利用臺灣人體生物資料庫分析族群粒線體DNA變異與表型關聯研究

Abstract

粒線體在細胞能量代謝中具有重要的功用，因此粒線體DNA (mtDNA) 的變異在許多疾病的發病機制中扮演著重要的角色。然而，非歐洲族群的粒線體DNA多樣性仍未被充分探索，並且需要更全面的分析與探究。本研究使用臺灣人體生物資料庫 (Taiwan Biobank, TWB) 中基因體資料，探討粒線體DNA上的變異及其與複雜性狀之間的相關性。本研究使用GATK Mutect2分析流程進行粒線體DNA變異檢測，包含單核苷酸變異 (single nucleotide variant, SNV) 與小片段插入與缺失 (insertion and deletion, Indel)，並分析這些變異屬於同質性 (homoplasmy) 或是異質性 (heteroplasmy)。 透過重新分析1,492個全基因體定序資料 (whole-genome sequencing, WGS)，找到了2,361個粒線體DNA變異，其中包括77個在gnomAD database v3.1中未曾報導的新變異。此外，本研究分析了臺灣人體生物資料庫中參與者的粒線體單倍群 (haplogroup)，發現多數人屬於M、D及F單倍群，而這些單倍群在分類上也確實都屬於亞洲的分支。 為了進一步探索粒線體DNA變異對複雜性狀的潛在影響，本研究使用120,163筆全基因體定型資料 (whole-genome genotyping) 對多種性狀進行了粒線體基因組的關聯性分析。首先，我們從WGS資料構建了專為臺灣人群建立的mtDNA基因型差補方法 (imputation panel)，並確認了進行粒線體DNA基因型差補的可行性。隨後利用全基因體定型資料進行關聯分析，發現了粒線體DNA變異和複雜性狀的相關性。首先，我們發現MT-ND2上的基因變異與高度近視相關；另一個位於粒線體DNA上調控複製的重要區域D-loop上的變異則與骨質密度分數相關，表明這個變異可能與骨質疏鬆症的風險有關。此外，本研究還發現了14個與腎功能指標相關的粒線體DNA變異。這些與腎功能相關的變異可以依照關聯性進一步被分為兩組，第一組是在M和N單倍群中的常見變異，屬於演化樹較上游的單倍群標誌 (haplogroup marker)，這些變異位點廣泛分佈在其下游分支中，並顯示了與腎功能惡化的風險相關。另一組變異則散佈在演化數中較下游的B4b單倍群分支中，顯示了與保護腎功能相關。這項研究補足了臺灣人體生物資料庫中對於粒線體DNA分析的不足，也拓展了對臺灣人群中粒線體DNA多樣性的理解。

The genetic variations on mitochondrial DNA (mtDNA) play a significant role in the pathogenesis of various diseases due to their influence on cellular energy metabolism. However, the diversity in mitochondrial genetics among non-European populations remains insufficiently explored and requires more comprehensive genetic insights. This study leverages the extensive genomic data from the Taiwan Biobank (TWB), encompassing over 200,000 individuals, to explore mtDNA variations and their phenotypic associations. This study employed the GATK Mutect2 analysis workflow for mitochondrial single nucleotide variant (SNV), insertion/deletion (Indel) calling to detect both homoplasmy and heteroplasmy. By reanalyzing 1,492 whole-genome sequences (WGS), this study identified 2,361 mtDNA variants, including 77 novel variants not previously reported in the gnomAD v3.1 database. Additionally, the mitochondrial haplogroup analysis underscored the predominance of haplogroups M, D, and F, demonstrating the distribution of Asian lineage mitochondrial haplogroups within the Taiwanese population. To further explore the potential implications of mtDNA variants on complex traits, this study conducted mitochondrial-wide association analyses with a wide range of phenotypes using genotyping array data from 120,163 participants. First, a Taiwanese population-specific mtDNA imputation panel based on 1,492 WGS data has been established, and the feasibility of mtDNA imputation has been evaluated. Subsequently, we performed the association analyses to discover relationships between mtDNA variants and complex traits. We identified variants in the MT-ND2 gene associated with high myopia. A variant in the mitochondrial control region was associated with bone mineral density score, suggesting a potential risk for osteoporosis. Additionally, this study discovered 14 mtDNA variants correlated with renal function biomarkers, including serum creatinine and eGFR. These variants can be divided into two independent sets. The first set includes ancestral variants in haplogroups M and N, which are broadly distributed in their downstream haplogroups. These markers are associated with decreased eGFR levels, indicating a potential risk correlation with renal dysfunction. The other set contained variants in lineage B4b and was associated with elevated eGFR and reduced creatinine, suggesting a protective correlation with renal function. This study significantly enriches our understanding of mtDNA diversity in the Taiwanese population and underscores the importance of including diverse genetic backgrounds in mitochondrial research to uncover relevant genetic insights that may be masked in predominantly European studies.