Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Molecular Pharmacology Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Int J Mol Sci. 2020 Jan 30;21(3):896. doi: 10.3390/ijms21030896.
To ensure accuracy of (rs3064744) genotyping for use in pharmacogenomics-based irinotecan dosing, we tested the concordance of several commonly used genotyping technologies. Heuristic genotype groupings and principal component analysis demonstrated concordance for Illumina sequencing, fragment analysis, and fluorescent PCR. However, Illumina sequencing and fragment analysis returned a range of fragment sizes, likely arising due to PCR "slippage". Direct sequencing was accurate, but this method led to ambiguous electrophoregrams, hampering interpretation of heterozygotes. Gel sizing, pyrosequencing, and array-based technologies were less concordant. Pharmacoscan genotyping was concordant, but it does not ascertain genotypes that are common in African populations. Method-based genotyping differences were also observed in the publication record ( < 0.0046), although fragment analysis and direct sequencing were concordant ( = 0.11). Genotyping errors can have significant consequences in a clinical setting. At the present time, we recommend that all genotyping for this allele be conducted with fluorescent PCR (fPCR).
为了确保基于药物基因组学的伊立替康剂量使用中（rs3064744）基因分型的准确性，我们测试了几种常用基因分型技术的一致性。启发式基因型分组和主成分分析表明，Illumina 测序、片段分析和荧光 PCR 具有一致性。然而，Illumina 测序和片段分析返回了一系列片段大小，可能是由于 PCR“滑动”引起的。直接测序是准确的，但这种方法导致电泳图谱不明确，阻碍了杂合子的解释。凝胶大小分析、焦磷酸测序和基于阵列的技术一致性较差。Pharmacoscan 基因分型是一致的，但它不能确定在非洲人群中常见的基因型。在文献记录中也观察到基于方法的基因分型差异（<0.0046），尽管片段分析和直接测序是一致的（=0.11）。在临床环境中，基因分型错误可能会产生重大影响。目前，我们建议使用荧光 PCR（fPCR）对该等位基因进行所有基因分型。
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