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• Whole Exome sequencing of colorectal cancer patients (SG-BULK)

  The study was approved by the institutional review board of Singhealth (2018-2795). Ten 5-µm tissue sections were cut using standard microtomy techniques. Each collected cell population was then extracted using the allprep kit. Extracted material was then quantified using a Qubit fluorometer. DNA-seq libraries were captured to exome regions using xGen Exome Research Panel v1.0 (IDT), and libraries were prepared using the KAPA Hyper prep kit. DNA libraries were sequenced to a target depth of ×200 for tumor sample, ×100 for normal samples on the Illumina HiSeq platform.

  Study EGAS00001006006

• Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in cancer patients

  The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient’s immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry and RNA-seq to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types, and gene expression profiles.

  Study EGAS50000000286

• DNA Repair Capacity for Lung Disease Risk Assessment

  A focus of this work was to address the extent to which susceptibility for lung cancer varies by gene-environment-phenotype interactions involving DNA repair capacity and differences in risk from environmental stressors. GWAS from a subset of subjects from the Lovelace Smokers Cohort and New Mexico Lung Cancer cohort were used to derive polygenic risk scores for DNA repair pathways (nucleotide excision, base excision, single strand break, non-homologous, homologous recombination). Logistic regression analysis was used to examine the association between polygenic risk score and lung cancer status. Polygenic risk scores were grouped by quartiles. Only diminished base excision repair was associated with increased risk for lung cancer at the 25-50% quartile and approached significance at the 50-75% quartile.

  Study phs004063

• Next-generation molecular analysis of surgical margins in oral squamous cell carcinoma for assessment of microscopic residual disease and personalized postoperative treatment decision

  Background : Patients operated for an early oral squamous cell carcinoma (OSCC) with clear margins have a 5-year local relapse rate of around 15%. Assessing the microscopic residual disease (MRD) remains a challenge. In a phase II prospective trial, we evaluated the tetranucleotide microsatellite instability markers in the surgical margins in T1-T2 OSCC resected with pathologically clear margins. Goal : Detect MRD in surgical margins and adapt the postoperative decision-making Details : Whole exome sequencing (WES) on early oral squamous cell carcinoma (OSCC) with clear margins, and on resection margins, 86 patients with a median follow-up of 58 months (range 30.4-83 months)

  Study EGAS50000000823

• Evolution of a FLT3-TKD mutated subclone at meningeal relapse in acute promyelocytic leukemia (H021)

  Here we report the case of an acute promyelocytic leukemia (APL) patient who, though negative for FLT3 mutations at diagnosis, developed isolated FLT3-TKD positive meningeal relapse, which, in retrospect, could be traced back to a minute bone marrow subclone present at first diagnosis. Initially, the 48-year old female diagnosed with high-risk APL had achieved complete molecular remission after standard treatment with all-trans retinoic acid (ATRA) and chemotherapy according to the AIDA protocol. 13 months after start of ATRA maintenance the patient suffered clinically overt meningeal relapse along with minute molecular traces of PML/RARA in the bone marrow. Following treatment with arsenic trioxide (ATO) and ATRA in combination with intrathecal cytarabine and methotrexate, the patient achieved a complete molecular remission in both cerebrospinal fluid (CSF) and bone marrow, which currently lasts for two years after completion of therapy. Whole exome sequencing and subsequent ultradeep targeted re-sequencing revealed a heterozygous FLT3-TKD mutation in CSF leukemic cells (p.D835Y, c.2503G>T, 1000/1961 reads (51%)), which was undetectable in the concurrent bone marrow sample. Interestingly, the FLT3-TKD mutated meningeal clone originated from a small bone marrow subclone present in a variant allele frequency of 0.4% (6/1553 reads) at initial diagnosis. This case highlights the concept of clonal evolution with a subclone harboring an additional mutation being selected as the “fittest” and leading to meningeal relapse. It also further supports earlier suggestions that FLT3 mutations may play a role for migration and clonal expansion in the CSF sanctuary site.H021

  Study EGAS00001001848

• Large Cancer Fingerprint Screening for Detection of Minimal Residual Disease.

  We describe an approach for large cancer fingerprint screening and its application to cell-free DNA from patients with cancer. Our approach involves tracking somatic mutations identified from patients' tumor biopsies, in the cell-free DNA from a blood draw.

