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Series GSE136702 Query DataSets for GSE136702
Status Public on Feb 11, 2020
Title Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]
Organisms Homo sapiens; unidentified plasmid
Experiment type Other
Summary Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants. 
Overall design Massively parallel reporter assays to study variant effects on reporter expression, 2-3 replicates, 3 cell types, 4 cell lines, lentiviral and transfection
Contributor(s) Ray JP, de Boer CG
Citation(s) 32144282
Submission date Aug 30, 2019
Last update date Apr 01, 2020
Contact name Carl G de Boer
Organization name The Broad Institute
Lab Aviv Regev
Street address 415 Main St
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL25362 Illumina HiSeq 2500 (unidentified plasmid)
Samples (33)
GSM4055618 MPRAv2_BJAB_stim_rep1
GSM4055619 MPRAv2_BJAB_stim_rep2
GSM4055620 MPRAv2_BJAB_unstim_rep1
This SubSeries is part of SuperSeries:
GSE136703 Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits
BioProject PRJNA563094
SRA SRP219970

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136702_20190823_MPRA_tag_count_matrix.txt.gz 41.9 Mb (ftp)(http) TXT
GSE136702_MPRA90823_MPRA_probe_SNP_allele_map.txt.gz 189.0 Kb (ftp)(http) TXT
GSE136702_MPRA_probes_and_barcodeNs_as_in_vector_for_association.fasta.gz 258.2 Kb (ftp)(http) FASTA
GSE136702_ProbeSequences_and_SNP_Genotypes_all.txt.gz 323.0 Kb (ftp)(http) TXT 103.7 Mb (ftp)(http) MAP
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Raw data are available in SRA
Processed data are available on Series record

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