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Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction
2012
JAMIA Journal of the American Medical Informatics Association
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Objective We demonstrate a genome-wide method for the integration of many studies of gene expression of phenotypically similar disease processes, a method of multiplex meta-analysis. ...
Our method may be extended to other disease processes, using RNA levels to prioritize genes likely to contain disease associated DNA variants. ...
Acknowledgments Special thanks to Rong Chen and Alex Skrenchuk for the development of database resources. ...
doi:10.1136/amiajnl-2011-000657
pmid:22319178
pmcid:PMC3277634
fatcat:dhebtuhnjfavhj6zfxdrvbifgq
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
2020
Journal for ImmunoTherapy of Cancer
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particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. ...
These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy ...
They have identified the epigenetic processes associated with dysfunctional immune cells and surface biomarkers to identify reprogrammable T cells. ► Chromatin states define tumour-specific T cell dysfunction ...
doi:10.1136/jitc-2020-000705
pmid:33268350
fatcat:iuqgiddv4ra63bz7ge3rq2ppk4
Genome-wide association study in frontal fibrosing alopecia identifies four susceptibility loci including HLA-B*07:02
2019
Nature Communications
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We undertake genome-wide association studies in females from a UK cohort, comprising 844 cases and 3,760 controls, a Spanish cohort of 172 cases and 385 controls, and perform statistical meta-analysis. ...
Transcriptomic analysis of affected scalp tissue highlights overrepresentation of transcripts encoding components of innate and adaptive immune response pathways. ...
We are thankful to Prof Kathryn Lewis, Dr. Raquel Iniesta, Dr. Ken Hanscombe and Dr. Leo Bottolo for their input and advice with the statistical analysis aspects of the metabolomic exploration. ...
doi:10.1038/s41467-019-09117-w
pmid:30850646
pmcid:PMC6408457
fatcat:v2pkria2gjfltaou6jy5g6g4di
Autism risk factors: genes, environment, and gene-environment interactions
2012
Dialogues in Clinical Neuroscience
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One aspect of this search that has been neglected so far is the study of interactions between genes and environmental factors. ...
The identification of specific alleles contributing to the autism spectrum has supplied important pieces for the autism puzzle. ...
of common variants in autism, a recent analysis of genetic variations associated with ASD suggests that common and rare C l i n i c a l r e s e a r c h variants contribute to ASD by perturbation of common ...
pmid:23226953
pmcid:PMC3513682
fatcat:quomgjutbjenblrp5wq5vou5la
Molecular Dysregulation in Autism Spectrum Disorder
2021
Journal of Personalized Medicine
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Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. ...
non-coding RNAs and CRISPR/Cas9 models. ...
Gene-based association analysis on primary ASD meta-analysis using MAGMA identified the top associated genes KIZ and XRN2 (Chr 20), MFHAS1, XKR6, MSRA, and SOX7 (Chr 8). ...
doi:10.3390/jpm11090848
pmid:34575625
fatcat:7z7li3qltvgsvotzhyf4ibmrxu
Advances of genomic science and systems biology in renal transplantation: a review
2011
Seminars in Immunopathology
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To develop the most appropriate molecular criteria, there have been studies by multiple groups applying omics technologies in attempts to identify biomarkers of rejection. ...
In this review, we discuss studies using genome-wide data sets of the transcriptome and proteome to investigate acute rejection, chronic allograft dysfunction, and tolerance. ...
In a multiplex meta-analysis designed to identify the core immune response genes as defined by the Molecular Signatures Database [24] , a comparative analysis of five studies of AR from kidney, lung, ...
doi:10.1007/s00281-011-0243-2
pmid:21318414
pmcid:PMC3082700
fatcat:thrm2xmd7rhvjfqgt5mexusvry
90PMolecular feature and clinical use development of gene expression profile "TP53 signature" in early stage breast cancer
2017
Annals of Oncology
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As with BRCA, the acquisition of additional mutations predicted to restore at least some PALB2 function and thus potentially confer resistance to therapies dependent on HRD, can be observed in tumors such ...
Conclusions: In addition to the commonly sequenced genes BRCA1/2, PALB2 mutation can lead to homologous recombination deficiency. ...
To identify potential driver alterations enriched in MSI-H tumors, variants in regions likely to be affected by polymerase slippage were excluded. ...
doi:10.1093/annonc/mdx363.006
fatcat:ifholazkkbc7dk3jmbsafpq5xe
Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons
2017
PLoS Genetics
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Acknowledgments We are grateful to all the individuals with Sjögren's syndrome and those serving as healthy controls who participated in this study. ...
We would like to thank the following individuals for their help in the collection and ascertainment of the samples used in this study: Erin We would also like to thank Jared Ning for the ongoing assistance ...
Therefore, we identified a variant associated with both SS susceptibility and gene expression in the IFN signature gene OAS1. ...
doi:10.1371/journal.pgen.1006820
pmid:28640813
pmcid:PMC5501660
fatcat:m4nhejcw25aq5jwyarlekg3uce
EBV infection determines the immune hallmarks of plasmablastic lymphoma
2018
Oncoimmunology
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Unsupervised hierarchical clustering analysis of PBL samples revealed they segregate according to their tumor EBV-status. ...