  Study phs001977

• NCI's Collection of Datasets for Health, Medical, and Biomedical Research Purposes

  This collection provides access to NCI's collections of datasets for the purpose of performing health, medical, or biomedical (HMB) research. This collection would not support ancestry lineage research not related to a specific medical or health conditions.

  Study phs003044

• Division of Cancer Epidemiology and Genetics (DCEG) Imputation Reference Dataset

  We have built a new resource for imputation of SNPs for existing and future genome-wide association studies (GWAS), known as the Division of Cancer Epidemiology and Genetics (DCEG) Reference Set. The first build of the data set includes 728 cancer-free individuals of European descent from three large prospectively sampled studies, 98 African-American individuals from the Prostate, Lung, Colon, and Ovary Cancer Screening Trial (PLCO), 74 Chinese individuals from a Chinese clinical trial in Shanxi, China (SHNX), and 349 unrelated individuals from the HapMap Project (see Molecular Data Section for details on arrays used). The final harmonized dataset includes 2.8 million autosomal polymorphic SNPs on 1,249 subjects after rigorous quality control metrics were applied.

  Study phs000396

• MYOSEQ project

  The MYOSEQ project focuses on the application of next generation sequencing, in particular whole exome sequencing (WES), in a large cohort of patients with unexplained limb‐girdle weakness (LGW). Focusing on undiagnosed patients with a clearly defined clinical phenotype enables increased diagnostic rates for known genes (in particular Pompe disease, GNE related pathologies and other known LGMD subtypes) in this cohort, while the use of WES provides scope both for new gene discovery and for additional research into disease modifiers and genotype‐phenotype correlation with substantial cost effectiveness. The LGW patient cohort was collated by Newcastle University in collaboration with clinical centers across Europe. The sequencing was performed at the Broad Institute and jointly analyzed with Newcastle University.

  Study EGAS00001002069

• Single cell transcriptional evolution of myeloid leukaemia of Down syndrome – scRNA

  Abstract: Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), and via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from a rich collection of primary patient samples through single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We distilled the transcriptional consequence of each genetic step in the evolution of ML-DS, showing that TAM-defining GATA1 mutations account for most of the ML-DS transcriptome, including those of progressive disease. This transcriptional backbone may thus represent a common vulnerability in ML-DS. We extracted the transcriptional difference between TAM and ML-DS which, unexpectedly, reflected features shared across childhood leukaemia. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations directly from patient samples.

  Dataset EGAD00001015452

• RNA sequencing of a glioblastoma PDX cohort

  Patient-derived xenograft (PDX) models represent an essential tool for the preclinical evaluation of novel targeted therapies and their combinations. In this project, we molecularly characterized a comprehensive panel of glioma PDX models with well conserved molecular and pathological features over multiple passages. PDX samples were subjected to next generation sequencing (NGS). Characterization of cancer-relevant features including driver mutations or cellular processes was performed using mutational and gene expression data in order to identify potential biomarker or treatment targets in glioblastoma. In summary, we reported a newly established and molecularly characterized panel of glioma PDX models with high relevance for translational preclinical research.

  Study EGAS00001007119

• Ultra-Low-Pass Whole Genome Sequencing of Cell-Free DNA for Large B-Cell Lymphoma

  While deep targeted DNA sequencing of liquid biopsies has shown prognostic utility in large B-cell lymphoma (LBCL), the routine clinical adoption of these assays remains limited due to their high costs. Here, leveraging a well-annotated cohort of encompassing both frontline and relapsed/refractory (R/R) LBCL, we profiled patient plasma samples with two complementary modalities – ultra-low-pass whole genome sequencing (ulpWGS) and deep targeted DNA sequencing, the former being a cost-effective method to profile large scale chromosomal abnormalities and estimate tumor burden. Our findings revealed a strong association of high cell-free tumor burden by both genomic profiling modalities with established measures of tumor burden and patient survival. Notably, the associations with survival remained statistically significant after accounting for international prognostic index scoring. Furthermore, we showed that del(17p) in circulating tumor DNA as detected by ulpWGS was strongly associated with TP53 mutation status and predicted for significantly inferior patient outcome in frontline but not R/R LBCL patients. Our study demonstrates that ulpWGS can provide robust prognostic biomarkers for both frontline and R/R LBCL, highlighting its broad applicability for risk stratification.

