BACKGROUND Phenylketonuria (PKU) is the most common inborn error of amino acid metabolism in Europe. The reasons underlying the high prevalence of heterozygous carriers are not clearly understood. We aimed to look for pathogenic PAH variant enrichment according to geographical areas and patients' ethnicity using a multiethnic nationwide cohort of patients with PKU in France. We subsequently appraised the population differentiation, balancing selection and the molecular evolutionary history of the PAH locus. METHODS The French nationwide PKU study included patients who have been referred at the national level to the University Hospital of Nancy, and for whom a molecular diagnosis of phenylketonuria was made by Sanger sequencing. We performed enrichment analyses by comparing alternative allele frequencies using Fisher's exact test with Bonferroni adjustment. We estimated the amount of genetic differentiation among populations using Wright's fixation index (Fst). To estimate the molecular evolutionary history of the PAH gene, we performed phylogenetic and evolutionary analyses using whole-genome and exome-sequencing data from healthy individuals and non-PKU patients, respectively. Finally, we used exome-wide association study to decipher potential genetic loci associated with population divergence on PAH. FINDINGS The study included 696 patients and revealed 132 pathogenic PAH variants. Three geographical areas showed significant enrichment for a pathogenic PAH variant: North of France (p.Arg243Leu), North-West of France (p.Leu348Val), and Mediterranean coast (p.Ala403Val). One PAH variant (p.Glu280Gln) was significantly enriched among North-Africans (OR = 23·23; 95% CI: 9·75-55·38). PAH variants exhibiting a strong genetic differentiation were significantly enriched in the 'Biopterin_H' domain (OR = 6·45; 95% CI: 1·99-20·84), suggesting a balancing selection pressure on the biopterin function of PAH. Phylogenetic and timetree analyses were consistent with population differentiation events on European-, African-, and Asian-ancestry populations. The five PAH variants most strongly associated with a high selection pressure were phylogenetically close and were located within the biopterin domain coding region of PAH or in its vicinity. Among the non-PAH loci potentially associated with population divergence, two reached exome-wide significance: SSPO (SCO-spondin) and DBH (dopamine beta-hydroxylase), involved in neuroprotection and metabolic adaptation, respectively. INTERPRETATION Our data provide evidence on the combination of evolutionary and adaptive events in populations with distinct ancestries, which may explain the overdominance of some genetic variants on PAH. FUNDING French National Institute of Health and Medical Research (INSERM) UMR_S 1256.

中文翻译：

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PAH 基因座的群体和进化遗传学揭示苯丙酮尿症的过度优势和适应性机制：多种族研究的结果。


背景苯丙酮尿症（PKU）是欧洲最常见的氨基酸代谢先天性疾病。杂合子携带者高患病率的原因尚不清楚。我们的目的是利用法国多民族全国 PKU 患者队列，根据地理区域和患者种族寻找致病性 PAH 变异富集情况。我们随后评估了 PAH 基因座的群体分化、平衡选择和分子进化历史。方法 法国全国 PKU 研究纳入了在国家一级转诊至南锡大学医院的患者，并通过桑格测序对这些患者进行了苯丙酮尿症分子诊断。我们通过使用 Fisher 精确检验和 Bonferroni 调整比较替代等位基因频率来进行富集分析。我们使用赖特固定指数（Fst）估计了人群之间遗传分化的程度。为了估计 PAH 基因的分子进化史，我们分别使用健康个体和非 PKU 患者的全基因组和外显子组测序数据进行系统发育和进化分析。最后，我们利用全外显子组关联研究来破译与 PAH 群体差异相关的潜在遗传位点。结果 该研究纳入了 696 名患者，发现了 132 种致病性 PAH 变异。三个地理区域显示出致病性 PAH 变异的显着富集：法国北部 (p.Arg243Leu)、法国西北部 (p.Leu348Val) 和地中海沿岸 (p.Ala403Val)。一种 PAH 变异 (p.Glu280Gln) 在北非人中显着富集 (OR = 23·23；95% CI：9·75-55·38)。 表现出强烈遗传分化的 PAH 变体在“Biopterin_H”结构域中显着富集（OR = 6·45；95% CI：1·99-20·84），表明 PAH 的生物蝶呤功能存在平衡选择压力。系统发育和时间树分析与欧洲、非洲和亚洲血统群体的群体分化事件一致。与高选择压力最密切相关的五个 PAH 变体在系统发育上接近，并且位于 PAH 的生物蝶呤结构域编码区域内或其附近。在可能与群体差异相关的非 PAH 位点中，有两个达到了外显子组范围内的显着性：SSPO（SCO-spondin）和 DBH（多巴胺 β-羟化酶），分别参与神经保护和代谢适应。解释我们的数据提供了具有不同祖先的人群中进化和适应事件相结合的证据，这可能解释了某些遗传变异对多环芳烃的过度支配。资助法国国家健康与医学研究所 (INSERM) UMR_S 1256。