ArticleBMC medical genomics2016
Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.
Article in BMC medical genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 2 of them syntheses that pooled it.
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Who cites it
23 citing papers in PubMed, 2 syntheses or guidelines pooled it, 42 citations in OpenAlex.
- Tumor infiltrating lymphocytes as an endpoint in cancer vaccine trials.Frontiers in immunology · 2023Pooled it
- Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group.Annals of oncology : official journal of the European Society for Medical Oncology · 2020Pooled it
- The compositional behavior of the human T cell receptor repertoire in ovarian cancer compared to healthy donors.Scientific data · 2025Article
- Effect of NK cell receptor genetic variation on allogeneic stem cell transplantation outcome and in vitro NK cell cytotoxicity.Scientific reports · 2024Article
- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.PLoS computational biology · 2024Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- The temporal behavior of the murine T cell receptor repertoire following Immunotherapy.Scientific data · 2023Article
- GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data.BMC bioinformatics · 2023Article
- TCR_Explore: A novel webtool for T cell receptor repertoire analysis.Computational and structural biotechnology journal · 2023Article
- T-cell repertoire diversity: friend or foe for protective antitumor response?Journal of experimental & clinical cancer research : CR · 2022Review
- Safety and efficacy of atezolizumab with obinutuzumab and bendamustine in previously untreated follicular lymphoma.Blood advances · 2022Article
- Article
- Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort.NAR genomics and bioinformatics · 2020Article
- Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites.Biomedical reports · 2019Article
- Best practices for bioinformatic characterization of neoantigens for clinical utility.Genome medicine · 2019Review
- Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing.Clinical epigenetics · 2019Article
- Long-read sequence capture of the haemoglobin gene clusters across codfish species.Molecular ecology resources · 2019Article
- Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits.European journal of human genetics : EJHG · 2019Article
- Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation.Leukemia · 2019Article
- Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT.Frontiers in immunology · 2019Article
Corrections and comments
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Authors and funding
17 authors at 6 institutions in 3 countries.
Funding
Abstract
backgroundThe observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - "Immunoseq".
resultsWe performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations.
conclusionsWe show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.