  Study EGAS50000001027

• Methotrexate Clearance GWAS in Acute Lymphoblastic Leukemia (ALL) Patients

  We estimated the plasma clearance of methotrexate from 1279 acute lymphoblastic leukemia (ALL) patients treated on the Children Oncology Group 9904 and 9905 trials (http://clinicaltrials.gov/show/NCT00005585 and http://clinicaltrials.gov/show/NCT00005596). Patients received either a 24-hour infusion of a 1 g/m2 dose or 4-hour infusion of a 2 g/m2 dose). Methotrexate clearance was lower in older children (p=7 x 10-7), females (p=2.7 x 10-4), and patients who received a delayed intensification phase (p=0.0022). In a genome-wide analysis, methotrexate clearance was associated with polymorphisms in the SLCO1B1 gene (p=2.1 x 10-11), which encodes for an organic anion transporter. This replicates findings using different schedules of high-dose methotrexate in ALL patients treated on St. Jude protocols. A combined meta-analysis yields a p-value of 5.7 x 10-19 for the association of methotrexate clearance with SLCO1B1 SNP rs4149056 (Trevino et al, PMID 19901119 and Ramsey et al, PMID 23233662). This data set includes the dependent variable of methotrexate clearance and all of the SNP data available from arrays.

  Study phs000637

• Prediction of Trastuzumab Benefit in Adjuvant Breast Cancer: Gene Expression Profiling in NSABP B31

  Background National Surgical Adjuvant Breast and Bowel Project (NSABP) trial B-31 suggested the efficacy of adjuvant trastuzumab, even in HER2-negative breast cancer. This finding prompted us to develop a predictive model for degree of benefit from trastuzumab using archived tumor blocks from B-31. Methods Case subjects with tumor blocks were randomly divided into discovery (n = 588) and confirmation cohorts (n = 991). A predictive model was built from the discovery cohort through gene expression profiling of 462 genes with nCounter assay. A predefined cut point for the predictive model was tested in the confirmation cohort. Gene-by-treatment interaction was tested with Cox models, and correlations between variables were assessed with Spearman correlation. Principal component analysis was performed on the final set of selected genes. All statistical tests were two-sided. Results Eight predictive genes associated with HER2 (ERBB2, c17orf37, GRB7) or ER (ESR1, NAT1, GATA3, CA12, IGF1R) were selected for model building. Three-dimensional subset treatment effect pattern plot using two principal components of these genes was used to identify a subset with no benefit from trastuzumab, characterized by intermediate-level ERBB2 and high-level ESR1 mRNA expression. In the confirmation set, the predefined cut points for this model classified patients into three subsets with differential benefit from trastuzumab with hazard ratios of 1.58 (95% confidence interval [CI] = 0.67 to 3.69; P = .29; n = 100), 0.60 (95% CI = 0.41 to 0.89; P = .01; n = 449), and 0.28 (95% CI = 0.20 to 0.41; P < .001; n = 442; P interaction between the model and trastuzumab < .001). Conclusions We developed a gene expression-based predictive model for degree of benefit from trastuzumab and demostrated that HER2-negative tumors belong to the moderate benefit group, thus providing justification for testing trastuzumab in HER2-negative patients (NSABP B-47). ** Reprinted from J Natl Cancer Inst;2013;105:1782-1788 with permission from Oxford University Press.

  Study phs000826

• Evolution of Core Archetypal Phenotypes in High-Grade Serous Ovarian Cancer (HGSOC)