Moreover, EBV+ PBL displays abundant leucocyte infiltrates and T-cell activation signatures, together with high expression levels of mRNA and protein markers of immune escape. ...
Conflict-of-interest disclosure The authors declare no conflict of interest. ...
doi:10.1080/2162402x.2018.1486950
pmid:30288350
pmcid:PMC6169584
fatcat:7os4rb6y4fgdxbmkwrqd7gdoqa
Genetic architecture, epigenetic influence and environment exposure in the pathogenesis of Autism
2015
Science China Life Sciences
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and gastrointestinal microbiota are two prominent ones. autism spectrum disorder, genetic architecture, genomic disorder, gene mutation, copy number variants, single nucleotide variants, genetic pathways ...
, epigenetic influence, DNA methylation, chromatin remodeling, long non-coding RNAs, environment exposure, immune dysregulation, gastrointestinal microbiota Citation: Yu L, Wu YM, Wu BL. ...
Meta-analysis identified three single-nucleotide polymorphisms and related haplotypes; all were mapped to a previously reported linkage region (1p13.2) with autism [26] . ...
doi:10.1007/s11427-015-4941-1
pmid:26490976
fatcat:erjhekqbsralhhinx5ykc6k6we
Beyond Single-Nucleotide Polymorphisms
2014
Clinics in Chest Medicine
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As future GWAS are published, new candidates will undoubtedly emerge and meta-analysis will be possible to harness the power of multiple populations. ...
This article summarizes the contributions of high throughput genomic, proteomic, metabolomic, and gene expression investigations to our understanding of inherited or acquired risk for acute respiratory ...
that gene variants associated with ARDS may be specific to ARDS risk factor. 54 In the first published human genome-wide association study (GWAS) for ARDS susceptibility, Christie and colleagues identified ...
doi:10.1016/j.ccm.2014.08.006
pmid:25453417
pmcid:PMC5629971
fatcat:pehfkke25za7tib4zoziwxaq6q
The Meta-Genome of Sepsis: Host Genetics, Pathogens and the Acute Immune Response
2014
Journal of Innate Immunity
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The pathogen is discussed with particular emphasis upon the modern era of microbiome analysis and nucleic acid diagnostics. ...
Finally, we discuss the host clinical and immune responses and present new data to suggest that the immune response is the key to understanding sepsis and improving a death rate of nearly 30%. ...
Acknowledgements Support for this study was obtained through SONRIS CIHR Network grant, Heart and Stroke Foundation, and the National Sanitorium Association. ...
doi:10.1159/000358835
pmid:24525633
pmcid:PMC6741586
fatcat:4ulmyzigkfagnggpip4oqqovyi
SAGES 2018, Symposium on Advances in Genomics, Epidemiology and Statistics 2018, Philadelphia, PA, USA, June 1, 2018: Abstracts
2018
Human Heredity
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We expect that screening for deleterious variants in the subset of candidate genes involved in cognition may be useful to identifying genetic factors contributing to expression of phenotype differences ...
and GTEx eQTL data from 44 tissues to identify target genes regulated by variants overlapping enhancers in matching tissue categories. ...
Capabilities to Predict Gene Expression Levels and Prioritize Variant-Based Associations Using Datasets with Varied Population Background
QC Software for Analysis of Sequence Data in Family-Based Studies ...
doi:10.1159/000490340
pmid:29852479
fatcat:c24yw4b2vngd5hnvf2nluajrfa
Discovery and application of immune biomarkers for hematological malignancies
2017
Expert Review of Molecular Diagnostics
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Moreover, the analysis of multidimensional, clinically annotated data sets obtained from public repositories such as Array Express, TCGA and GEO is crucial to identify immune biomarkers, to inform the ...
Although high-throughput transcriptomic and proteomic approaches are being employed to interrogate immune surveillance and escape mechanisms in patients with solid tumours, and to identify actionable targets ...
Importantly, immune-related gene signatures, and not tumour-related gene expression
patterns, have been identified as being the main parameters associated with dissemination of
CRC to distant metastases ...
doi:10.1080/14737159.2017.1381560
pmid:28927305
fatcat:w6xgbthnm5gyjcbeouh4bx4rja
Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
2021
Journal of Neuroinflammation
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A previous meta-analysis of seven microarray studies and one RNA sequencing (RNA-seq) study using the blood of children with ASD identified dysregulation of gene expressions relevant to the immune system ...
Conclusions The dysregulated gene expressions confirmed in the blood of adults with ASD were relevant to the dysfunction of innate and adaptive immunity. ...
Acknowledgments We would like to thank Ms. Chiemi Onishi for the technical assistance. We also wish to thank Dr. Naohito Tokunaga for the technical advice on RNAsequencing. ...
doi:10.1186/s12974-021-02154-7
pmid:33931079
pmcid:PMC8086363
fatcat:5fxoxx3rlfey5pyuuh444ji7ye
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