| Literature DB >> 26064965 |
Yun Kyoung Kim1, Ji Hee Oh1, Young Jin Kim1, Mi Yeong Hwang1, Sanghoon Moon1, Siew-Kee Low2, Atsushi Takahashi2, Koichi Matsuda3, Michiaki Kubo2, Juyoung Lee1, Bong-Jo Kim1.
Abstract
Hematological traits are important health indicators and are used as diagnostic clinical parameters for human disorders. Recently, genome-wide association studies (GWAS) identified many genetic loci associated with hematological traits in diverse ethnic groups. However, additional GWAS are necessary to elucidate the breadth of genetic variation and the underlying genetic architecture represented by hematological metrics. To identify additional genetic loci influencing hematological traits (such as hematocrit, hemoglobin concentration, white blood cell count, red blood cell count, and platelet count), we conducted GWAS and meta-analyses on data from 12,509 Korean individuals grouped into population-based cohorts. Of interest is EGF, a factor plays a role in the proliferation and differentiation of hematopoietic progenitor cells. We identified a novel EGF variant, which associated with platelet count in our study (P combined = 2.44 × 10(-15)). Our study also replicated 16 genetic associations related to five hematological traits with genome-wide significance (P < 5 × 10(-8)) that were previously established in other ethnic groups. Of these, variants influencing platelet count are distributed across several genes and have pleiotropic effects in coronary artery disease and dyslipidemia. Our findings may aid in elucidating molecular mechanisms underlying not only hematopoiesis but also inflammatory and cardiovascular diseases.Entities:
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Year: 2015 PMID: 26064965 PMCID: PMC4430676 DOI: 10.1155/2015/914965
Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411
Results of genome-wide association analyses for hematological traits.
| Trait | CHR | SNP | Cytoband | Gene |
Minor | Discovery ( | Replication ( | Combined ( | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF | Effect size |
| Effect size |
| Effect size |
|
| ||||||
| Novel | |||||||||||||
| PLT | 4 | rs2282786 | 4q25 | EGF | C | 0.25 | −6.66 ± 1.123 | 3.18 × 10−9 | −6.58 ± 1.741 | 1.58 × 10−4 | −6.64 ± 0.944 | 2.05 × 10−12 | 0.97 (0.00) |
| Previously reported | |||||||||||||
| Hb | 22 | rs2076086 | 22q12.3 | TMPRSS6 | T | 0.49 | 0.09 ± 0.018 | 7.33 × 10−7 | 0.11 ± 0.026 | 3.24 × 10−5 | 0.09 ± 0.015 | 1.19 × 10−10 | 0.52 (0.41) |
| Hct | 6 | rs9376090 | 6q23.3 | HBS1L-MYB | C | 0.32 | −0.35 ± 0.055 | 1.68 × 10−10 | −0.18 ± 0.081 | 2.68 × 10−2 | −0.30 ± 0.045 | 6.20 × 10−11 | 0.08 (3.05) |
| RBC | 6 | rs7775698 | 6q23.3 | HBS1L-MYB | T | 0.33 | −0.07 ± 0.006 | 6.82 × 10−34 | −0.06 ± 0.009 | 4.92 × 10−12 | −0.07 ± 0.005 | 2.69 × 10−44 | 0.20 (1.68) |