  The evolution of resistance in high-grade serous ovarian cancer (HGSOC) cells in response to chemotherapy is only partially understood. To uncover phenotypic changes associated with chemotherapy resistance, we performed single-cell RNA-sequencing (scRNA-seq) or whole-genome sequencing of 23 total patients, with longitudinal samples collected from 9, treatment-naïve samples from 8 patients, and post-treatment samples from 6 patients. Our study revealed that the HGSOC transcriptome could be described using three core archetypal phenotypes, defined as oncogenic tasks that describe majority of the transcriptional data. We implemented a multi-task learning approach to identify the biological tasks of each archetype and identified metabolism and proliferation, cellular defense response, and DNA repair signaling. The “metabolism and proliferation” archetype evolved during treatment and was enriched in cancer cells from patients that received multiple-lines of treatment and had elevated tumor burden indicated by CA-125 levels. The emergence of archetypes was not consistently linked to specific whole-genome driver mutations. However, archetypes were closely associated with sub-clonal clusters at the single-cell level, indicating that cancer cell sub-populations specialize in particular biological tasks. Our study reveals a defining principle of ovarian tumor evolution using temporal scRNA-seq profiles, identifies the key phenotypic features across patients and links metabolic shifts with a response to chemotherapy.

  Study phs002294

• PD-L1 blockade immunotherapy rewires cancer-induced emergency myelopoiesis

  Introduction Immune checkpoint blockade (ICB) immunotherapy has revolutionized cancer treatment, demonstrating exceptional clinical responses in a wide range of cancers. Despite the success, a significant proportion of patients still fail to respond, highlighting the existence of unappreciated mechanisms of immunotherapy resistance. Delineating such mechanisms is paramount to minimize immunotherapy failures and optimize the clinical benefit. Methods In this study, we treated tumour-bearing mice with PD-L1 blockage antibody (aPD-L1) immunotherapy, to investigate its effects on cancer-induced emergency myelopoiesis, focusing on bone marrow HSPCs. We examined the impact of aPD-L1 treatment on HSPC quiescence, proliferation, transcriptomic profile, and functionality. Results Herein, we reveal that aPD-L1 in tumour-bearing mice targets the hematopoietic stem and progenitor cells (HSPCs) in the bone marrow (ΒΜ), mediating their exit from quiescence and promoting their proliferation. Notably, disruption of the PDL1/PD1 axis induces transcriptomic reprogramming in HSPCs, observed in both individuals with Hodgkin lymphoma (HL) and tumour-bearing mice, shifting towards an inflammatory state. Furthermore, HSPCs from aPDL1-treated mice demonstrated resistance to cancer-induced emergency myelopoiesis, evidenced by a lower generation of MDSCs compared to control-treated mice. Discussion: Our findings shed light on unrecognized mechanisms of action of ICB immunotherapy in cancer, which involves targeting of BM-driven HSPCs and reprogramming of cancer-induced emergency myelopoiesis.

  Study EGAS00001007873

• Exome sequencing of patient samples from study

  Exome sequencing data from FFPE preserved patient samples and patient-derived cultures. The goal of the study is to validate patient-derived cultures. Additional goal is to understand the relationship between omics and drug response.

  Study EGAS50000000171

• Whole transcriptome seq from patient samples

  Exome sequencing data from FFPE preserved patient samples and patient-derived cultures. The goal of the study is to validate patient-derived cultures. Additional goal is to understand the relationship between omics and drug response.

  Study EGAS50000000172

• minION fastq files of 10 different tumor samples from the Master program (H021)

  Nanopore RNA Sequencing was done for 10 tumor samples. Direct cDNA sequencing was performed using the SQK-DCS109 kit (Oxford Nanopore Technologies). For analysis of a single sample on a MinION flow cell (version R9.4.1), 5 μg RNA was used as input. For multiplexing on a MinION flow cell, 2.5 μg RNA per sample was used as input, and the native barcoding expansion kit EXP-NBD104 was employed in conjunction with SQK-DCS109. After reverse transcription with Maxima H Minus Reverse Transcriptase (Thermo Scientific), second-strand synthesis was performed using the 2x LongAmp Taq Master Mix (New England Biolabs). The resulting double-stranded cDNA was subjected to end-repair and dA-tailing using the NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs). For multiplexed libraries, this step was followed by barcode ligation and library pooling. Next, libraries were quantified with a Qubit Fluorometer 3.0 (Life Technologies). Finally, sequencing adapters were added to the library preparations and ligated with Blunt/TA Ligase Master Mix (New England Biolabs), followed by further quality control using a Qubit. Samples ACC1 and ACC2 were analyzed on individual MinION flow cells, while the remaining eight samples were sequenced as multiplexed libraries on two MinION flow cells by pooling four samples for each run. Five ACC samples were also analyzed individually on Flongle flow cells

