Due to its distinct phenotype and relatively simple inheritance pattern, the phenylthiocarbamide (PTC) loci is frequently utilized in teaching laboratories to demonstrate genetic concepts such as Mendelian inheritance and population genetics. We have developed a next-generation sequencing and bioinformatics approach to analyze the PTC gene locus to reveal single nucleotide polymorphism (SNP) variation at nucleotide position 785 that predicts tasting ability in humans. Here students purify DNA from their own cheek cells, perform polymerase chain reaction (PCR) amplification of the PTC gene followed by cleaved amplified polymorphic sequence (CAPS) testing. Students perform a second PCR on the PTC loci using high-fidelity Taq to create bar-coded amplicons for next-generation sequencing on the Ion Torrent Personal Genome Machine. Bioinformatic verification reveals polymorphic variation by aligning the entire class PTC PCR fragment sequence to the human gene using Bowtie2 and visualizing the results in the Integrated Genome Viewer. This exercise presents a learning opportunity for students to use next-generation sequencing to predict their own PTC taste sensitivity phenotype coupled with the standard CAPS method. This approach brings the PTC teaching method into the genomics era.

中文翻译：

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使用 Integrated Genome Viewer 揭示教学实验室中苯硫脲基因座富集的扩增子衍生多态性

由于其独特的表型和相对简单的遗传模式，苯硫脲 (PTC) 基因座经常被用于教学实验室来展示遗传概念，如孟德尔遗传和群体遗传学。我们开发了下一代测序和生物信息学方法来分析 PTC 基因位点，以揭示核苷酸位置 785 处的单核苷酸多态性 (SNP) 变异，该变异可预测人类的品尝能力。在这里，学生从自己的脸颊细胞中纯化 DNA，对 PTC 基因进行聚合酶链反应 (PCR) 扩增，然后进行切割扩增多态性序列 (CAPS) 测试。学生使用高保真 Taq 对 PTC 基因座进行第二次 PCR，以在 Ion Torrent 个人基因组机器上创建用于下一​​代测序的条形码扩增子。生物信息学验证通过使用 Bowtie2 将整个类 PTC PCR 片段序列与人类基因对齐并在集成基因组查看器中可视化结果来揭示多态性变异。本练习为学生提供了一个学习机会，可以使用下一代测序来预测他们自己的 PTC 味觉敏感性表型以及标准 CAPS 方法。这种方法将PTC教学方法带入了基因组学时代。