title: Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism.
abstract: BACKGROUND
  Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group of monogenic disorders with highly variable clinical presentation, often with acute, nonspecific initial symptoms. In many cases irreversible damage can be reduced by initiation of specific treatment, provided that a correct molecular diagnosis can be rapidly obtained. MPS thus has the potential to significantly improve both diagnostics and outcome for affected patients in this highly specialized area of medicine.
  
  
  RESULTS
  We have developed a conceptually novel approach for acute MPS, by analysing pulsed whole genome sequence data in real time, using automated analysis combined with data reduction and parallelization. We applied this novel methodology to an in-house developed customized work flow enabling clinical-grade analysis of all IEM with a known genetic basis, represented by a database containing 474 disease genes which is continuously updated. As proof-of-concept, two patients were retrospectively analysed in whom diagnostics had previously been performed by conventional methods. The correct disease-causing mutations were identified and presented to the clinical team after 15 and 18 hours from start of sequencing, respectively. With this information available, correct treatment would have been possible significantly sooner, likely improving outcome.
  
  
  CONCLUSIONS
  We have adapted MPS to fit into the dynamic, multidisciplinary work-flow of acute metabolic medicine. As the extent of irreversible damage in patients with IEM often correlates with timing and accuracy of management in early, critical disease stages, our novel methodology is predicted to improve patient outcome. All procedures have been designed such that they can be implemented in any technical setting and to any genetic disease area. The strategy conforms to international guidelines for clinical MPS, as only validated disease genes are investigated and as clinical specialists take responsibility for translation of results. As follow-up in patients without any known IEM, filters can be lifted and the full genome investigated, after genetic counselling and informed consent.
authors.affiliation: Department of Molecular Medicine and Surgery, Science for Life Laboratory, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden. Henrik.Stranneheim@scilifelab.se.
authors.forename: Henrik
authors.initials: H
authors.lastname: Stranneheim
authors.forename: Martin
authors.initials: M
authors.lastname: Engvall
authors.forename: Karin
authors.initials: K
authors.lastname: Naess
authors.forename: Nicole
authors.initials: N
authors.lastname: Lesko
authors.forename: Pontus
authors.initials: P
authors.lastname: Larsson
authors.forename: Mats
authors.initials: M
authors.lastname: Dahlberg
authors.forename: Robin
authors.initials: R
authors.lastname: Andeer
authors.forename: Anna
authors.initials: A
authors.lastname: Wredenberg
authors.forename: Chris
authors.initials: C
authors.lastname: Freyer
authors.forename: Michela
authors.initials: M
authors.lastname: Barbaro
authors.forename: Helene
authors.initials: H
authors.lastname: Bruhn
authors.forename: Tesfail
authors.initials: T
authors.lastname: Emahazion
authors.forename: Måns
authors.initials: M
authors.lastname: Magnusson
authors.forename: Rolf
authors.initials: R
authors.lastname: Wibom
authors.forename: Rolf H
authors.initials: RH
authors.lastname: Zetterström
authors.forename: Valtteri
authors.initials: V
authors.lastname: Wirta
authors.forename: Ulrika
authors.initials: U
authors.lastname: von Döbeln
authors.forename: Anna
authors.initials: A
authors.lastname: Wedell
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008661:Metabolism, Inborn Errors / Q000175:diagnosis* / Q000235:genetics; D030481:Pyruvate Dehydrogenase (Lipoamide) / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D030481:Pyruvate Dehydrogenase (Lipoamide); C065640:pyruvate dehydrogenase E1alpha subunit