  Dataset EGAD00001008970

• Tam-Seq of HGSOC samples for fixative comparison study

  Targeted amplicon sequencing of samples as part of the study "Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples. The amplicon panel consists of 48 amplicons in TP53, PTEN, EGFR, PIK3CA, KRAS and BRAF genes as described previously [Forshew, STM 2012]. All libraries were pooled and quantify using DNA 1000 kit on Agilent 2100 Bioanalyzer and KAPA SYBR FAST ABI Prism qPCR Kit (KAPA Biosystems) on 7900HT Fast Real-Time PCR System (Applied Biosystems) according to the supplier's recommendations. Reads were aligned using bwa-mem v0.7.12-r1039 to the 1000 genomes version of human genome build GRCh37, retaining duplicate reads.

  Dataset EGAD00001001937

• COMPARE study: participants typed during UK Biobank version 2 array development phase

  The COMPARE study enrolled 29,066 British blood between donors between February 2016 and March 2017, the study aim is to find the optimum technology for haemoglobin screening (ISRCTN 90871183). All participants were at the time of recruitment active blood donors. The 4,796 participants in this dataset have consented to join the NIHR BioResource. Genotyping data was produced using the Thermo Fisher Scientific Axiom Genotyping platform. The UK Biobank version 2 array design was used, content on this array has been added to allow for accurate DNA based identification of human blood group antigens.

  Dataset EGAD00001005023

• Transcriptomics for IMMU-SCCHN1 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 confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.

  Dataset EGAD50000002206

• Targeted Validation Samples

  The dataset consists of targeted sequencing data obtained from an independent cohort of 11 patients to validate discriminative DMRs (differentially methylated regions) for Acute coronary syndrome (ACS) subtypes. The cohort includes 2 healthy subjects, 4 STEMI (ST-segment elevation myocardial infarction), 3 NSTEMI (non-ST-segment elevation myocardial infarction), and 2 UA (unstable angina) patients. The sequencing panel targeted 18,831 CpGs for analysis, reaching at least 5 reads coverage for 75% of the targeted CpGs in each sample. The sequencing was performed using the NEBNext Enzymatic Methyl-seq Module and the Nonacus Cell3TMTarget: Library Preparation kit, followed by probe hybridization, capture enrichment, and sequencing on the Novaseq 6000 platform, generating 400 million reads. The dataset is in raw fastq format.

  Dataset EGAD00001010934

• Genomic Data of Pediatric MDS

  The dataset consists of - 126 whole exome sequencings (SAMD9/9Lmut: 64; GATA2mut 24, MDS wildtype 38/471) performed using SureSelect Human All Exon V6 enrichment (Agilent, cat# 5190-8863). The generated libraries were sequenced on the Illumina Hiseq 2500 with 150bp paired-end reads. FASTQ files were processed using SeqNext platform (JSI medical system, Germany), with gene-based alignment to a virtual panel of 300 genes (including 28 MDS-associated genes, SAMD9, and SAMD9L), consisting of genes relevant to bone marrow failure, MDS predisposition, and hematological cancers as per the Pan-Cancer studies with cohorts of >10,000 cancers. The respective BAM files are provided. - Custom panel targeting SAMD9, SAMD9L, and 22 single nucleotide polymorphisms (SNP) on chromosome 7q (allele frequency >35% in all ethnic sub-populations in gnomAD) (Ampliseq #IAD104171) were performed in 666/669 cases. And Custom panel targeting 28 MDS-associated genes (GATA2, RUNX1, HOXA9, CEBPA, GATA1, KRAS, NRAS, CBL, PTPN11, ASXL1, EZH2, SETBP1, FLT3, KIT, JAK2, JAK3, CSF3R, MPL, SH2, BCOR, BCORL1; RAD21, STAG2, CTCF, TP53, PTEN, CALR, VPS45) was performed in 544 cases (Ampliseq #IAD51150). Both custom panel libraries were prepared using NEBNext Ultra II DNA library prep kit (New England BioLabs, cat#E7645S/L) per manufacturer’s instruction and samples were sequenced on an Illumina Miseq 2000 with 2 x 150 bp reads. The respective BAM files are provided - 4 SAMD9/9L patients were subjected to MissionBio custom single-cell panel (CO-112) targeting 250 heterozygous gnomAD population polymorphisms on 7q arm and 69 amplicons in SAMD9/9L and other cancer genes. All libraries were sequenced on an Illumina NovaSeq6000 with 150 base-paired ending multiplexed runs. Fastq files were processed using the Tapestri Pipeline V2 and python-based Mosaic package (multi-omics analysis, data visualization). The derived BAM and loom files are provided.

