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• 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

• T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis

  Data Access Committee means the following members of the Institute of Experimental Immunology, UZH, and investigators of the publication, to which the Data Access refers and who are responsible for making the data access decisions for the genotype and gene expression generated by UZH or respectively the epigenetic data, which had been generated at Karolinska Institute. Christian Münz, PhD; Co-Director of Institute of Experimental Immunology, University of Zurich Roland Martin, MD; Affiliated Group Leader (to Institute Münz) of Institute of Experimental Immunology Institute of Experimental Immunology Ivan Jelcic, PhD, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland Maja Jagodic, PhD, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden

  Dac EGAC50000000464

• SUM-seq data for Primary T-cells differentiated to helper subtypes

  Briefly, naive CD4+ T cells were isolated from PBMCs obtained from buffy coats from three healthy human donors, and differentiated into Th0, iTreg, Th2, Th1, Th17, and IFN-β-activated subsets. This allowed us to study the differentiation of naive CD4+ T cells into distinct helper subsets under the influence of a specific cytokine environment. Following 5 days of differentiation, T cells were left unstimulated or re-stimulated with phorbol 12-myristate 13-acetate (PMA) and ionomycin to assess their functional responses. Thus, this SUM-seq experiment consisted of 36 multiplexed conditions (3 donors x 6 stimulations x with/without re-stimulation). Single-cell chromatin accessibility and gene expression data is provided as demultiplexed fastq files.

  Dataset EGAD50000001204

• 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

• Evaluation of clonal hematopoiesis regarding TP53 mutation status in 140,597 individuals

  The existence of clonal hematopoiesis, in which somatic mutations accumulate in the peripheral blood with age and expand clonally, is becoming clear, and various clinical implications are being suggested. This study analyzed clonal hematopoiesis regarding TP53 mutation status by targeted sequencing in 140,597 individuals, including those with breast cancer, gastric cancer, colorectal cancer, heart failure, stroke, etc. The clinical characteristics of clonal hematopoietic carriers were evaluated.

  Study JGAS000782

• Molecular profiling for a patient with lipoblastoma-like tumor of the vulva

  Lipoblastoma-like tumors of the vulva (LLTVs) are exceptionally rare indolent adipocytic mesenchymal tumors arising in adults. Only total 19 cases have been reported previously and has just been categorized as mesenchymal tumours of the lower genital tract on the latest WHO classification of tumours, 5th edition. This is the first case of LLTV assessed for RNA-seq, WES, and WGS by next generation sequencing.

  Study JGAS000529

• Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing

  The aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.

  Study EGAS50000001541

• A single-cell atlas of the early COPD lung

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways.

  Study EGAS50000000720

• Meta-analysis of Genome-Wide-Association Sudies for plasma Factor XI

  Coagulation factor XI (FXI) has become increasingly interesting for its role in pathogenesis of thrombosis. We performed a genome-wide association study (GWAS) for plasma FXI levels, using novel data imputed to the 1000 Genomes reference panel. Individual GWAS analyses, including a total of 16,169 European individuals from the ARIC, GHS, MARTHA and PROCARDIS studies, were meta-analyzed, and results are presented here.

  Study EGAS00001002123

• Inherited damaging mutations in immune-related genes favour the development of genetically heterogeneous synchronous colorectal cancer.

  Synchronous colorectal cancers are physically separated tumours that develop simultaneously in the intestine. To understand how common genetic and environmental backgrounds influence the development of multiple tumours, we conduct a genome-wide comparative analysis of somatic alterations of 20 syCRCs from 10 patients. We show that syCRCs have independent genetic origins, acquire discordant somatic alterations, and follow different clonal developments.

  Study EGAS00001001461

• Mutational profiling of LUAD in young never-smokers

  NSCLC has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients with lung adenocarcinomas (LUADs). Our study provides a detailed mutational portrait of LUADs occurring in young never-smokers and gives insights into the molecular pathogenesis of this NSCLC subgroup

  Study EGAS00001002773

• Whole_Genome_sequencing_of_individuals_from_Val_Borbera__Italy

  This study includes Phase 2 whole-genome sequencing data (at 4x depth)of 100 individuals from an Italian genetic isolate population (Val Borbera, abbreviated VBI) of the Italian Network of Genetic Isolates (INGI). The INGI-VBI_SEQ2 project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Study EGAS00001000458

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Spastic Paraplegia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002021

• HipSci HumanHT 12v4 Expression BeadChip analysis-Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001276

• Whole exome sequencing data for patients with Bosma arhinia microphthalmia syndrome (BAMS).

  The datasets includes 21 samples from 7 families with Bosma arhinia microphthalmia (BAMS). For details of the study please refer to the manuscript "De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development", Nature Genetics 2017. Each sample was exome sequenced and the family ID in sample description refers to the Individual ID in Supplementary figure 2 of the manuscript.

  Study EGAS00001002193

• HipSci whole exome sequencing for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed whole exome sequencing using Agilent whole exome pulldown method.

  Study EGAS00001001726

• HipSci expression microarray for embryonic stem cell control lines

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we use commercially available embryonic stem cell lines as control samples against which to compare HipSci's iPS cell lines. We performed expression analysis using the Illumina HumanHT -12 Expression BeadChip.

  Study EGAS00001001729

• HipSci HumanHT 12v4 Expression BeadChip analysis - monogenic diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001277

• GILD_ExomeSeq_PTNHL

  This study is meant to gain further knowledge in haematological cancers. Patients samples (mainly DNAs or PCR products) from haematolocical cancer patients will be sequenced, and the outputs will be correlated to their diagnosis and/or prognosis; the findings may also add more insight into the understanding of biology in this type of tumour. We will be sequencing Primary Testicular Lymphomas (PTL) to identify genetic drivers of this rare cancer

  Study EGAS00001001613

• Roma Sequencing Study

  Present day Roma genome were shaped by the extensive inbreeding and admixture during their Diaspora. Here, we shed light on the Roma demographic history by analyzing the whole genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. The strong reduction in effective population size (~44%), that occurred around 2kya, was not masked by the subsequent high admixture in Middle Eastern and European countries.

  Study EGAS00001004287

• Splenic_Marginal_Zone_Lymphoma_with_villous_lymphocytes_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from ~3 Splenic Marginal Zone Lymphoma with villous lymphocytes samples and matched normal DNA from the same patients. Samples will be multiplexed in one lane of Illumina HiSeq. Sequencing to a coverage of at least 30x will be performed and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000139

• ATAC_SEQ_MAIN___PHASE_1

  This is a study to test ATAC-seq protocols. CD4+ and CD8+ cells have been obtained from three different anatomical compartments. We aim to assay open-chromatin regions across these cells and perform comparative analyses.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000947

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Cerebellar Ataxias

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002020

• Genomewide detection of cytosine methylation by single molecule real-time sequencing

  5-methylcytosine (5mC) is an important type of epigenetic modification. 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. This methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses. 

  Study EGAS00001004642

• Foetal_phylogeny_8pcw___WGS_of_LCM_tissues

  This study relates to the overall project of constructing the phylogeny of foetal haematopoiesis. This is an additional project relating to pre-existing work in projects 2043, 2169, 2243 and 2244. This project is to perform WGS (to around 40X) of polyclonal LCM tissues from the 8pcw foetus that have previously undergone library prep and targeted sequencing only. This work is to address reviewers comments for the publication of this work.

  Study EGAS00001004674