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M.J. Stubbs et al.
Table 1. Lead single nucleotide polymorphisms identified in the UK discovery cohort.
mal region (see the Online Supplementary Table S1).19 All markers were functionally annotated with information from the UCSC Genome Browser (Human Assembly GRCh37/hg19)23,24) (see the Online Supplementary Table S1). One variant was particularly noted, rs71767581 (Ch3, 119187422 AC/-del), which is a 2-basepair deletion in the promoter of POGLUT1. This may be functionally important as the haploblock identified is associated with reduced expression in POGLUT1. Upon analysis of ChipSeq data in UCSC Genome Browser 14 transcription factors were predicted to bind at this site (see the Online Supplementary Table S2), adding further evidence that rs71767581 may be functionally important for POGLUT1 expression.
Discussion
This GWAS, involving two European populations, is the first to be performed in iTTP and shows consistent evidence of association at loci on chromosome 6 and chromosome 3. The associated alleles on chromosome 6 lie within the HLA region and imputation of HLA types and conditional analyses indicated independent associa- tion between HLA-DRB1*11:01 (OR 2.79; P=3.25x10-17) and HLA-DQA1*03:01 (OR 0.47; P=1.49x10-6, post condi- tional analysis), which are consistent, and in linkage with previously published risk and protective associations with iTTP at this locus.5–7 A recent case-control study comparing frequency of alleles only at immune loci in 190 Italian TTP patients and 1,255 controls identified the HLA variant rs6903608, (in addition to HLA-DQB1*05:03) as conferring a 2.5-fold increase of developing TTP.25
Here we also identified a novel association of iTTP with alleles on chromosome 3 tagged by the lead SNP rs9884090. Five genes are located within the associated haploblock: ARHGAP31, TMEM39A, POGLUT1, TIM- MDC1, and CD80. ARHGAP31 (rho GTPase activating protein 31) is associated with the autosomal dominant condition Adams-Oliver Syndrome (OMIM 100300).26 Mutations within ARHGAP31 have been implicated with abnormal vascular development and VEGF (vascular endothelial growth factor) angiogenesis.27 Little is under- stood regarding the function of TMEM39A (transmem- brane protein 39A). While variants have been implicated in autoimmune disease such as systemic lupus erythe- matosus28,29 and multiple sclerosis,30,31 understanding of
rsID (position)
rs9884090
(ch3:119116150)
rs28383233
(ch6:32584153)
rs1064994
(ch6:32611195)
Minor allele / MAF cases /
Logistic regression P-value
P = 5.22x10-10 P = 2.20x10-23 P = 1.13x10-10
Odds
Ratio (95% CI)
0.40
(0.29-0.56)
3.12
(2.49-3.93)
2.20
(2.06-3.37)
Major allele
A/G G/A C/T
MAF controls
0.08/0.19 0.64/0.40 0.25/0.11
Displayed are Minor/Major Alleles, Minor Allele Frequencies (MAF), logistic regression P-value (corrected for principal component analysis stratification), and odds ratio (with 95% Confidence Intervals [CI]). Genomic positions refer to Human Assembly GRCh37/hg19.
ciation testing was performed using a logistic regression model with PCA correction, and l was 1.0830 (Online Supplementary Figure S5).
The association with the lead SNP in the chromosome 3 haploblock, rs9884090(A) was replicated with a P-value of 0.001 (OR 0.52), and the two independent lead SNP with the class II HLA peak on chromosome 6 were also replicated (Table 2). The locus zoom plots are shown (Online Supplementary Figures S6 to S8). Imputed HLA type analysis was also consistent with the UK discovery cohort with HLA-DRB1*11:01 and HLA-DQA1*03:01 representing two independent HLA signals.
In addition, a meta-analysis was performed combining the UK and French cohorts (cases 241/112, controls 3,200/2,603 respectively), which demonstrated strength- ening of the previously observed signal (rs9884090 P=1.60x10-10, OR 0.47, rs28383233 P=1.22x10-42, OR 3.70, rs1064994 P=5.03x10-25, OR 2.89) (Table 3; Online Supplementary Figure S9).
Expression quantitative trait loci and functional DNA analysis
eQTL data from the Genotype Tissue Expression Project and Blood eQTL Browser for the lead SNP at the chromosome 3 locus (rs9884090) demonstrated signifi- cant reduction in expression of POGLUT1 with the pro- tective allele in the majority of tissues tested, including blood cells (P<0.001).18,22 LD-link identified 20 markers found to be in tight linkage disequilibrium (R2 and D’ >0.80) with rs9884090 contained within the chromoso-
Table 2. French cohort replication of lead single nucleotide polymor- phisms identified in the UK discovery cohort.
rsID (position)
rs9884090
(ch3:119116150)
Minor Allele / MAF Cases / Logistic MajorAllele MAFControls Regression
Odds Ratio (95%CI)
0.52
(0.34-0.81)
2.57
(1.87-3.53)
2.86
(2.06-3.99)
rs28383233 G/A
(ch6:32584153)
rs1064994 C/T
(ch6:32611195)
A/G
0.10/0.18 0.68/0.40 0.42/0.11
P-value P = 0.001
P = 3.87x10-9 P = 5.015x10-9
Displayed are Minor/Major Alleles,Minor Allele Frequencies (MAF),logistic regression P-value (corrected for principal component analysis stratification), and odds ratio (with 95% Confidence Intervals [CI]). Genomic positions refer to Human Assembly GRCh37/hg19.
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Table 3. Meta-analysis combining UK and French Cohorts, showing lead single nucleotide polymorphisms identified in the UK discover cohort.
rsID (position)
Minor Allele / MAF Cases /
Logistic Regression P-value
Odds Ratio (95% CI)
rs9884090 (ch3:119116150) rs28383233 (ch6:32584153) rs1064994 (ch6:32611195)
A/G G/A
0.08/0.19 0.64/0.41
P =1.60x10-10 P = 1.22x10-42
0.47 (0.36-0.60) 3.70 (2.81-4.03) 2.89 (2.39-3.49)
Major Allele
MAF Controls
C/T
0.22/0.11
P = 5.03x10-25
Displayed are Minor/Major Alleles,Minor Allele Frequencies (MAF),logistic regression P-value (corrected for principal component analysis stratification), and odds ratio (with 95% Confidence Intervals [CI]). Genomic positions refer to Human Assembly GRCh37/hg19.