每个 CFTR 变异体都很重要——基于靶向捕获的下一代测序在德国 CF 登记处的分子诊断中的应用。

Every CFTR variant counts - Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry.

机构信息

Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany.

Department of Pediatrics, Justus-Liebig-University Giessen, Giessen, Germany.

出版信息

J Cyst Fibros. 2024 Jul;23(4):774-781. doi: 10.1016/j.jcf.2023.10.009. Epub 2023 Oct 21.

DOI:10.1016/j.jcf.2023.10.009

PMID:37867076

Abstract

BACKGROUND

In times of genotype guided therapy options, a total of 3.2 % of people with CF (pwCF) in the German CF Registry[1] only have one or no CFTR-variant detected after genetic analysis. Additionally, genetic data in the Registry can be documented as free text and can therefore be prone to error. In order to allow the greatest possible amount of pwCF access to modern therapies, we conducted a re-evaluation of free text entries and established a custom-whole-CFTR-locus NGS-approach for all pwCF who remained without genetic confirmation afterwards.

METHODS

To this end, we assembled 731 free text variants of 655 pwCF in the German CF Registry. All variants were evaluated using ClinVar, HGMD and CFTR1/2, corrected in the Registries' database and uploaded to ClinVar. PwCF whose diagnosis remained uncertain as well as additional pwCF or pwCFTR-RD that were assembled through a nationwide call for testing of unclear cases were offered genetic analysis. Samples were analysed using a target-capture based NGS-custom-design-panel covering the entire CFTR-locus.

RESULTS

Evaluation of free text variants led to the discovery of 43 variants not formerly reported in the context of CF. The Registries' dropdown list was extended by 497 variants and over 500 pwCF were provided with their most up-to-date genotype. Samples of 47 pwCF/pwCFTR-RD were sequenced via NGS with an overall success rate of 61.7 %, resulting in implementation of entire CFTR-genotyping into routine diagnostics.

CONCLUSION

Entire CFTR-genotyping can greatly increase the genetic diagnostic rate of pwCF/pwCFTR-RD and should be considered after inconspicuous CFTR screening panels in CFTR-diagnostics.

摘要

背景

在基因型指导治疗方案的时代，德国 CF 注册中心[1]中总共有 3.2%的 CF 患者（pwCF）在基因分析后仅检测到一种或没有 CFTR 变异。此外，注册中心的遗传数据可以以纯文本形式记录，因此容易出错。为了让尽可能多的 pwCF 能够获得现代治疗方法，我们对纯文本条目进行了重新评估，并为所有随后仍未获得基因确认的 pwCF 建立了一个定制的全 CFTR 基因座 NGS 方法。

方法

为此，我们在德国 CF 注册中心汇集了 731 名 pwCF 的 655 个自由文本变体。所有变体均使用 ClinVar、HGMD 和 CFTR1/2 进行评估，在注册中心的数据库中进行校正，并上传至 ClinVar。诊断仍不确定的 pwCF 以及通过全国性的不明病例检测呼吁而聚集的额外 pwCF 或 pwCFTR-RD 被提供基因分析。使用基于目标捕获的 NGS 定制设计面板对样本进行分析，该面板覆盖整个 CFTR 基因座。

结果

对自由文本变体的评估导致发现了 43 种以前未在 CF 背景下报告的变体。注册中心的下拉列表扩展了 497 种变体，为 500 多名 pwCF 提供了最新的基因型。通过 NGS 对 47 名 pwCF/pwCFTR-RD 进行了测序，总体成功率为 61.7%，从而将整个 CFTR 基因分型纳入常规诊断。