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. 2020 Sep 2;15(9):e0238467.
doi: 10.1371/journal.pone.0238467. eCollection 2020.

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

Rowida Almomani  1   2   3 , Margherita Marchi  4 , Maurice Sopacua  2   5 , Patrick Lindsey  1 , Erika Salvi  4 , Bart de Koning  6 , Silvia Santoro  7 , Stefania Magri  4 , Hubert J M Smeets  1   2 , Filippo Martinelli Boneschi  7 , Rayaz R Malik  8   9 , Dan Ziegler  10   11 , Janneke G J Hoeijmakers  2   5 , Gidon Bönhof  10 , Sulayman Dib-Hajj  12   13   14 , Stephen G Waxman  12   13   14 , Ingemar S J Merkies  5   15 , Giuseppe Lauria  4   16 , Catharina G Faber  2   5 , Monique M Gerrits  6 ; on behalf on the PROPANE Study Group
Affiliations

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

Rowida Almomani et al. PLoS One. .

Erratum in

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® 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.

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Conflict of interest statement

FMB, RM and DZ report a grant from European Union 7th Framework Programme (grant n°602273) for the PROPANE study. JH reports personal fees from Pfizer Inc. (travel funding and speakers’ honorarium) and grants from Prinses Beatrix Spierfonds (W.OK17-09), outside the submitted work. SDH reports grants from European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie grant for PAIN-Net, Molecule-to-man pain network (grant no. 721841) and European Union 7th Framework Programme (grant n°602273) for the PROPANE study, was supported in part by the Rehabilitation Research and Development Service and Biomedical Laboratory Research Service, Department of Veterans Affairs, and served as a paid consultant to Koro Bio, Inc, SiteOne Therapeutics and GLG Group, outside the submitted work. SW reports grants from European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie grant for PAIN-Net, Molecule-to-man pain network (grant no. 721841) and European Union 7th Framework Programme(grant n°602273) for the PROPANE study, was supported in part by the Rehabilitation Research and Development Service and Biomedical Laboratory Research Service,Department of Veterans Affairs, served as a paid consultant to Amgen, Biogen, Glaxo Smith Kline, ChromoCell and RedPin Therapeutics, and serves on the Scientific Advisory Board of SiteOne Therapeutics, outside the submitted work. IM reports grants from Talecris Talents program, GSB CIDP Foundation International, Prinses Beatrix Spierfonds and European Union 7th Framework Programme (grant n°602273), participates Steering committees of the Talecris ICE Study, LFB, CSL Behring,Novartis, Grifols, and Octapharma, serves on the editorial board of the Journal of Peripheral Nervous system, and is a member of the Inflammatory Neuropathy Consortium (INC) and Peripheral Nerve Society, outside the submitted work. GL reports grants from European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie grant for PAIN-Net, Molecule-to-man pain network (grant no. 721841) and European Union 7th Framework Programme (grant n°602273) for the PROPANE study, and participates in Steering committees/advisory boards for studies in small fibre neuropathy of CLS Behring, Biogen, Vertex and Chromocell, outside the submitted work. CF reports grants from European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie grant for PAIN-Net, Molecule-to-man pain network (grant no. 721841), European Union 7th Framework Programme (grant n°602273) for the PROPANE study, Prinses Beatrix Spierfonds, Grifols and Lamepro for a trial on IVIg in small fibre neuropathy, and participates in Steering committees/advisory boards for studies in small fibre neuropathy of Biogen, Vertex and Chromocell, outside the submitted work. Other authors have no conflicts of interests to declare. Above mentioned competing interests do not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. MIPs-NGS and TSCA-NGS workflows summary.
Graphical depiction of MIPs-NGS (A) and TSCA-NGS (B) methods for library construction and capture protocol for targeted next-generation sequencing.
See this image and copyright information in PMC

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