| 4 | rs17084406 | 4q12 | PDGFRA-KIT | G | 0.26 | −0.04 ± 0.006 | 2.09 × 10−11 | −0.05 ± 0.010 | 1.81 × 10−8 | −0.05 ± 0.005 | 2.85 × 10−18 | 0.36 (0.85) | |
| 6 | rs3218108 | 6p21.1 | CCND3 | T | 0.22 | 0.04 ± 0.007 | 2.15 × 10−10 | 0.05 ± 0.010 | 2.54 × 10−6 | 0.04 ± 0.006 | 2.59 × 10−15 | 0.79 (0.07) | |
| 12 | rs7138216 | 12p13.3 | PARP11-CCND2 | C | 0.27 | −0.03 ± 0.006 | 2.70 × 10−7 | −0.03 ± 0.009 | 4.73 × 10−3 | −0.03 ± 0.005 | 5.19 × 10−9 | 0.54 (0.37) | |
| 9 | rs8176743 | 9q34.2 | ABO | T | 0.21 | 0.03 ± 0.007 | 9.88 × 10−7 | 0.03 ± 0.010 | 5.73 × 10−3 | 0.03 ± 0.006 | 2.12 × 10−8 | 0.62 (0.25) | |
| 2 | rs2218660 | 2p21 | PRKCE | G | 0.18 | −0.03 ± 0.007 | 2.90 × 10−6 | −0.03 ± 0.011 | 2.90 × 10−3 | −0.03 ± 0.006 | 2.94 × 10−8 | 0.85 (0.04) | |
| WBC | 17 | rs8070454 | 17q21.1 | PSMD3-CSF3 | T | 0.47 | 0.16 ± 0.028 | 3.62 × 10−9 | 0.11 ± 0.043 | 8.68 × 10−3 | 0.15 ± 0.023 | 1.74 × 10−10 | 0.31 (1.04) |
| 7 | rs11981340 | 7q21.2 | CDK6 | C | 0.34 | −0.13 ± 0.029 | 4.99 × 10−6 | −0.20 ± 0.045 | 9.58 × 10−6 | −0.15 ± 0.024 | 4.33 × 10−10 | 0.21 (1.58) | |
| PLT | 22 | rs1977081 | 22q13.31 | PNPLA3 | C | 0.41 | −5.84 ± 0.997 | 4.70 × 10−9 | −3.76 ± 1.608 | 1.94 × 10−2 | −5.27 ± 0.847 | 5.10 × 10−10 | 0.27 (1.21) |
| 6 | rs9469032 | 6p21.33 | LY6G5C | G | 0.03 | 12.7 ± 2.757 | 4.42 × 10−6 | 16.6 ± 4.336 | 1.35 × 10−4 | 13.8 ± 2.327 | 3.12 × 10−9 | 0.45 (0.58) | |
| 6 | rs9277053 | 6p21.32 | HLA-DOA-HLA-DPA1 | A | 0.34 | 5.18 ± 1.049 | 7.95 × 10−7 | 5.27 ± 1.622 | 1.18 × 10−3 | 5.21 ± 0.881 | 3.43 × 10−9 | 0.96 (0.00) | |
| 12 | rs739496 | 12q24.12 | SH2B3 | A | 0.11 | −8.36 ± 1.572 | 1.06 × 10−7 | −5.75 ± 2.385 | 1.06 × 10−2 | −7.57 ± 1.313 | 8.00 × 10−9 | 0.36 (0.84) | |
| 6 | rs9399137 | 6q23.3 | HBS1L-MYB | C | 0.33 | 5.24 ± 1.072 | 1.06 × 10−6 | 5.00 ± 1.630 | 2.20 × 10−3 | 5.17 ± 0.896 | 8.07 × 10−9 | 0.90 (0.02) | |
| 3 | rs13091574 | 3q27.1 | THPO | C | 0.16 | 6.39 ± 1.319 | 1.28 × 10−6 | 6.22 ± 2.142 | 3.73 × 10−3 | 6.34 ± 1.123 | 1.62 × 10−8 | 0.94 (0.01) | |
CHR, chromosome; BP, base position; MAF, minor allele frequency; Hb, hemoglobin; Hct, hematocrit; RBC, red blood cell count; WBC, white blood cell count; PLT, platelet count. Effect sizes are shown as beta ± S.E. A test of heterogeneity (P het) was conducted; Q, Cochrane's Q value based on chi-squared statistics. Age and gender were used in analyses as covariates.
Figure 1Manhattan plots of the GWAS for five hematological traits in discovery stage. Vertical axis indicates −log10 P values of SNPs in the GWAS for Hb, Hct, RBC, WBC, and PLT, and horizontal axis represents chromosomal position. The genetic loci that exceeded the genome-wide significance threshold of P < 5.0 × 10−8 are marked in red in each of the traits.
