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

Journal: PloS one 2020;15(9):e0238467

PMID: 32877464

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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.

Address: Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands.; MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.; Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.; Neuroalgology Units, Fondazione IRCCS Istituto Neurologico "Carlo Besta" Milan, Milan, Italy.; MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.; Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands.; Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands.; Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, the Netherlands.; Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.; Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands.; MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.; Institute of Human Development, Centre for Endocrinology and Diabetes, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, United Kingdom.; Department of Medicine, Weill Cornell Medicine, Doha, Qatar.; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Düsseldorf, Germany.; Department of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Düsseldorf, Germany.; Department of Neurology, Yale University School of Medicine, Yale, New Haven, United States of America.; Center for Neuroscience and Regeneration Research, Yale University School of Medicine, Yale, New Haven, United States of America.; Center for Neuroscience and Regeneration Research, Veterans Affairs Medical Center, West Haven, Connecticut, United States of America.; Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands.; Department of Neurology, St Elisabeth Hospital, Willemstad, Curaçao.; Neuroalgology Units, Fondazione IRCCS Istituto Neurologico "Carlo Besta" Milan, Milan, Italy.; Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy.

DOI: 10.1371/journal.pone.0238467

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MeSH Terms: Chromosome Inversion, DNA Probes, Genetic Testing, High-Throughput Nucleotide Sequencing, Humans, Molecular Probes, Mutation, Neuralgia, Sensitivity and Specificity, Sequence Analysis, DNA