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

被引：16

作者：

Almomani, Rowida ^{[1
,2
,3
]}

Marchi, Margherita ^{[4
]}

Sopacua, Maurice ^{[2
,5
]}

Lindsey, Patrick ^{[1
]}

Salvi, Erika ^{[4
]}

Koning, Bart de ^{[6
]}

Santoro, Silvia ^{[7
]}

Magri, Stefania ^{[4
]}

Smeets, Hubert J. M. ^{[1
,2
]}

Martinelli Boneschi, Filippo ^{[7
]}

Malik, Rayaz R. ^{[8
,9
,10
]}

Ziegler, Dan ^{[11
,12
]}

Hoeijmakers, Janneke G. J. ^{[2
,5
]}

Boenhof, Gidon ^{[11
]}

Dib-Hajj, Sulayman ^{[13
,14
,15
]}

Waxman, Stephen G. ^{[13
,14
,15
]}

Merkies, Ingemar S. J. ^{[5
,16
]}

Lauria, Giuseppe ^{[4
,17
]}

Faber, Catharina G. ^{[2
,5
]}

Gerrits, Monique M. ^{[6
]}

机构：

[1] Maastricht Univ, Dept Genet & Cell Biol, Clin Genom Unit, Maastricht, Netherlands

[2] Maastricht Univ, MHeNs Sch Mental Hlth & Neurosci, Maastricht, Netherlands

[3] Jordan Univ Sci & Technol, Dept Med Lab Sci, Irbid, Jordan

[4] Fdn IRCCS Ist Neurol Carlo Besta, Neuroalgol Units, Milan, Italy

[5] Maastricht Univ, Med Ctr, Dept Neurol, Maastricht, Netherlands

[6] Maastricht Univ, Med Ctr, Dept Clin Genet, Maastricht, Netherlands

[7] Ist Sci San Raffaele, Lab Human Genet Neurol Disorders, Inst Expt Neurol INSPE, Div Neurosci, Milan, Italy

[8] Univ Manchester, Ctr Endocrinol & Diabet, Inst Human Dev, Manchester, Lancs, England

[9] Manchester Acad Hlth Sci Ctr, Cent Manchester NHS Fdn Trust, Manchester, Lancs, England

[10] Weill Cornell Med, Dept Med, Doha, Qatar

[11] Leibniz Ctr Diabet Res, German Diabet Ctr, Inst Clin Diabetol, Dusseldorf, Germany

[12] Heinrich Heine Univ, Fac Med, Dept Endocrinol & Diabetol, Dusseldorf, Germany

[13] Yale Univ, Sch Med, Dept Neurol, New Haven, CT 06510 USA

[14] Yale Univ, Sch Med, Ctr Neurosci & Regenerat Res, New Haven, CT USA

[15] Vet Affairs Med Ctr, Ctr Neurosci & Regenerat Res, West Haven, CT USA

[16] St Elizabeth Hosp, Dept Neurol, Willemstad, Curacao

[17] Univ Milan, Dept Biomed & Clin Sci Luigi Sacco, Milan, Italy

来源：

PLOS ONE | 2020年 / 15卷 / 09期

关键词：

ASSOCIATIONS; DISORDERS; GENES;

D O I：

10.1371/journal.pone.0238467

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：15

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