Abstract：
BACKGROUND: Determination of DPYD and UGT1A1 polymorphisms prior to 5-fluorouracil and irinotecan therapy is crucial for avoiding severe adverse drug effects. Hence, there is a pressing need for accurate and reliable genotyping methods for the most common DPYD and UGT1A1 polymorphisms. In this study, we introduce a novel polymerase chain reaction (PCR) melting curve analysis method for discriminating DPYD c.1236G > A, c.1679 T > G, c.2846A > T, IVS14 + 1G > A and UGT1A1*1, *28, *6 (G71R) genotypes.
METHODS: Following protocol optimization, this technique was employed to genotype 28 patients, recruited between March 2023 and October 2023, at the First Affiliated Hospital of Xiamen University. These patients included 20 with UGT1A1 *1/*1, 8 with UGT1A1 *1/*28, 4 with UGT1A1 *28/*28, 22 with UGT1A1*6 G/G, 6 with UGT1A1*6 G/A, 4 with UGT1A1*6 A/A, 27 with DPYD(c.1236) G/G, 3 with DPYD(c.1236) G/A, 2 with DPYD(c.1236) A/A, 27 with DPYD(c.1679) T/T, 2 with DPYD(c.1679) T/G, 3 with DPYD(c.1679) G/G, 28 with DPYD(c.2846A/T) A/A, 2 with DPYD(c.2846A/T) A/T, 2 with DPYD(c.2846A/T) T/T, 28 with DPYD(c.IVS14 + 1) G/G, 2 with DPYD(c.IVS14 + 1) G/G, and 2 with DPYD(c.IVS14 + 1) G/G, as well as 3 plasmid standards. Method accuracy was assessed by comparing results with those from Sanger sequencing or Multiplex quantitative PCR(qPCR). Intra- and inter-run precision of melting temperatures (Tms) were calculated to evaluate reliability, and sensitivity was assessed through limit of detection examination.
RESULTS: The new method accurately identified all genotypes and exhibited higher accuracy than Multiplex qPCR. Intra- and inter-run coefficients of variation for Tms were both ≤1.97 %, with standard deviations ≤0.95 °C. The limit of detection was 0.09 ng/μL of input genomic DNA.
CONCLUSIONS: Our developed PCR melting curve analysis offers accurate, reliable, rapid, simple, and cost-effective detection of DPYD and UGT1A1 polymorphisms. Its application can be easily extended to clinical laboratories equipped with a fluorescent PCR platform.
METHODS: Following protocol optimization, this technique was employed to genotype 28 patients, recruited between March 2023 and October 2023, at the First Affiliated Hospital of Xiamen University. These patients included 20 with UGT1A1 *1/*1, 8 with UGT1A1 *1/*28, 4 with UGT1A1 *28/*28, 22 with UGT1A1*6 G/G, 6 with UGT1A1*6 G/A, 4 with UGT1A1*6 A/A, 27 with DPYD(c.1236) G/G, 3 with DPYD(c.1236) G/A, 2 with DPYD(c.1236) A/A, 27 with DPYD(c.1679) T/T, 2 with DPYD(c.1679) T/G, 3 with DPYD(c.1679) G/G, 28 with DPYD(c.2846A/T) A/A, 2 with DPYD(c.2846A/T) A/T, 2 with DPYD(c.2846A/T) T/T, 28 with DPYD(c.IVS14 + 1) G/G, 2 with DPYD(c.IVS14 + 1) G/G, and 2 with DPYD(c.IVS14 + 1) G/G, as well as 3 plasmid standards. Method accuracy was assessed by comparing results with those from Sanger sequencing or Multiplex quantitative PCR(qPCR). Intra- and inter-run precision of melting temperatures (Tms) were calculated to evaluate reliability, and sensitivity was assessed through limit of detection examination.
RESULTS: The new method accurately identified all genotypes and exhibited higher accuracy than Multiplex qPCR. Intra- and inter-run coefficients of variation for Tms were both ≤1.97 %, with standard deviations ≤0.95 °C. The limit of detection was 0.09 ng/μL of input genomic DNA.
