αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia
αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia
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DOI：
10.1073/pnas.1422238112
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发表时间：
2015-04-14
影响因子：
11.1
通讯作者：
Coller, Barry S.
中科院分区：
文献类型：
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作者：
Buitrago, Lorena;Rendon, Augusto;Coller, Barry S.
下一代测序正在改变我们对人类遗传变异的理解，但评估新变异的功能影响提出了挑战。我们分析了整合素α IIb β 3受体亚基基因ITGA2B和ITGB3的错义变异体，这些错义变异体由来自16108个个体的32000个等位基因组成，这些基因是通过血小板基因组项目的全外显子组或全基因组测序鉴定的。我们对这些基因的111个错义变异进行了分析，这些基因先前报道与Glanzmann血栓减少症（GT）相关，20个与同种免疫性血小板减少症相关，5个与异源性/巨量血小板减少症相关。我们在ITGA2B中鉴定出114种新的错义变异（影响类似于11%的氨基酸），在ITGB3中鉴定出68种新的错义变异（影响类似于9%的氨基酸）。96%的变异小等位基因频率(MAF) < 0.1%，表明其罕见性。基于序列保守、MAF和在完整的α IIb β 3模型上的定位，我们选择了三个影响先前与GT相关的氨基酸在HEK293细胞中表达的新变体。α IIb P176H和β 3 C547G严重降低α IIb β 3表达，而aIIb P943A部分降低α IIb β 3表达，对纤维蛋白原结合无影响。我们使用结合注释依赖耗尽、Polyphen 2-HDIV的受体工作特征曲线，并将不耐受和耐受进行分类，以估计可能有害的新变异的百分比。在最佳临界值（检测GT突变的灵敏度为69-98%）下，预计27%至71%的新型aIIb或β 3错义变体是有害的。我们的数据有助于理解α IIb β 3的进化压力，并强调了预测新型错义变异的临床意义所面临的挑战。
Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin alpha IIb beta 3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the Thrombo-Genomics project, comprising similar to 32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting similar to 11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting similar to 9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of alpha IIb beta 3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. alpha IIb P176H and beta 3 C547G severely reduced alpha IIb beta 3 expression, whereas aIIb P943A partially reduced alpha IIb beta 3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69-98% sensitivity in detecting GT mutations, between 27% and 71% of the novel aIIb or beta 3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on alpha IIb beta 3 and highlight the challenges in predicting the clinical significance of novel missense variants.