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.
| Original language | English |
|---|---|
| Article number | 0238467 |
| Number of pages | 15 |
| Journal | PLOS ONE |
| Volume | 15 |
| Issue number | 9 |
| DOIs | |
| Publication status | Published - 2 Sept 2020 |
Keywords
- ASSOCIATIONS
- DISORDERS
- GENES
Access to Document
- 10.1371/journal.pone.0238467Licence: CC BY
Cite this
- APA
- Author
- BIBTEX
- Harvard
- Standard
- RIS
- Vancouver
}
In: PLOS ONE, Vol. 15, No. 9, 0238467, 02.09.2020.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing
AU - Almomani, Rowida
AU - Marchi, Margherita
AU - Sopacua, Maurice
AU - Lindsey, Patrick
AU - Salvi, Erika
AU - Koning, Bart de
AU - Santoro, Silvia
AU - Magri, Stefania
AU - Smeets, Hubert J. M.
AU - Martinelli Boneschi, Filippo
AU - Malik, Rayaz R.
AU - Ziegler, Dan
AU - Hoeijmakers, Janneke G. J.
AU - Boenhof, Gidon
AU - Dib-Hajj, Sulayman
AU - Waxman, Stephen G.
AU - Merkies, Ingemar S. J.
AU - Lauria, Giuseppe
AU - Faber, Catharina G.
AU - Gerrits, Monique M.
AU - PROPANE Study Grp
N1 - Funding Information: This study was supported by grants from European Union 7th Framework Programme for the PROPANE study (grant n°602273) and European Union’s Horizon 2020 research and innovation programme Marie Sklodowska-Curie grant for PAIN-Net, Molecule-to-man pain network (grant no. 721841). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Lead author PROPANE Study Group: G. Lauria, Neuroalgology Units, Fondazione IRCCS Istituto Neurologico “Carlo Besta” Milan, Italy and Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy, Email: Giuseppe.LauriaPinter@istituto-besta.it. Members Propane Study Group: Bianca M. de Greef (Maastricht UMC+, Maastricht, the Netherlands); Jo M. Vanoevelen (Maastricht UMC+, Maastricht, the Netherlands); Ivo Eijkenboom (Maastricht University, Maastricht, the Netherlands); Michela M. Taiana (IRCCS Foundation Neurological Institute “Carlo Besta”, Milan, Italy); Raffaella Lombardi ((IRCCS Foundation Neurological Institute “Carlo Besta”, Milan, Italy); Daniele Cazzato (IRCCS Foundation Neurological Institute “Carlo Besta”, Milan, Italy); Andrea Zauli (San Raffaele Scientific Institute, Milan, Italy); Ferdinando Clarelli (San Raffaele Scientific Institute, Milan, Italy); Ignazio D. Lopez (San Raffaele Scientific Institute, Milan, Italy); Angelo Quattrini (San Raffaele Scientific Institute, Milan, Italy); Mitra Tavakoli (University of Manchester, Manchester, United Kingdom); Dimos Kapetis (IRCCS Foundation Neurological Institute “Carlo Besta”, Milan, Italy); Markos N. Xenakis (Maastricht University, Maastricht, the Netherlands); Massimo Mantegazza (University of Côte d’Azur, Sophia Antipolis, France); Francesco Battiato (German Diabetes Center, Düsseldorf, Germany); Alexander Strom (German Diabetes Center, Düsseldorf, Germany); Sandrine Cestèle (University of Côte d’Azur, Sophia Antipolis, France); Oana Chever (Collège de France, Paris, France). Funding Information: Competinginterests:FMB,RMandDZreporta grantfromEuropeanUnion7thFramework Programme(grantn˚602273)forthePROPANE study.JHreportspersonalfeesfromPfizerInc. (travelfundingandspeakers’honorarium)and grantsfromPrinsesBeatrixSpierfonds(W.OK17-09),outsidethesubmittedwork.SDHreports grantsfromEuropeanUnion’sHorizon2020 researchandinnovationprogrammeMarie Sklodowska-CuriegrantforPAIN-Net,Molecule-to-manpainnetwork(grantno.721841)and EuropeanUnion7thFrameworkProgramme(grant n˚602273)forthePROPANEstudy,wassupported inpartbytheRehabilitationResearchand DevelopmentServiceandBiomedicalLaboratory ResearchService,DepartmentofVeteransAffairs, andservedasapaidconsultanttoKoroBio,Inc, SiteOneTherapeuticsandGLGGroup,outsidethe submittedwork.SWreportsgrantsfromEuropean Union’sHorizon2020researchandinnovation programmeMarieSklodowska-Curiegrantfor PAIN-Net,Molecule-to-manpainnetwork(grant no.721841)andEuropeanUnion7thFramework Programme(grantn˚602273)forthePROPANE study,wassupportedinpartbytheRehabilitation ResearchandDevelopmentServiceand BiomedicalLaboratoryResearchService, DepartmentofVeteransAffairs,servedasapaid consultanttoAmgen,Biogen,GlaxoSmithKline, ChromoCellandRedPinTherapeutics,andserves ontheScientificAdvisoryBoardofSiteOne Therapeutics,outsidethesubmittedwork.IM reportsgrantsfromTalecrisTalentsprogram,GSB CIDPFoundationInternational,PrinsesBeatrix SpierfondsandEuropeanUnion7thFramework Programme(grantn˚602273),participatesSteering committeesoftheTalecrisICEStudy,LFB,CSL Behring,Novartis,Grifols,andOctapharma,serves ontheeditorialboardoftheJournalofPeripheral Nervoussystem,andisamemberofthe InflammatoryNeuropathyConsortium(INC)and PeripheralNerveSociety,outsidethesubmitted work.GLreportsgrantsfromEuropeanUnion’s Horizon2020researchandinnovationprogramme MarieSklodowska-CuriegrantforPAIN-Net, Molecule-to-manpainnetwork(grantno.721841) andEuropeanUnion7thFrameworkProgramme (grantn˚602273)forthePROPANEstudy,and participatesinSteeringcommittees/advisory boardsforstudiesinsmallfibreneuropathyofCLS Behring,Biogen,VertexandChromocell,outside thesubmittedwork.CFreportsgrantsfrom EuropeanUnion’sHorizon2020researchand innovationprogrammeMarieSklodowska-Curie grantforPAIN-Net,Molecule-to-manpainnetwork Publisher Copyright: © 2020 Almomani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2020/9/2
Y1 - 2020/9/2
N2 - 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.
AB - 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.
KW - ASSOCIATIONS
KW - DISORDERS
KW - GENES
U2 - 10.1371/journal.pone.0238467
DO - 10.1371/journal.pone.0238467
M3 - Article
C2 - 32877464
SN - 1932-6203
VL - 15
JO - PLOS ONE
JF - PLOS ONE
IS - 9
M1 - 0238467
ER -