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GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms
  1. Ian M Carr1,
  2. Nick Camm2,
  3. Graham R Taylor1,2,
  4. Ruth Charlton2,
  5. Sian Ellard3,
  6. Eamonn G Sheridan1,2,
  7. Alexander F Markham1,
  8. David T Bonthron1
  1. 1Division of Molecular & Translational Medicine, Leeds Institute of Molecular Medicine, University of Leeds, UK
  2. 2Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
  3. 3Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
  1. Correspondence to Dr Ian M Carr, Leeds Institute for Molecular Medicine, Level 9, Wellcome Trust Brenner Building, St James's University Hospital, Leeds LS9 7TF, UK; i.m.carr{at}leeds.ac.uk

Abstract

Background 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.

Aim To provide a freely available, intuitive software application for highly efficient mutation screening of large sequence batches.

Methods and results 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.

Conclusion 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.

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Footnotes

  • Funding Cancer Research UK, Sir Jules Thorn Award for Biomedical Research.

  • Competing interests None.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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