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Series GSE115828 Query DataSets for GSE115828
Status Public on Feb 11, 2019
Title Integrated analysis of genetic variants regulating retinal transcriptome (GREx) identifies genes underlying age-related macular degeneration
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility. To gain functional understanding of AMD genetics, we generated transcriptional profiles of retina from 453 individuals including both controls and cases at distinct stages of AMD. We integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at over 9 million common single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets. Cis-eQTL analysis revealed 10,474 genes under genetic regulation, including 4,541 eQTLs detected only in the retina. We then integrated the AMD-genome-wide association studies (GWAS) data with eQTLs and ascertained target genes at six loci. Furthermore, using transcriptome wide association analysis (TWAS), we identified 23 additional AMD-associated genes, including RLBP1, HIC1 and PARP12. Our studies expand the genetic landscape of AMD leading to direct targets for biological evaluation and establish the Genotype-Retina Expression (GREx) database as a resource for post-GWAS interpretation of retina-associated traits including glaucoma and diabetic retinopathy.
Overall design Retinal samples from 523 aged post-mortem human subjects from a spectrum of age-related macular degeneration (AMD) were RNA-seq profiled.
Contributor(s) Ratnapriya R, Starostik M, Kayode S, Kwicklis M, Kapphahn R, Fritsche L, Walton A, Arvanitis M, Geiser L, Pietraszkiewicz A, Montezuma S, Chew E, Battle A, Abecasis G, Ferrington D, Chatterjee N, Swaroop A
Citation(s) 30742112, 31631019, 35307029
Submission date Jun 14, 2018
Last update date Mar 31, 2022
Contact name Matthew J Brooks
Phone 301-443-4906
Organization name NIH
Department NEI
Street address 6 Center Dr Bldg 6, Rm 303
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (523)
GSM3190962 R42015-419pf_1-IR_L7
GSM3190963 R42015-490pf_100-IR_L2
GSM3190964 R42016-137pf_101-IR_L5
BioProject PRJNA476171
SRA SRP151763

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

Supplementary file Size Download File type/resource
GSE115828_DE_analysis.txt.gz 1.3 Mb (ftp)(http) TXT
GSE115828_Normalized_CPM.txt.gz 62.7 Mb (ftp)(http) TXT
GSE115828_README_for_retina_TWAS_wgts.tar.txt 847 b (ftp)(http) TXT
GSE115828_RSEM_gene_counts.tsv.gz 20.3 Mb (ftp)(http) TSV
GSE115828_retina_TWAS_wgts.tar.gz 3.3 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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