King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia.
King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia.
Genes (Basel). 2023 Oct 9;14(10):1919. doi: 10.3390/genes14101919.
Sickle cell disease (SCD) is a Mendelian disease characterized by multigenic phenotypes. Previous reports indicated a higher rate of thromboembolic events (TEEs) in SCD patients. A number of candidate polymorphisms in certain genes (e.g., FVL, PRT, and MTHFR) were previously reported as risk factors for TEEs in different clinical conditions. This study aimed to genotype these genes and other loci predicted to underlie TEEs in SCD patients.
A multi-center genome-wide association study (GWAS) involving Saudi SCD adult patients with a history of TEEs (n = 65) and control patients without TEE history (n = 285) was performed. Genotyping used the 10× Affymetrix Axiom array, which includes 683,030 markers. Fisher's exact test was used to generate p-values of TEE associations with each single-nucleotide polymorphism (SNP). The haplotype analysis software tool version 1.05, designed by the University of Göttingen, Germany, was used to identify the common inherited haplotypes.
No association was identified between the targeted single-nucleotide polymorphism rs1801133 in MTHFR and TEEs in SCD ( = 0.79). The allele frequency of rs6025 in FVL and rs1799963 in PRT in our cohort was extremely low (<0.01); thus, both variants were excluded from the analysis as no meaningful comparison was possible. In contrast, the GWAS analysis showed novel genome-wide associations ( < 5 × 10) with seven signals; five of them were located on Chr 11 (rs35390334, rs331532, rs317777, rs147062602, and rs372091), one SNP on Chr 20 (rs139341092), and another on Chr 9 (rs76076035). The other 34 SNPs located on known genes were also detected at a signal threshold of < 5 × 10. Seven of the identified variants are located in olfactory receptor family 51 genes (OR51B5, OR51V1, OR51A1P, and OR51E2), and five variants were related to family 52 genes (OR52A5, OR52K1, OR52K2, and OR52T1P). The previously reported association between rs5006884-A in OR51B5 and fetal hemoglobin (HbF) levels was confirmed in our study, which showed significantly lower levels of HbF ( = 0.002) and less allele frequency ( = 0.003) in the TEE cases than in the controls. The assessment of the haplotype inheritance pattern involved the top ten significant markers with no LD (rs353988334, rs317777, rs14788626882, rs49188823, rs139349992, rs76076035, rs73395847, rs1368823, rs8888834548, and rs1455957). A haplotype analysis revealed significant associations between two haplotypes (a risk, TT-AA-del-AA-ins-CT-TT-CC-CC-AA, and a reverse protective, CC-GG-ins-GG-del-TT-CC-TT-GG-GG) and TEEs in SCD ( = 0.024, OR = 6.16, CI = 1.34-28.24, and = 0.019, OR = 0.33, CI = 0.13-0.85, respectively).
Seven markers showed novel genome-wide associations; two of them were exonic variants (rs317777 in OLFM5P and rs147062602 in OR51B5), and less significant associations ( < 5 × 10) were identified for 34 other variants in known genes with TEEs in SCD. Moreover, two 10-SNP common haplotypes were determined with contradictory effects. Further replication of these findings is needed.
镰状细胞病（SCD）是一种多基因表型的孟德尔疾病。先前的报告表明，SCD 患者发生血栓栓塞事件（TEEs）的比率更高。先前有报道称，某些基因中的一些候选多态性（如 FVL、PRT 和 MTHFR）是不同临床情况下 TEEs 的危险因素。本研究旨在对这些基因以及其他预测与 SCD 患者 TEEs 相关的基因座进行基因分型。
本研究是一项多中心全基因组关联研究（GWAS），纳入了沙特阿拉伯有 TEEs 病史的成年 SCD 患者（n=65）和无 TEEs 病史的对照患者（n=285）。基因分型使用了 10× Affymetrix Axiom 阵列，该阵列包含 683030 个标记物。Fisher 精确检验用于生成每个单核苷酸多态性（SNP）与 TEEs 关联的 p 值。德国哥廷根大学设计的哈普洛特分析软件工具版本 1.05 用于识别常见的遗传性单倍型。
在 MTHFR 中的靶向单核苷酸多态性 rs1801133 与 SCD 中的 TEEs 之间未发现关联（ = 0.79）。我们队列中 FVL 中的 rs6025 和 PRT 中的 rs1799963 的等位基因频率极低（<0.01）；因此，由于无法进行有意义的比较，这两个变体都被排除在分析之外。相比之下，GWAS 分析显示出与七个信号具有全新的全基因组关联（<5×10）；其中五个位于 11 号染色体（rs35390334、rs331532、rs317777、rs147062602 和 rs372091），一个 SNP 位于 20 号染色体（rs139341092），另一个位于 9 号染色体（rs76076035）。在已知基因中还检测到另外 34 个位于信号阈值<5×10 的 SNP。鉴定出的七个变体中有七个位于嗅觉受体家族 51 基因（OR51B5、OR51V1、OR51A1P 和 OR51E2）中，五个变体与家族 52 基因（OR52A5、OR52K1、OR52K2 和 OR52T1P）相关。OR51B5 中的 rs5006884-A 与胎儿血红蛋白（HbF）水平之间先前报道的关联在我们的研究中得到了证实，该研究表明 TEE 病例的 HbF 水平明显降低（ = 0.002），等位基因频率也较低（ = 0.003）。对没有 LD（rs353988334、rs317777、rs14788626882、rs49188823、rs139349992、rs76076035、rs73395847、rs1368823、rs8888834548 和 rs1455957）的前十个显著标记物的单倍型遗传模式的评估显示，两个单倍型（风险 TT-AA-del-AA-ins-CT-TT-CC-CC-AA 和逆转保护 CC-GG-ins-GG-del-TT-CC-TT-GG-GG）与 SCD 中的 TEEs 之间存在显著关联（ = 0.024，OR = 6.16，CI = 1.34-28.24， = 0.019，OR = 0.33，CI = 0.13-0.85）。
七个标记物显示出全新的全基因组关联；其中两个是外显子变体（rs317777 在 OLFM5P 中和 rs147062602 在 OR51B5 中），对于与 SCD 中的 TEEs 具有较小显著关联（<5×10）的 34 个其他已知基因中的变体也进行了识别。此外，确定了两个具有相反作用的 10-SNP 常见单倍型。需要进一步复制这些发现。
