台灣布魯蓋達症候群全基因插補暨關聯性研究

A genome-wide association and imputation study of Brugada Syndrome in Taiwan

鄭凱元(Kai-Yuan Cheng)

指導教授 ： 盧子彬

國立臺灣大學/公共衛生學院/流行病學與預防醫學研究所/碩士(2020年)

https://doi.org/10.6342/NTU202001846

摘要

背景：布魯蓋達症候群為一遺傳性心律不整之罕見疾病，此疾病會造成心臟電流出現異常而提升心因性猝死之風險。布魯蓋達症候群於歐洲之盛行率約為0.01-0.05%，在亞洲地區較高約為0.12%。目前布魯蓋達症候群被認為是體染色體顯性遺傳疾病，其中位於第三條染色體上的SCN5A基因變異為主要的風險因子，不過在臨床上約有20-30%的患者帶有SCN5A基因變異，另外仍有其他離子通道相關基因被發現與布魯蓋達症候群有關，故布魯蓋達症候群在臨床上僅約30-35%之病人其致病原因是由於遺傳因素所導致，反之則代表有超過65%的患者其致病過程仍屬未知。過去研究針對歐洲地區族群進行布魯蓋達症候群全基因體關聯性研究，其結果顯示在歐洲地區族群中有兩個顯著的遺傳變異位點(rs10628132及rs9388451)，然而由於族群與地區間的布魯蓋達症候群發病機率有所差異，因此本研究預期針對台灣布魯蓋達症候群患者之基因資料找出重要的遺傳變異位點，並驗證過去研究所提出的布魯蓋達症候群相關遺傳變異，以提供布魯蓋達症候群遺傳因子以及致病機轉更進一步的了解。
研究方法：本研究之病例組來自於全台灣各地醫療院所共190位患者，此190位患者中又依照SCN5A基因是否變異分為SCN5A變異組28人以及野生型SCN5A組162人；正常對照組資料自台灣人體生物資料庫15,981人中抽樣760人。這些個體透過Affymetrix公司出品之Axiom Genome_Wide TWB Array Plate微陣列晶片進行基因型鑑定。本論文透過基因插補增加台灣族群基因序列的覆蓋率，接著使用費雪精確檢定針對整體布魯蓋達症候群患者、SCN5A變異組以及野生型SCN5A組進行單一因子分析。另外，針對整體布魯蓋達症候群患者分別建立相加、顯性及隱性模式的單一因子Cox比例風險模型，以了解不同遺傳模式的單一因子對於布魯蓋達症候群之風險情形。最後使用多基因遺傳風險評分以評估多個遺傳位點同時對疾病的影響。
結果：針對全基因體進行基因插補後，從原始晶片上的648,629個遺傳位點擴展至8,081,033個遺傳位點後進行後續分析。在單一因子分析上，整體布魯蓋達症候群患者全基因體中共有19個顯著位點(p value < 6.187×〖10〗^(-9)(邦費羅尼校正))。單一因子Cox比例風險模型則可以若病患在特定遺傳位點中帶有風險位點，則該病患之平均發病年齡相較於其他病患而言將會提前大約十五年。多基因遺傳風險分數模型中，分數落在較低區間的健康族群帶有布魯蓋達症候群的風險顯著的低於分數落在較高區間的健康族群。
結論：本研究於發現了許多在台灣族群中特有的布魯蓋達症候群相關遺傳變異，未來仍需透過其他外部資料進行驗證。此研究結果有助於了解布魯蓋達症候群致病機轉及生物傳導途徑，以協助未來尋找布魯蓋達症候群早期診斷的生物標記以及藥物上開發提供參考依據。

關鍵字

布魯蓋達症候群 ； 基因插補 ； 全基因體關聯性研究 ； 存活分析 ； 多基因遺傳風險評分

並列摘要

Introduction: Brugada syndrome (BrS) is a rare disease that increases the risk of abnormal heart rhythms and sudden cardiac death. The prevalence of BrS is estimated to be 1-5 cases per 10,000 people, and its incidence and prevalence rates are higher in the Asia populations (12 cases per 10,000 people). BrS is a genetic disorder in which the electrical activity within the heart is abnormal, and SCN5A is considered as the major genetic risk factor. However, there are about 20-30% of BrS patients can be attributed to SCN5A; furthermore, since BrS patients can also be attributed to some ion channel related SNPs, the cause of BrS among 30-35% BrS patients is due to genetic factors, which means that there are more than 65% BrS patients remain unknown genetic disorder pattern. In a previous GWAS study, two SNP loci (rs10428132, rs9388451) were reported in the Europe population. Although these two SNP loci were validated in Taiwanese, whether other important SNPs exist in Taiwanese patients only remains unclear. Therefore, the aim of this study is to identify novel SNPs associated with BrS in Taiwanese by using the imputed whole genome variants.
Materials and method: A total of 190 BrS cases were recruited from hospitals and medical centers in Taiwan, and the BrS cases can be further divided into SCN5A mutation (28 cases) and SCN5A wild type (162 cases) by whether the patient’s SCN5A is mutated. A total of 760 matched healthy controls were selected from Taiwan Biobank, which has collected 15,981 healthy samples. The genotyping experiments were performed by using the Axiom Genome_Wide TWB Array Plate from the Affymetirx company. The DNA variants of all 950 samples were imputed based on the allele frequencies obtained from the East Asian populations in the 1000 genome project after quality control, which also increased the coverage of SNP in Taiwanese population. In addition, a Fisher exact test based on the imputed data of three groups of cases (total BrS, SCN5A mutation, SCN5A wild type) were used to evaluate the effect of SNP locus. A Cox proportional hazard model was built by using three genetic models (additive, dominant, recessive) for total BrS cases to investigate the diagnostic effect. Lastly, a polygenic risk score model was used to evaluate the combination effects of multi-markers.
Result: All 950 samples passing the quality control steps, and the SNP number was increased to 8,081,033 from 648,629 after the genome-wide imputation process. A total of 19 SNPs were significant in Logistic regression of total BrS cases(p value < 6.187×〖10〗^(-9) (bonferroni correction)). In Cox proportional hazard model analysis, if a patient carries risk allele on specific SNPs, the average offset age was found to be 15 years earlier than the patients without risk allele. In the result of Polygenic Risk Score model, the healthy population with lower score have a significantly lower risk of suffering from BrS.
Conclusion: Several novel DNA variants were identified in Taiwanese BrS patients, and further investigations were warranted to elucidate their etiology and functional impact in BrS.

並列關鍵字

Brugada syndrome ； genetic imputation ； GWAS ； survival ； PRS

參考文獻

1. Vatta, M., et al., Genetic and biophysical basis of sudden unexplained nocturnal death syndrome (SUNDS), a disease allelic to Brugada syndrome. Hum Mol Genet, 2002. 11(3): p. 337-45.

2. Nademanee, K., Sudden unexplained death syndrome in Southeast Asia. Am J Cardiol, 1997. 79(6a): p. 10-1.

3. Brugada, J., P. Brugada, and R. Brugada, The syndrome of right bundle branch block ST segment elevation in V1 to V3 and sudden death--the Brugada syndrome. Europace, 1999. 1(3): p. 156-66.

4. Matsuo, K., et al., The circadian pattern of the development of ventricular fibrillation in patients with Brugada syndrome. European Heart Journal, 1999. 20(6): p. 465-470.

5. Brugada, R., et al., Brugada syndrome. Methodist DeBakey cardiovascular journal, 2014. 10(1): p. 25-28.