GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms

• Published in: Journal of medical genetics Vol. 48; no. 2; pp. 123 - 130
• Main Authors: Carr, Ian M, Camm, Nick, Taylor, Graham R, Charlton, Ruth, Ellard, Sian, Sheridan, Eamonn G, Markham, Alexander F, Bonthron, David T
• Format: Journal Article
• Language: English
• Published: London BMJ Publishing Group Ltd 01.02.2011; BMJ Publishing Group; BMJ Publishing Group LTD
• Subjects: Automation; Base Sequence - genetics; Biological and medical sciences; diagnostics; DNA Mutational Analysis - methods; DNA sequencing; Fundamental and applied biological sciences. Psychology; General aspects. Genetic counseling; genetic screening/counselling; Genetic Variation; genetics; Genetics of eukaryotes. Biological and molecular evolution; Humans; Medical genetics; Medical sciences; Methods; Molecular and cellular biology; molecular genetics; Mutation; Mutation detection; Operating systems; Software; Human; Genetics; Mutation; Nucleotide sequence; Detection; Diagnostics; Molecular genetics; Genetic screening/counselling
• ISSN: 0022-2593; 1468-6244; 1468-6244
• DOI: 10.1136/jmg.2010.082081

BackgroundWhile 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.AimTo provide a freely available, intuitive software application for highly efficient mutation screening of large sequence batches.Methods and resultsThe 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.ConclusionUsing 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.