Pharmaceutical Sciences Department, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
Genome Res. 2012 Jan;22(1):1-8. doi: 10.1101/gr.129668.111. Epub 2011 Dec 6.
Methotrexate is used to treat autoimmune diseases and malignancies, including acute lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results in heterogeneous systemic exposure, clinical efficacy, and toxicity. In a genome-wide association study of children with ALL, we identified SLCO1B1 as harboring multiple common polymorphisms associated with methotrexate clearance. The extent of influence of rare versus common variants on pharmacogenomic phenotypes remains largely unexplored. We tested the hypothesis that rare variants in SLCO1B1 could affect methotrexate clearance and compared the influence of common versus rare variants in addition to clinical covariates on clearance. From deep resequencing of SLCO1B1 exons in 699 children, we identified 93 SNPs, 15 of which were non-synonymous (NS). Three of these NS SNPs were common, with a minor allele frequency (MAF) >5%, one had low frequency (MAF 1%-5%), and 11 were rare (MAF <1%). NS SNPs (common or rare) predicted to be functionally damaging were more likely to be found among patients with the lowest methotrexate clearance than patients with high clearance. We verified lower function in vitro of four SLCO1B1 haplotypes that were associated with reduced methotrexate clearance. In a multivariate stepwise regression analysis adjusting for other genetic and non-genetic covariates, SLCO1B1 variants accounted for 10.7% of the population variability in clearance. Of that variability, common NS variants accounted for the majority, but rare damaging NS variants constituted 17.8% of SLCO1B1's effects (1.9% of total variation) and had larger effect sizes than common NS variants. Our results show that rare variants are likely to have an important effect on pharmacogenetic phenotypes.
甲氨蝶呤用于治疗自身免疫性疾病和恶性肿瘤，包括急性淋巴细胞白血病（ALL）。甲氨蝶呤清除率的个体间差异导致系统暴露、临床疗效和毒性的异质性。在一项 ALL 患儿的全基因组关联研究中，我们发现 SLCO1B1 含有多个与甲氨蝶呤清除率相关的常见多态性。罕见变体与药物基因组表型的影响程度在很大程度上仍未得到探索。我们检验了 SLCO1B1 中的罕见变体是否会影响甲氨蝶呤清除率的假设，并比较了常见变体与罕见变体以及临床协变量对清除率的影响。通过对 699 名儿童 SLCO1B1 外显子的深度重测序，我们鉴定了 93 个 SNP，其中 15 个是非同义突变（NS）。这三个 NS SNP 是常见的，其次要等位基因频率（MAF）>5%，一个是低频的（MAF 1%-5%），11 个是罕见的（MAF<1%）。预测具有功能破坏性的 NS SNP（常见或罕见）在清除率最低的患者中比清除率高的患者更有可能被发现。我们验证了与甲氨蝶呤清除率降低相关的四个 SLCO1B1 单倍型在体外功能降低。在调整其他遗传和非遗传协变量的多元逐步回归分析中，SLCO1B1 变体解释了清除率的 10.7%的人群变异性。在该变异性中，常见的 NS 变体占大多数，但罕见的破坏性 NS 变体构成了 SLCO1B1 效应的 17.8%（总变异的 1.9%），并且比常见的 NS 变体具有更大的效应大小。我们的结果表明，罕见变体很可能对药物遗传学表型有重要影响。
