DataSheet1_Whole-genome sequencing reveals rare variants associated with gout in Taiwanese males.PDF

To identify rare variants (RVs) of gout, we sequenced the whole genomes of 321 male gout patients and combined these with those of 64 male gout patients and 682 normal controls at Taiwan Biobank. We performed ACAT-O to identify 682 significant RVs (p < 3.8 × 10−8) clustered on chromosomes 1, 7, 10, 16, and 18. To prioritize causal variants effectively, we sifted them by Combined Annotation-Dependent Depletion score >10 or |effect size| ≥ 1.5 for those without CADD scores. In particular, to the best of our knowledge, we identified the rare variants rs559954634, rs186763678, and 13-85340782-G-A for the first time to be associated with gout in Taiwanese males. Importantly, the RV rs559954634 positively affects gout, and its neighboring gene NPHS2 is involved in serum urate and expressed in kidney tissues. The kidneys play a major role in regulating uric acid levels. This suggests that rs559954634 may be involved in gout. Furthermore, rs186763678 is in the intron of NFIA that interacts with SLC2A9, which has the most significant effect on serum urate. Note that gene-gene interaction NFIA-SLC2A9 is significantly associated with serum urate in the Italian MICROS population and a Croatian population. Moreover, 13-85340782-G-A significantly affects gout susceptibility (odds ratio 6.0; P = 0.038). The >1% carrier frequencies of these potentially pathogenic (protective) RVs in cases (controls) suggest the revealed associations may be true; these RVs deserve further studies for the mechanism. Finally, multivariate logistic regression analysis shows that the rare variants rs559954634 and 13-85340782-G-A jointly are significantly associated with gout susceptibility.

为鉴定痛风的罕见变异（rare variants, RVs），我们对321名男性痛风患者开展全基因组测序，并将该测序数据与台湾生物库（Taiwan Biobank）收录的64名男性痛风患者及682名正常对照的全基因组数据进行整合。我们采用ACAT-O方法进行关联分析，最终鉴定出682个显著罕见变异（P < 3.8 × 10⁻⁸），这些变异聚集于1号、7号、10号、16号及18号染色体。为高效筛选致病变异，我们通过以下规则进行筛选：联合注释依赖型剔除（Combined Annotation-Dependent Depletion, CADD）评分>10，或对无CADD评分的变异设置|效应量|≥1.5。尤为关键的是，据我们所知，本研究首次在台湾男性人群中鉴定出与痛风相关的罕见变异rs559954634、rs186763678及13-85340782-G-A。值得注意的是，罕见变异rs559954634对痛风具有正向致病效应，其邻近基因NPHS2参与血清尿酸调控且在肾脏组织中特异性表达。肾脏是调控机体尿酸水平的核心器官，这提示rs559954634可能直接参与痛风的发病过程。此外，rs186763678位于NFIA基因的内含子区域，该基因可与SLC2A9发生相互作用，而SLC2A9是目前已知对血清尿酸水平影响最显著的基因。已有研究证实，NFIA与SLC2A9的基因-基因相互作用在意大利MICROS队列及克罗地亚人群中与血清尿酸水平显著相关。另外，变异位点13-85340782-G-A对痛风易感性具有显著影响（比值比=6.0；P=0.038）。上述潜在致病性（保护性）罕见变异在病例组（对照组）中的携带者频率均>1%，提示本研究揭示的关联具有真实性，上述罕见变异值得开展进一步的机制研究。最后，多变量logistic回归分析显示，罕见变异rs559954634与13-85340782-G-A联合后，与痛风易感性显著相关。