Ruchi Rupam, Genovese Giulio, Lee Jessica, Charoonratana Victoria T, Bernhardy Andrea J, Alper Seth L, Kopp Jeffrey B, Thadhani Ravi, Friedman David J, Pollak Martin R
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America; Division of Nephrology, Department of Medicine, University of Florida, Gainesville, Florida, United States of America; Harvard Medical School, Boston, Massachusetts, United States of America.
Stanley Center, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
PLoS One. 2015 May 1;10(5):e0125410. doi: 10.1371/journal.pone.0125410. eCollection 2015.
Two coding variants in the APOL1 gene (G1 and G2) explain most of the high rate of kidney disease in African Americans. APOL1-associated kidney disease risk inheritance follows an autosomal recessive pattern: The relative risk of kidney disease associated with inheritance of two high-risk variants is 7-30 fold, depending on the specific kidney phenotype. We wished to determine if the variability in phenotype might in part reflect structural differences in APOL1 gene. We analyzed sequence coverage from 1000 Genomes Project Phase 3 samples as well as exome sequencing data from African American kidney disease cases for copy number variation. 8 samples sequenced in the 1000 Genomes Project showed increased coverage over a ~100kb region that includes APOL2, APOL1 and part of MYH9, suggesting the presence of APOL1 copy number greater than 2. We reasoned that such duplications should be enriched in apparent G1 heterozygotes with kidney disease. Using a PCR-based assay, we observed the presence of this duplication in additional samples from apparent G0G1 or G0G2 individuals. The frequency of this APOL1 duplication was compared among cases (n = 123) and controls (n = 255) with apparent G0G1 heterozygosity. The presence of APOL1 duplication was observed in 4.06% of cases and 0.78% controls, preliminary evidence that this APOL1 duplication may alter susceptibility to kidney disease (p = 0.03). Taqman-based copy number assays confirmed the presence of 3 APOL1 copies in individuals positive for this specific duplication by PCR assay, but also identified a small number of individuals with additional APOL1 copies of presumably different structure. These observations motivate further studies to better assess the contribution of APOL1 copy number on kidney disease risk and on APOL1 function. Investigators and clinicians genotyping APOL1 should also consider whether the particular genotyping platform used is subject to technical errors when more than two copies of APOL1 are present.
载脂蛋白L1基因（APOL1）中的两个编码变体（G1和G2）解释了非裔美国人中大多数肾病的高发病率。与APOL1相关的肾病风险遗传遵循常染色体隐性模式：与两个高风险变体遗传相关的肾病相对风险为7至30倍，具体取决于特定的肾脏表型。我们希望确定表型的变异性是否可能部分反映APOL1基因的结构差异。我们分析了来自千人基因组计划第三阶段样本的序列覆盖情况以及非裔美国人肾病病例的外显子组测序数据，以检测拷贝数变异。在千人基因组计划中测序的8个样本显示，在一个约100kb的区域（包括APOL2、APOL1和部分MYH9）覆盖增加，这表明存在大于2个拷贝数的APOL1。我们推断，这种重复在患有肾病的明显G1杂合子中应该更为常见。使用基于聚合酶链反应（PCR）的检测方法，我们在来自明显G0G1或G0G2个体的其他样本中观察到了这种重复的存在。在明显为G0G1杂合性的病例（n = 123）和对照（n = 255）中比较了这种APOL1重复的频率。在4.06%的病例和0.78%的对照中观察到了APOL1重复的存在，这是该APOL1重复可能改变肾病易感性的初步证据（p = 0.03）。基于Taqman的拷贝数检测方法通过PCR检测确认了在对这种特定重复呈阳性的个体中存在3个APOL1拷贝，但也鉴定出了少数具有可能不同结构的额外APOL1拷贝的个体。这些观察结果促使进一步的研究，以更好地评估APOL1拷贝数对肾病风险和APOL1功能的贡献。当存在超过两个APOL1拷贝时，对APOL1进行基因分型的研究人员和临床医生还应考虑所使用的特定基因分型平台是否会出现技术错误。
