Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data.
Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data.
复制标题
使用 SNP 阵列数据对已知和新型 CYP2A6 结构变体进行基因分型、表征和插补。
DOI：
10.1038/s10038-023-01148-y
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发表时间：
2023
影响因子：
3.5
通讯作者：
Tyndale,RachelF
中科院分区：
文献类型：
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作者：
Langlois,AlecWR;El-Boraie,Ahmed;Pouget,JennieG;Cox,LisaSanderson;Ahluwalia,JasjitS;Fukunaga,Koya;Mushiroda,Taisei;Knight,Jo;Chenoweth,MeghanJ;Tyndale,RachelF
CYP 2A 6代谢灭活尼古丁。更快的CYP 2A 6活性与更严重的吸烟和更高的肺癌风险有关。CYP 2A 6基因具有多态性，包括基因缺失（CYP 2A 6 *4）、重复（CYP 2A 6 *1×2）和与CYP 2A 7假基因的杂交（CYP 2A 6 *12、CYP 2A 6 *34）等功能结构变异。SV由于其复杂的遗传结构而对基因型具有挑战性。本研究的目的是建立一种可靠的SV基因分型方法，对已知的SV和新的SV进行功能表型分析，并探讨用SNP芯片数据对两个祖先群体进行CYP 2A 6SV插补的可行性。欧洲-（欧元; n= 935）和非洲（AFR;n= 964）血统的个体使用Illumina阵列进行SNP基因分型，使用Taqman拷贝数（CN）测定法进行CYP 2A 6SV基因分型。SV特异性PCR扩增和桑格测序用于表征一种新的SV。使用尼古丁代谢物比率（CYP 2A 6活性的生物标志物）对SV患者进行表型分析。整合SV二倍型和SNP阵列数据并定相以产生祖先特异性SV参考组。采用留一法交叉验证法考察CYP 2A 6SV插补的可行性。开发了一个最小的方案，需要三个Taqman CN测定CYP 2A 6SV基因分型，并复制了已知的SV与活性的相关性。第一个结构域交换CYP 2A 6-CYP 2A 7杂合SV，CYP 2A 6 *53，被鉴定，测序，并与较低的CYP 2A 6活性相关。在EUR和AFR中，大多数SV等位基因都是通过插补确定的（分别>70%和> 60%）;重要的是，假阳性率<1%。这些结果证实，CYP 2A 6 SV插补可以识别大多数SV等位基因，包括一个新的SV。
CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. TheCYP2A6gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1×2), and hybrids with theCYP2A7pseudogene (CYP2A6*12,CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility ofCYP2A6SV imputation from SNP array data in two ancestry populations. European- (EUR;n= 935) and African- (AFR;n= 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and forCYP2A6SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility ofCYP2A6SV imputation. A minimal protocol requiring three Taqman CN assays forCYP2A6SV genotyping was developed and known SV associations with activity were replicated. The first domain swapCYP2A6-CYP2A7hybrid SV,CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm thatCYP2A6SV imputation can identify most SV alleles, including a novel SV.