  Dataset EGAD00001007856

• Somatic mutations of non-malignant T cells

  Somatic mutations in T cells can cause cancer but also have implications for immunological diseases and cell therapies. The mutation spectrum in non-malignant T cells is unclear. Here, we examined somatic mutations in CD4+ and CD8+ T cells from 90 patients with hematological and immunological disorders and used T cell receptor (TCR) and single-cell sequencing to link mutations with T cell expansions and phenotypes. CD8+ cells had higher mutation burden than CD4+ cells. Notably, the biggest variant allele frequency (VAF) of non-synonymous variants was higher than synonymous variants in CD8+ T cells, indicating non-random occurrence. The non-synonymous VAF in CD8+ T cells strongly correlated with the TCR frequency, but not age. We identified mutations in pathways essential for T cell function and often affected in lymphoid neoplasia. Single-cell sequencing revealed cytotoxic Temra phenotypes of mutated T cells. Our findings suggest that somatic mutations contribute to CD8+ T cell expansions without malignant transformation.

  Study EGAS50000000237

• SSBP1 sample

  The dataset includes exome sequencing results for a patient with SSBP1 mutations that cause a complex optic atrophy spectrum disorder

  Dataset EGAD00001005475

• Sequencing_of_patient_samples_who_received_immune_checkpoint_inhibition___WES___NKI

  DNA and RNA isolated from FFPE blocks of patients who received immune checkpoint inhibition (ICI) are sequenced with the aim to identify therapeutically tractable vulnerabilities in tumors to prevent ICI resistance.

  Study EGAS00001003154

• COLORS_in_IBD__Whole_exome_sequencing_of_early_onset_IBD_patients

  Exome sequence analysis of individuals with severe early onset inflammatory bowel disease, and their families. Individuals are ascertained through the COLORS in IBD study, which includes centres throughout UK and Europe.

  Study EGAS00001000513

• IMSGC and MultipleMS project MS patients from Norway

  Genotype and phenotype data on 575 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002485

• IMSGC and MultipleMS project MS patients from Greece

  Genotype and phenotype data on 140 MS patients from Greece. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002493

• IMSGC and MultipleMS project MS patients from Spain

  Genotype and phenotype data on 151 MS patients from Spain. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002492

• IMSGC and MultipleMS project MS patients from UK

  Genotype and phenotype data on 943 MS patients from UK. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002491

• IMSGC and MultipleMS project MS patients from Netherlands

  Genotype and phenotype data on 209 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002488

• IMSGC and MultipleMS project MS patients from Austria

  Genotype and phenotype data on 246 MS patients from Austria. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002487

• Dataset of whole-exome sequencing of intravascular large B-cell lymphoma

  This dataset includes 44 bam files derived of 21 patients with IVL. Tumor samples are derived from cfDNA (n = 18), PDX (n = 4) and bone marrow (n = 2). Normal samples are derived from peripheral blood.

  Dataset EGAD00001005445

• Comprehensive survey for the construction of an integrated database of food, gut microbiome, and health information (the "Sukoyaka Health Survey") A data collection study exploring the relationship between the gut microbiome, food, health, and the genome.

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 51 healthy Japanese. We analyzed some participants living in Nagahama. The SNP array (Japonica Array v2) was used for genotyping. Shotgun metagenomic sequencing of fecal microbiome were analyzed.

