Whole-genome sequencing and the clinician: a tale of two cities
- A Reghan Foley1,
- Robert D S Pitceathly2,
- Jie He3,4,
- Jihee Kim5,
- Nathaniel M Pearson3,6,
- Francesco Muntoni1,
- Michael G Hanna2
- 1Dubowitz Neuromuscular Centre, MRC Centre for Neuromuscular Diseases, University College London Institute of Child Health and Great Ormond Street Hospital for Children, London, UK
- 2MRC Centre for Neuromuscular Diseases, University College London Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
- 3Knome, Inc., Cambridge, Massachusetts, USA
- 4Foundation Medicine, Inc., Cambridge, Massachusetts, USA
- 5Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
- 6Ingenuity Systems/QIAGEN, Redwood City, California, USA
- Correspondence to Professor Michael G Hanna, MRC Centre for Neuromuscular Diseases, University College London Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK;
- Received 1 December 2013
- Revised 11 March 2014
- Accepted 12 March 2014
- Published Online First 4 April 2014
Background Clinicians are faced with unprecedented opportunities to identify the genetic aetiologies of hitherto molecularly uncharacterised conditions via the use of high-throughput sequencing. Access to genomic technology and resultant data is no longer limited to clinicians, geneticists and bioinformaticians, however; ongoing commercialisation gives patients themselves ever greater access to sequencing services. We report an increasingly common medical scenario by describing two neuromuscular patients—a mother and adult son—whose consumer access to whole-genome sequencing affected their diagnostic journey.
Results Whole-genome sequencing initiated by the patients—to predict their risk of common diseases—revealed that they share several variants potentially relevant to neuromuscular diseases, which initially sidetracked diagnostic efforts. Since eventual clinical reassessment, including muscle imaging, pointed towards Bethlem myopathy, a collagen VI-related myopathy, we pursued Sanger sequencing of COL6A1, COL6A2 and COL6A3. This targeted approach revealed a heterozygous causative variant in COL6A3 (c.6365G>T (p.Gly2122Val)), shared by both individuals, that was not flagged by the interpretation of the whole-genome sequencing data.
Conclusions This report highlights the essential interplay of clinical and genomic expertise in realising the potential of high-throughput sequencing. In an era when patients themselves may bring their own data to the table, definitively identifying clinically significant genomic variants will require close collaboration among clinicians, geneticists and bioinformaticians.
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