CONCLUSIONS: Our developed PCR melting curve analysis offers accurate, reliable, rapid, simple, and cost-effective detection of DPYD and UGT1A1 polymorphisms. Its application can be easily extended to clinical laboratories equipped with a fluorescent PCR platform.
摘要：
背景：在5-氟尿嘧啶和伊立替康治疗之前确定DPYD和UGT1A1多态性对于避免严重的药物不良反应至关重要。因此，对于最常见的DPYD和UGT1A1多态性,迫切需要准确可靠的基因分型方法.在这项研究中,我们介绍了一种新的聚合酶链反应（PCR）熔解曲线分析方法，用于区分DPYDc.1236G>A，c.1679T>G，c.2846A>T，IVS14+1G>A和UGT1A1*1、*28、*6(G71R)基因型。
方法：在协议优化之后，这项技术被用于对28名患者进行基因分型，2023年3月至2023年10月在厦门大学第一附属医院招募。这些患者包括20例UGT1A1*1/*1，8例UGT1A1*1/*28，4例UGT1A1*28/*28，22例UGT1A1*6G/G，6与UGT1A1*6G/A，4与UGT1A1*6A/A，27与DPYD（c.1236）G/G，3与DPYD（c.1236）G/A，2与DPYD（c.1236）A/A，27与DPYD（c.1679）T/T，2与DPYD（c.1679）T/G，3与DPYD（c.1679）G/G，28与DPYD（c.2846A/T）A/A，2与DPYD（c.2846A/T）A/T，2与DPYD（c.2846A/T）T/T，28与DPYD（c。IVS14+1)G/G,2与DPYD（c。IVS14+1)G/G,和2与DPYD（c。IVS14+1)G/G,以及3个质粒标准。通过将结果与来自Sanger测序或多重定量PCR(qPCR)的结果进行比较来评估方法准确性。计算熔融温度(Tms)的运行内和运行间精度以评估可靠性，通过检测限检查评估灵敏度。
结果：新方法准确地鉴定了所有基因型，并表现出比MultiplexqPCR更高的准确性。Tms的运行内和运行间变异系数均≤1.97%，标准偏差≤0.95°C。检测限为0.09ng/μL输入基因组DNA。
结论：我们开发的PCR熔解曲线分析提供了准确的，可靠,快速,简单,以及DPYD和UGT1A1多态性的经济有效检测。它的应用可以很容易地扩展到配备荧光PCR平台的临床实验室。
方法：在协议优化之后，这项技术被用于对28名患者进行基因分型，2023年3月至2023年10月在厦门大学第一附属医院招募。这些患者包括20例UGT1A1*1/*1，8例UGT1A1*1/*28，4例UGT1A1*28/*28，22例UGT1A1*6G/G，6与UGT1A1*6G/A，4与UGT1A1*6A/A，27与DPYD（c.1236）G/G，3与DPYD（c.1236）G/A，2与DPYD（c.1236）A/A，27与DPYD（c.1679）T/T，2与DPYD（c.1679）T/G，3与DPYD（c.1679）G/G，28与DPYD（c.2846A/T）A/A，2与DPYD（c.2846A/T）A/T，2与DPYD（c.2846A/T）T/T，28与DPYD（c。IVS14+1)G/G,2与DPYD（c。IVS14+1)G/G,和2与DPYD（c。IVS14+1)G/G,以及3个质粒标准。通过将结果与来自Sanger测序或多重定量PCR(qPCR)的结果进行比较来评估方法准确性。计算熔融温度(Tms)的运行内和运行间精度以评估可靠性，通过检测限检查评估灵敏度。
结果：新方法准确地鉴定了所有基因型，并表现出比MultiplexqPCR更高的准确性。Tms的运行内和运行间变异系数均≤1.97%，标准偏差≤0.95°C。检测限为0.09ng/μL输入基因组DNA。
结论：我们开发的PCR熔解曲线分析提供了准确的，可靠,快速,简单,以及DPYD和UGT1A1多态性的经济有效检测。它的应用可以很容易地扩展到配备荧光PCR平台的临床实验室。