  Study JGAS000680

• M116 Proteome Extracellular Vesicle Profiling

  For extracellular vesicles (ECV) extraction from plasma, 1M ammonium acetate was added to precipitate ECVs on ice for 45 min. Then, 100 mM ammonium acetate was added to the mixture, and ECVs were precipitated by centrifugation at 20,000g for 30 min. ECVs were washed with 50 mM ammonium bicarbonate (Sigma-Aldrich, Cat. 1066-33-7). Then, 600 µl of 1% ammonium deoxycholate (Sigma Aldrich, Cat. K2755-1MG) were added. The concentration of protein in each sample was measured using a bicinchoninic acid assay (BCA assay). Ammonium bicarbonate was used to dilute 500 µg of protein into a final volume of 500 µl. Next, dithiothreitol (Sigma-Aldrich, Cat. D9779) was added to obtain a final concentration of 20 mM, followed by iodoacetamide (Sigma-Aldrich, Cat. I6125) to a final concentration of 40 mM. Next, trypsin (Roche, Cat. RTRYP-RO) was added to the sample in a 1:25 protein ratio and incubated at 37°C overnight. Next day, formic acid (ThermoFisher Scientific, Cat. 28905) in a final concentration of 0.1% was added and extraction of proteins was done using Empore™ Solid Phase Extraction Cartridges (3M), following manufacturer’s instructions. The eluted samples were then centrifuged for 90 min. using a speed vacuum centrifuge (Thermo, RC1010), followed by snap freezing in liquid nitrogen. Then, the samples were kept in a freeze dryer (LyoDry Compact Benchtop, MechaTech) overnight. Next, the samples were reconstituted in 30 µl of 0.1% formic acid (FA) and an o-Phthaladehyde (Oparil) assay was performed to determine the concentration of each sample. After that, the sample was prepared in a concentration of 0.5 µg/µl using 0.1% FA and alcohol dehydrogenase (ADH). The samples were prepared in glass mass spectrometry vials for proteomic analysis using a Waters Synapt G2Si High-Definition Mass Spectrometry (Waters Corporation) operated by the MassLynx 4.1., 110 min. running time with 2 µl of an injection containing 1 µg of peptide. Quality controls were also run along with samples to guarantee consistency. Pooled quality controls were made from all samples, in which the samples were run at the beginning, middle and end of the mass spectrometry run. Samples were randomized before running the experiment. The proteomic data was then imported into Progenesis software 4.2 (Nonlinear Dynamic, UK) to identify and quantify peptides and proteins.

  Dataset EGAD50000001679

• Characterization of Autosomal CNV Among the Negrito from Peninsular Malaysia

  Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However the CNV data from diverse populations is rather limited. Here we report the first investigation of copy number variation (CNV) in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 62 putative novel CNVs, consisting of 25 gains and 37 losses. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), as well as the metabolic pathways (GO:0001852). Copy number gains in CNVRs enriched with genes were significantly higher than the losses (P value <0.001). Therefore, in view of the small population size, relative isolation and semi-normadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.

  Study phs000664

• Linking the epigenetic landscape in chronic lymphocytic leukemia to deregulated chromatin networks

  Aberrant chromatin features and epigenetic signaling emerge as an important part of the tumor disease state in chronic lymphocytic leukemia (CLL). However, an integrative analysis of the malignant chromatin landscape is currently missing. Here, we mapped DNA-methylation, nucleosome position, 7 histone modifications, ATAC-seq and the transcriptome in primary CD19+ sorted B-cells from the peripheral blood of CLL patients in comparison to non-malignant lymphocytes of healthy donor reference samples. On the > 50 kb scale we identified global differences with respect to DNA methylation, nucleosome positioning and histone modifications in CLL. Furthermore, a chromatin state annotation was developed to identify deregulated chromatin features of promoters and enhancers in CLL. By integrating these findings with an ATAC-seq based transcription factor binding analysis we identified a set of promoters and enhancers specific to CLL that were enriched in certain transcription factors binding motifs and genes of the BCR signaling pathway. Thus, our study provides an in-depth map of the CLL chromatin landscape and links chromatin state changes at promoters and enhancers to deregulated pathways.

  Study EGAS00001002518

• Predictive impact of rare genomic copy number variations in siblings of individuals with autism spectrum disorders

  Identification of genetic biomarkers associated with autism spectrum disorders (ASDs) could improve recurrence prediction for families with a child with ASD. Here, we describe clinical microarray findings for 253 longitudinally phenotyped ASD families from the Baby Siblings Research Consortium (BSRC), encompassing 288 infant siblings. By age 3, 103 siblings (35.8%) were diagnosed with ASD and 54 (18.8%) were developing atypically. Thirteen siblings have copy number variants (CNVs) involving ASD-relevant genes: 6 with ASD, 5 atypically developing, and 2 typically developing. Within these families, an ASD-related CNV in a sibling has a positive predictive value (PPV) for ASD or atypical development of 0.83; the Simons Simplex Collection of ASD families shows similar PPVs. Polygenic risk analyses suggest that common genetic variants may also contribute to ASD. CNV findings would have been pre-symptomatically predictive of ASD or atypical development in 11 (7%) of the 157 BSRC siblings who were eventually diagnosed clinically.

