PLoS ONE (Jan 2020)

Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing.

  • Rowida Almomani,
  • Margherita Marchi,
  • Maurice Sopacua,
  • Patrick Lindsey,
  • Erika Salvi,
  • Bart de Koning,
  • Silvia Santoro,
  • Stefania Magri,
  • Hubert J M Smeets,
  • Filippo Martinelli Boneschi,
  • Rayaz R Malik,
  • Dan Ziegler,
  • Janneke G J Hoeijmakers,
  • Gidon Bönhof,
  • Sulayman Dib-Hajj,
  • Stephen G Waxman,
  • Ingemar S J Merkies,
  • Giuseppe Lauria,
  • Catharina G Faber,
  • Monique M Gerrits,
  • on behalf on the PROPANE Study Group

DOI
https://doi.org/10.1371/journal.pone.0238467
Journal volume & issue
Vol. 15, no. 9
p. e0238467

Abstract

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Resolving the genetic architecture of painful neuropathy will lead to better disease management strategies. We aimed to develop a reliable method to re-sequence multiple genes in a large cohort of painful neuropathy patients at low cost. In this study, we compared sensitivity, specificity, targeting efficiency, performance and cost effectiveness of Molecular Inversion Probes-Next generation sequencing (MIPs-NGS) and TruSeq® Custom Amplicon-Next generation sequencing (TSCA-NGS). Capture probes were designed to target nine sodium channel genes (SCN3A, SCN8A-SCN11A, and SCN1B-SCN4B). One hundred sixty-six patients with diabetic and idiopathic neuropathy were tested by both methods, 70 patients were validated by Sanger sequencing. Sensitivity, specificity and performance of both techniques were comparable, and in agreement with Sanger sequencing. The average targeted regions coverage for MIPs-NGS was 97.3% versus 93.9% for TSCA-NGS. MIPs-NGS has a more versatile assay design and is more flexible than TSCA-NGS. The cost of MIPs-NGS is >5 times cheaper than TSCA-NGS when 500 or more samples are tested. In conclusion, MIPs-NGS is a reliable, flexible, and relatively inexpensive method to detect genetic variations in a large cohort of patients. In our centers, MIPs-NGS is currently implemented as a routine diagnostic tool for screening of sodium channel genes in painful neuropathy patients.