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| Status |
Public on Nov 24, 2015 |
| Title |
Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Genome-wide association studies have been tremendously successful in identifying genetic variants associated with complex diseases. The majority of association signals are intergenic and evidence is accumulating that a high proportion of signals lie in enhancer regions.We use Capture Hi-C to investigate, for the first time, the interactions between associated variants for four autoimmune diseases and their functional targets in B- and T-cell lines. Here we report numerous looping interactions and provide evidence that only a minority of interactions are common to both B- and T-cell lines, suggesting interactions may be highly cell-type specific; some disease-associated SNPs do not interact with the nearest gene but with more compelling candidate genes (for example, FOXO1, AZI2) often situated several megabases away; and finally, regions associated with different autoimmune diseases interact with each other and the same promoter suggesting common autoimmune gene targets (for example, PTPRC, DEXI and ZFP36L1).
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| Overall design |
Capture Hi-C was carried out to characterise the interactions of confirmed susceptibility loci for four autoimmune diseases: rheumatoid arthritis (RA), type 1 diabetes (T1D), psoriatic arthritis (PsA) and juvenile idiopathic arthritis (JIA) with the aim of linking associated variants with disease-causing genes. We have tested the interactions in two complementary experiments: the first, Region Capture, targets regions associated with disease; the second, Promoter Capture, provides independent validation through capturing all known promoters within 500kb of lead associated disease SNPs. All experiments were performed in human T-cell (Jurkat) and B-cell (GM12878) lines in duplicate.
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| Contributor(s) |
Martin P, McGovern A, Orozco G, Duffus K, Yarwood A, Barton A, Worthington J, Eyre S |
| Citation(s) |
26616563, 27861577 |
| Submission date |
Jun 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Martin |
| E-mail(s) |
paul.martin-2@manchester.ac.uk
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| Organization name |
Univeristy of Manchester
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| Department |
Centre for Genetics and Genomics Versus Arthritis
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| Street address |
Oxford Road
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| City |
Manchester |
| State/province |
Greater Manchester |
| ZIP/Postal code |
M13 9PT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (4)
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| GSM1704493 |
Region Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two |
| GSM1704494 |
Region Capture Hi-C, Jurkat T lymphocyte cells, replicate one & two |
| GSM1704495 |
Promoter Capture Hi-C, GM12878 Lymphoblastoid cells, replicate one & two |
| GSM1704496 |
Promoter Capture Hi-C, Jurkat T lymphocyte cells, replicate one & two |
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| Relations |
| BioProject |
PRJNA285958 |
| SRA |
SRP059186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69600_RAW.tar |
1.9 Gb |
(http)(custom) |
TAR (of BEDPE) |
| GSE69600_promoter_capture_bait_coordinates.bed.gz |
65.1 Kb |
(ftp)(http) |
BED |
| GSE69600_region_capture_bait_coordinates.bed.gz |
24.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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