  Study phs001876

• Memorial Sloan Kettering (MSKCC) Single Cell Mutational Profiling in Myeloid Malignancies

  Myeloid malignancies have previously been characterized by large scale bulk molecular profiling studies on patient samples. These studies, while clinically informative, are unable to delineate mutation order as well as clonal architecture and complexity. To investigate the clonal framework of myeloid malignancies, the Single Cell Mutational Profiling in Myeloid Malignancies study was designed. This study performed sequencing of 148 samples from 117 adult patients diagnosed with clonal hematopoiesis (n = 21), myeloproliferative neoplasms (MPN; n = 14), and acute myeloid leukemia (AML; n = 82) between 20 and 87 years of age. Sequencing of all samples was performed using the Tapestri single cell DNA sequencing platform from Mission Bio, Inc. The platform utilizes a custom amplicon panel covering 109 amplicons across 31 genes frequently mutated in myeloid malignancies (CH, MPN, AML). Using the single cell DNA sequencing data, we were capable of elucidating clonal architecture and clonal complexity in each sample. In a subset of samples, we also performed simultaneous single cell DNA sequencing and cell surface protein expression analysis using the Tapestri DNA + Protein platform. This study allowed us to determine the expression of 7 cell surface proteins (CD3, CD11b, CD19, CD34, CD38, CD45RA, and CD90) at single cell resolution. We performed DNA+ Protein sequencing on samples from CH patients (n = 7) as well as AML patients (n = 17).

  Study phs002049

• Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

  The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

  Study JGAS000240

• SG Peranakan Project: Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia

  The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ~300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ~5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ~1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ~190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.

  Study EGAS00001005379

• SMRT-seq

  In this study, we enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model.

  Dataset EGAD00001006875

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy iPSCs

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of induced pluripotent stem cells (iPSCs) derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and two patients carrying pathogenic variants in EHMT2 (P1 and P2). Poly(A)-selected RNA was used for library preparation, and strand-specific libraries were generated for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002344

• RNA-Seq data from study: Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  The ChRCC study RNA-Seq dataset contains raw whole transcriptome sequencing data of 16 tumor and 6 adjacent normal samples from 7 UTSW patients, who have consented to depositing their genomic data to public repository. RNA-Seq was performed using 50bp single-end on a HiSeq2500 platform (Illumina, San Diego, CA, USA). 50M reads per sample on average. The raw data is in fastq format.

  Dataset EGAD50000000416

• Chondromyxoid fibroma

  Chondromxoid fibroma is a benign tumour of bone with unknown underlying pathogenesis. To determine pathognomic genomic event in chondromyxoid fibroma whole genome sequencing will be undertaken to reconstruct rearrangements and find underlying mutations.

  Dataset EGAD00001001063

• Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor-like Melanoma

  Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. The genomics of MPNST-like melanoma have not been previously described. In this study, we performed whole exome sequencing analysis in 8 samples from 6 patients diagnosed with MPNST-like melanoma. Our results demonstrate that, although MPNST-like melanoma shares oncogenic alterations common to both cutaneous melanoma and MPNST, it also presents unique genomic alterations not previously described in neither of the malignancies.

  Dataset EGAD00001006999

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

  RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001009707

• Idiopathic Scoliosis (SNP-array & WES study)

  This study aimed to investigate the genetic basis of severe idiopathic scoliosis (IS) using whole exome sequencing (WES) and SNP array methods. We intended to identify structural and point genetic variations contributing to the development of IS. By analyzing intraoperatively collected articular processes (AP) and blood (BL) samples from 70 unrelated individuals with IS, we sought to uncover pathogenic copy number variants (CNVs), regions of homozygosity (ROH), and single-nucleotide variants (SNVs) linked to the condition. EGAD00001015758

  Study EGAS00001008152