Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5' and 5 kb 3' of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration. In phase 2, a 510 kb region, which included the entire topologically associated domain of CFTR, was sequenced in 276 F508del homozygotes drawn from extremes of lung function. An additional 163 individuals who carried F508del and a different CF-causing variant were sequenced to inform haplotype construction. Region-based burden testing of both common and rare variants revealed seven regions of significance (α=0.01), five of which overlapped known regulatory elements or chromatin interactions. Notably, the -80 kb locus known to interact with the CFTR promoter was associated with variation in both CF traits. Haplotype analysis revealed a single rare recombination event (1.9% frequency) in intron 15 of CFTR bearing the F508del variant. Otherwise, the majority of F508del chromosomes were markedly similar, consistent with a single origin of the F508del allele. Together, these high-resolution variant analyses of the CFTR locus suggest a role for non-coding regulatory motifs in trait variation among individuals carrying the common CF allele.

中文翻译：

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对 762 个 F508del 纯合子中的 CFTR 进行深度重测序揭示了与囊性纤维化疾病特征相关的非编码变异簇。


在患有孟德尔疾病的个体中，甚至在致病基因具有相同基因型的个体中，通常观察到广泛的表型变异。为了确定 CFTR 内部及其周围的变异是否会导致囊性纤维化 (CF) 的表型变异，我们对 762 名常见 CF 致病变异 F508del 纯合子的患者进行了 CFTR 深度测序。在第 1 阶段，对选自汗液氯化物浓度极端的 486 个 F508del 纯合子进行了约 200 kb 的测序，其中包含 CFTR 并延伸 10 kb 5' 和 5 kb 3' 基因。在第 2 阶段，对取自肺功能极端情况的 276 个 F508del 纯合子中的一个 510 kb 区域（包括 CFTR 的整个拓扑相关结构域）进行了测序。对另外 163 名携带 F508del 和不同 CF 致病变异的个体进行了测序，以了解单倍型构建。对常见和罕见变异的基于区域的负荷测试揭示了七个重要区域（α = 0.01），其中五个与已知的调控元件或染色质相互作用重叠。值得注意的是，已知与 CFTR 启动子相互作用的 -80 kb 基因座与两个 CF 性状的变异相关。单倍型分析揭示了带有 F508del 变体的 CFTR 内含子 15 中的单个罕见重组事件（频率为 1.9%）。除此之外，大多数 F508del 染色体明显相似，与 F508del 等位基因的单一起源一致。总之，这些 CFTR 基因座的高分辨率变异分析表明，非编码调控基序在携带常见 CF 等位基因的个体性状变异中发挥着作用。