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 Boenhof, Sulayman Dib-Hajj, Stephen G. Waxman, Ingemar S. J. Merkies, Giuseppe Lauria, Catharina G. Faber, Monique M. Gerrits*PROPANE Study Grp

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Web of Science)

Abstract

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 (R) Custom Amplicon-Next generation sequencing (TSCA-NGS). Capture probes were designed to target nine sodium channel genes (SCN3A,SCN8A-SCN11A, andSCN1B-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.

Original languageEnglish
Article number0238467
Number of pages15
JournalPLOS ONE
Volume15
Issue number9
DOIs
Publication statusPublished - 2 Sep 2020

Keywords

  • ASSOCIATIONS
  • DISORDERS
  • GENES

Cite this