PDF(Pubmed)
Abstract：
Cystic fibrosis is caused by biallelic pathogenic variants in the CFTR gene, which contains a polymorphic (TG)mTn sequence (the \"poly-T/TG tract\") in intron 9. While T9 and T7 alleles are benign, T5 alleles with longer TG repeats, e.g., (TG)12T5 and (TG)13T5, are clinically significant. Thus, professional medical societies currently recommend reporting the TG repeat size when T5 is detected. Sanger sequencing is a cost-effective method of genotyping the (TG)mTn tract; however, its polymorphic length substantially complicates data analysis. We developed CFTR-TIPS, a freely available web-based software tool that infers the (TG)mTn genotype from Sanger sequencing data. This tool detects the (TG)mTn tract in the chromatograms, quantifies goodness of fit with expected patterns, and visualizes the results in a graphical user interface. It is broadly compatible with any Sanger chromatogram that contains the (TG)mTn tract ± 15 bp. We evaluated CFTR-TIPS using 835 clinical samples previously analyzed in a CLIA-certified, CAP-accredited laboratory. When operated fully automatically, CFTR-TIPS achieved 99.8% concordance with our clinically validated manual workflow, while generally taking less than 10 s per sample. There were two discordant samples: one due to a co-occurring heterozygous duplication that confounded the tool and the other due to incomplete (TG)mTn tract detection in the reverse chromatogram. No clinically significant misclassifications were observed. CFTR-TIPS is a free, accurate, and rapid tool for CFTR (TG)mTn tract genotyping using cost-effective Sanger sequencing. This tool is suitable both for automated use and as an aid to manual review to enhance accuracy and reduce analysis time.
摘要：
囊性纤维化是由CFTR基因的双等位基因致病变异引起的，内含子9中包含多态性（TG）mTn序列（“poly-T/TGtract”）。虽然T9和T7等位基因是良性的，TG重复序列较长的T5等位基因，例如，(TG)12T5和(TG)13T5具有临床意义。因此，专业医学协会目前建议在检测到T5时报告TG重复大小.Sanger测序是对（TG）mTn束进行基因分型的一种经济有效的方法；但是，其多态长度实质上使数据分析复杂化。我们开发了CFTR-TIPS,一个免费提供的基于网络的软件工具，从Sanger测序数据推断（TG）mTn基因型。该工具检测色谱图中的(TG)mTn束,量化与预期模式的拟合优度，并在图形用户界面中可视化结果。它与包含（TG）mTn束±15bp的任何Sanger色谱图广泛兼容。我们使用先前在CLIA认证中分析的835个临床样本评估了CFTR-TIPS，CAP认证实验室。当全自动操作时，CFTR-TIPS与我们经过临床验证的手动工作流程实现了99.8%的一致性，而每个样本通常需要少于10s。有两个不一致的样品：一个是由于共同发生的杂合复制混淆了工具，另一个是由于反向色谱图中不完整的（TG）mTn束检测。没有观察到临床上显著的错误分类。CFTR-TIPS是免费的，准确,使用具有成本效益的Sanger测序进行CFTR（TG）mTn道基因分型的快速工具。该工具既适用于自动使用，也适用于手动检查，以提高准确性并减少分析时间。
