabling pain disorder with unclear cutaneous molecular mechanisms. To identify gene-expression signatures linked to pain intensity and disease progression, we profiled the local transcriptome of CRPS-affected skin. 42 patients agreed to skin biopsies from the CRPS-affected area, which underwent low-input total RNA-seq. Full experimental and bioinformatics protocols are provided in the associated publication and its supplementary material.

  Study EGAS50000001061

• Efficacy of dual KRAS G12D–EGFR blockade versus triple combinations in patient-derived models of KRAS G12D-mutant colorectal cancer

  RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to characterize the transcriptional landscape of KRAS-mutant mCRC cells in response to therapeutic strategies targeting the EGFR and KRAS signaling pathways. Transcriptomic profiling was conducted following drug treatments to investigate molecular changes associated with single and combination therapies. A total of 24 samples were analyzed.

  Study EGAS50000001700

• Breast Cancer Follow Up Series

  This study's purpose is to use data generated in whole genome and exome Breast Cancer sequencing to target specific areas in multiple other Breast Cancer samples. These areas will then be subjected to PCR in multiple cases, tagged and then pool the resultant amplicons. These amplicons will then be sequenced on the Illumina GAII. This is hoped to show the prevalence of previous findings in multiple individuals in a high throughput method.

  Study EGAS00001000002

• Single cell long read whole genome sequencing reveals somatic transposon activity in human brain

  The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover novel dynamics in three brains utilizing single cell long-read sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements.

  Study EGAS50000001156

• Illumina Human Exome (ExomeChip) genotype data from the Pomak villages in Greece (HELIC Pomak Isolate). 1040 samples all >=16 years old.

  Isolated populations can empower the identification of rare variation associated with complex traits through next generation association studies. Here we have genotyped individuals from a Greek population isolate on the Illumina HumanExome Beadchip. The HELIC (Hellenic Isolated Cohorts) Pomak collection focuses on the Pomak villages in Greece. Recruitment of this population-based sample was primarily carried out at the village medical centres. www.helic.org

  Study EGAS00001000658

• The origin of post-transplant clonal hematopoiesis can be traced to prenatal development.

  Clonal hematopoiesis (CH), a prevalent and premalignant state in the elderly, can occur in young individuals under selective pressures such as hematopoietic cell transplantation (HCT). However, the origin of CH and mutational processes underlying CH driver mutations in young individuals remain unclear. Here, we used genome-wide somatic mutation profiles to retrospectively trace the origin of DNMT3A-mutant CH in three individuals, 14-41 years after childhood HCT.

  Study EGAS50000000919

• Genomic landscape of poorly differentiated thyroid carcinoma

  Poorly differentiated thyroid carcinoma (PDTC) is a rare and aggressive subtype of thyroid cancer with limited molecular characterization. This study aims to define the somatic mutational landscape of PDTC using whole-genome sequencing. Paired tumour and matched normal blood samples were collected from six patients undergoing surgery. The overarching goal is to identify recurrent mutations, structural variants, and other genomic alterations associated with tumour aggressiveness and poor clinical outcomes.

  Study EGAS50000001134

• IMMUcan Lung NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001558

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells, peritoneal fluid, and peritoneal metastases from patients with colorectal cancer

  The data published here contains single-cell RNA- sequencing (scRNAseq) on peripheral blood mononuclear cells (PBMC), peritoneal fluid (PF), and peritoneal metastases (PM). PBMC, PF and, where possible, PM was acquired from patients with colorectal cancer (CRC) and subjected to 3' scRNAseq using the 10X Genomics (Chromium Single Cell 3’ Reagent). Sequencing was performed in a paired-ended fashion on either the HiSeq4000 or the NovaSeq6000.

  Study EGAS50000000173

• Single-cell RNA-sequencing and cellular indexing of transcriptomes and epitopes of peripheral blood mononuclear cells and peritoneal fluid from patients with achalasia

  The data published here contains cellular indexing of transcriptomes and epitopes (CITE-seq) and single-cell RNA- sequencing (scRNAseq) data on patients with achalasia. Paired PBMC and PF were subjected to 3' scRNAseq and CITE-seq, respectively. All single-cell data was generated using the 10X Genomics (Chromium Single Cell 3’ Reagent) and sequenced in a paired-ended fashion on the NovaSeq6000.

  Study EGAS50000000174

• Genomic Profile of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Multiple spiradenomas and spiradenocarcinoma from a single donor were subjected to exome sequencing. Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue, and genomic DNA was extracted. The DNA samples were subjected to library generation using the xGen ssDNA & Low-Input DNA Library Preparation Kit, followed by exome capture using the xGen Exome Research Panel v2. The libraries were sequenced on DNBSEQ G400RS. Reads were aligned to GRCh37 with BWA.

  Study EGAS50000000554

• Characterisation of Cyr61-enriched myeloid angiogenic cells

  We previously demonstrated the enrichment of an angiogenic precursor cell population from peripheral blood mononuclear cells by CYR61, a protein of the CCN family. In vivo, CYR61 mediates the binding of leukocytes and particular monocyte populations at sites of vascular inflammation. Here, we present an in vitro enrichment system mimicking (patho)physiology and at the same time representing an effective tool for enrichment of the CYR61-binding blood cells and analyzed this cell population in depth.

  Study EGAS50000000533

• Genomic profiling of fragile X syndrome unmethylated full mutation carriers

  Whole genome sequencing of two unrelated FMR1 unmethylated full mutation carriers. The existence of rare, unmethylated full mutation carriers who carry the mutation that causes fragile X syndrome but do not gain methylation at the locus offers a rare opportunity to study the mechanisms underlying fragile X syndrome. This study aims to investigate the genomic variants in these individuals alongside transcriptomic data to elucidate underlying genomic variants behind transcriptomic differences observed in UFM individuals.

  Study EGAS50000000648

• MOSAIC - Multi-Omics Spatial Atlas In Cancer

  MOSAIC is a collaborative initiative founded by Owkin, Lausanne University Hospital (CHUV), Charité Universitätsmedizin Berlin, University Hospital Erlangen (UKER), Gustave Roussy Institute in Paris, and University of Pittsburgh. The goal of MOSAIC is to build the largest collection of spatial omics data in cancer. By integrating comprehensive high quality clinical annotations with advanced deep profiling techniques, MOSAIC aims to uncover novel cancer subtypes and identify key drug targets and biomarkers within them.

  Study EGAS50000000689