CYP2A6及同源基因测序和分型方法的准确性及应用。

IF 1.7 3区 医学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Alec W R Langlois, Ahmed El-Boraie, Koya Fukunaga, Taisei Mushiroda, Michiaki Kubo, Caryn Lerman, Jo Knight, Steven E Scherer, Meghan J Chenoweth, Rachel F Tyndale
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引用次数: 1

摘要

目的:我们评估了19号染色体同源区域的多种基因分型/测序方法,并研究了两种常见的3'-UTR CYP2A6变异与体内活性的关系。方法:对1704名欧洲和非洲血统的个体(n = 1704)进行尼古丁代谢物比率(NMR)和CYP2A6活性指数的表型分析,并使用深度扩增子外显子测序、SNP阵列、基因型插入和靶向捕获测序进行基因分型/测序。扩增子外显子测序是金标准,其他方法在个体内比较CYP2A6、CYP2A7、CYP2A13和CYP2B6外显子,以确定高度不一致的位置。线性回归模型评估CYP2A6*1B和rs8192733基因型(加性编码)与loggnmr的关系。结果:所有方法与金标准的不一致性≤2.6%;不协调的呼叫集中在几个位置。>10%的个体中有15个位点不一致,其中12个位点出现在同源基因之间的高同源区域(例如CYP2A6和CYP2A7)。其中6个,我们的研究和在线数据库中的等位基因频率不一致,表明在线资源存在错误。在欧洲血统组(n = 935), CYP2A6*1B和rs8192733与loggnmr相关(P < 0.001)。一个组合模型发现了两种变体对增加logNMR的主要影响。非洲血统的人也有类似的趋势(n = 506)。结论:用于该19号染色体区域的多种基因分型/测序方法存在基因分型/测序错误,在线数据库也是如此。基因特异性引物和SNP阵列探针必须考虑基因同源性;应避免在单一反应中对相关基因进行短读测序。使用改进的测序方法,我们鉴定了两个功能获得的3'-UTR变体,包括相对较少研究的rs8192733。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Accuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes.

Accuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes.

Objectives: We evaluated multiple genotyping/sequencing approaches in a homologous region of chromosome 19, and investigated associations of two common 3'-UTR CYP2A6 variants with activity in vivo.

Methods: Individuals (n = 1704) of European and African ancestry were phenotyped for the nicotine metabolite ratio (NMR), an index of CYP2A6 activity, and genotyped/sequenced using deep amplicon exon sequencing, SNP array, genotype imputation and targeted capture sequencing. Amplicon exon sequencing was the gold standard to which other methods were compared within-individual for CYP2A6, CYP2A7, CYP2A13, and CYP2B6 exons to identify highly discordant positions. Linear regression models evaluated the association of CYP2A6*1B and rs8192733 genotypes (coded additively) with logNMR.

Results: All approaches were ≤2.6% discordant with the gold standard; discordant calls were concentrated at few positions. Fifteen positions were discordant in >10% of individuals, with 12 appearing in regions of high identity between homologous genes (e.g. CYP2A6 and CYP2A7). For six, allele frequencies in our study and online databases were discrepant, suggesting errors in online sources. In the European-ancestry group (n = 935), CYP2A6*1B and rs8192733 were associated with logNMR (P < 0.001). A combined model found main effects of both variants on increasing logNMR. Similar trends were found in those of African ancestry (n = 506).

Conclusion: Multiple genotyping/sequencing approaches used in this chromosome 19 region contain genotyping/sequencing errors, as do online databases. Gene-specific primers and SNP array probes must consider gene homology; short-read sequencing of related genes in a single reaction should be avoided. Using improved sequencing approaches, we characterized two gain-of-function 3'-UTR variants, including the relatively understudied rs8192733.

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来源期刊
Pharmacogenetics and genomics
Pharmacogenetics and genomics 医学-生物工程与应用微生物
CiteScore
3.20
自引率
3.80%
发文量
47
审稿时长
3 months
期刊介绍: ​​​​Pharmacogenetics and Genomics is devoted to the rapid publication of research papers, brief review articles and short communications on genetic determinants in response to drugs and other chemicals in humans and animals. The Journal brings together papers from the entire spectrum of biomedical research and science, including biochemistry, bioinformatics, clinical pharmacology, clinical pharmacy, epidemiology, genetics, genomics, molecular biology, pharmacology, pharmaceutical sciences, and toxicology. Under a single cover, the Journal provides a forum for all aspects of the genetics and genomics of host response to exogenous chemicals: from the gene to the clinic.
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