Division of Molecular & Translational Medicine, Leeds Institute for Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, UK.
J Med Genet. 2011 Feb;48(2):123-30. doi: 10.1136/jmg.2010.082081. Epub 2010 Oct 30.
While massively parallel DNA sequencing methods continue to evolve rapidly, the benchmark technique for detection and verification of rare (particularly disease-causing) sequence variants remains four-colour dye-terminator sequencing by capillary electrophoresis. The high throughput and long read lengths currently available have shifted the bottleneck in mutation detection away from data generation to data analysis. While excellent computational methods have been developed for quantifying sequence accuracy and detecting variants, either during de novo sequence assembly or for single-nucleotide polymorphism detection, the identification, verification and annotation of very rare sequence variants remains a rather labour-intensive process for which few software aids exist.
To provide a freely available, intuitive software application for highly efficient mutation screening of large sequence batches.
The authors developed GeneScreen, a desktop program that analyses capillary electropherograms and compares their sequences with a known reference for identification of mutations. The detected sequence variants are then made available for rapid assessment and annotation via a graphical user interface, allowing chosen variants to be exported for reporting and archiving. The program was validated using more than 16,000 diagnostic laboratory sequence traces.
Using GeneScreen, a single user requires only a few minutes to identify rare mutations in hundreds of sequence traces, with comparable sensitivity to expensive commercial products.
尽管大规模平行 DNA 测序方法不断快速发展，但用于检测和验证罕见（特别是致病）序列变体的基准技术仍然是毛细管电泳的四色染料终止测序。目前可获得的高通量和长读取长度已经将突变检测的瓶颈从数据生成转移到数据分析。虽然已经开发出了用于量化序列准确性和检测变体的优秀计算方法，无论是在从头序列组装期间还是用于单核苷酸多态性检测，但是非常罕见的序列变体的识别、验证和注释仍然是一个相当劳动密集型的过程，几乎没有软件辅助工具。
提供一个免费的、直观的软件应用程序，用于对大量序列批次进行高效的突变筛选。
作者开发了 GeneScreen，这是一个桌面程序，可分析毛细管电泳图谱并将其序列与已知参考序列进行比较，以识别突变。然后通过图形用户界面提供检测到的序列变体，以便快速评估和注释，允许选择的变体导出用于报告和存档。该程序使用了超过 16000 个诊断实验室序列迹线进行了验证。
使用 GeneScreen，单个用户只需几分钟即可在数百个序列迹线中识别罕见突变，其灵敏度与昂贵的商业产品相当。