Figure 2A regional association plot of the novel genetic locus associated with PLT. Round shaped dots represent −log10 P values of SNPs from combined meta-analyses (discovery and replication stages). Diamond shaped purple dot that is located in the center of 0.8 Mb of 4q25 genomic region indicates the strongest signal associated with PLT. The color of each dot indicates the level of linkage disequilibrium (LD), r 2, relative to the SNP rs2282786. At the bottom, the locations of RefSeq genes are represented. Plot was generated from JPT + CHB panel based on hg18 HapMap phase 2 using LocusZoom.
Association results of rs2282786 for platelet count.
| Trait | CHR | SNP | BP | Gene | Function | MA | KARE + CAVAS ( |
Health2∗ ( | BioBank Japan ( | Combined ( | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Effect size |
| Effect size |
| Effect size |
| Effect size |
|
| |||||||
| PLT | 4 | rs2282786 | 111141945 | EGF | Intronic | C | −6.64 ± 0.944 | 2.05 × 10−12 | −4.21 ± 1.11 | 1.59 × 10−4 | −4.78 ± 1.04 | 4.47 × 10−6 | −5.23 ± 0.66 | 2.44 × 10−15 | 0.41 (0.68) |
∗The association result of rs11098063, a proxy SNP of rs2282786 (r 2 > 0.9), in Health2 cohort is represented in this table. Effect sizes are shown as beta ± S.E.; CHR, chromosome; BP, base position; MA, minor allele.
Associations with CAD and lipid profiles for loci-associated PLT with genome-wide significance.
| Trait | SNP | Cytoband | Gene | CAD ( | TC ( | TG ( | LDL ( | HDL ( | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) |
| Effect size |
| Effect size |
| Effect size |
| Effect size |
| ||||
| PLT | rs13091574 | 3q27.1 | THPO | 0.96 (0.86–1.07) | 0.4571 | −0.39 ± 0.72 | 0.5944 | −1.63 ± 2.12 | 0.4426 | −0.67 ± 0.65 | 0.3096 | 0.37 ± 0.21 | 0.0704 |
| rs2282786 | 4q25 | EGF | 1.07 (0.97–1.17) | 0.1803 | −0.33 ± 0.62 | 0.5954 | −2.40 ± 1.82 | 0.188 | −0.05 ± 0.56 | 0.9282 | −0.05 ± 0.17 | 0.7807 | |
| rs9469032 | 6p21.33 | LY6G5C | 1.15 (0.93–1.42) | 0.1943 | 1.69 ± 1.51 | 0.2613 | 4.37 ± 4.47 | 0.3288 | 1.00 ± 1.37 | 0.4655 | 0.01 ± 0.43 | 0.9818 | |
| rs9277053 | 6p21.32 | HLA-DOA-HLA-DPA1 | — | — | 0.93 ± 0.57 | 0.1059 | 0.16 ± 1.67 | 0.9252 | 0.79 ± 0.52 | 0.1296 | 0.14 ± 0.16 | 0.3875 | |
| rs9399137 | 6q23.3 | HBS1L-MYB | — | — | −2.79 ± 0.58 | 1.87 × 10−6 | −5.75 ± 1.72 | 8.41 × 10−4 | −1.78 ± 0.53 | 8.02 × 10−4 | −0.05 ± 0.17 | 0.7750 | |
| rs739496 | 12q24.12 | SH2B3 | 0.82 (0.72–0.94) | 3.70 × 10−3 | 0.99 ± 0.86 | 0.2522 | 4.77 ± 2.54 | 0.06059 | 0.05 ± 0.78 | 0.9487 | 0.36 ± 0.24 | 0.1420 | |
| rs1977081 | 22q13.31 | PNPLA3 | 0.94 (0.87–1.03) | 0.182 | −2.03 ± 0.55 | 2.08 × 10−4 | −5.94 ± 1.60 | 2.00 × 10−4 | −1.30 ± 0.50 | 8.93 × 10−3 | 0.07 ± 0.16 | 0.6558 | |
CHR, chromosome; BP, base position; PLT, platelet count; CAD, coronary artery disease; TC, total cholesterol; TG, triglyceride; LDL, LDL-cholesterol; HDL, HDL-cholesterol. Logistic and linear regression analyses adjusted by age and gender were performed. Effect sizes are shown as beta ± S.E.