Characterizing the pharmacogenome using molecular inversion probes for targeted next-generation sequencing

被引：10

作者：

Suzuki, Oscar ^{[1
,2
]}

Dong, Olivia M. ^{[1
,2
]}

Howard, Rachel M. ^{[1
,2
]}

Wiltshire, Tim ^{[1
,2
,3
]}

机构：

[1] Univ N Carolina, Div Pharmacotherapy & Expt Therapeut, Eshelman Sch Pharm, Chapel Hill, NC 27599 USA

[2] Univ N Carolina, Ctr Pharmacogen & Individualized Therapy, Chapel Hill, NC 27599 USA

[3] Univ N Carolina, Dept Genet, Chapel Hill, NC 27599 USA

来源：

PHARMACOGENOMICS | 2019年 / 20卷 / 14期

关键词：

molecular inversion probes; next-generation sequencing; pharmacogenetic; pharmacogenome; precision medicine; IMPLEMENTATION CONSORTIUM GUIDELINES; DNA REFERENCE MATERIALS; CPIC GUIDELINES; CYP2C19; GENOTYPES; COPY NUMBER; CYP2D6; GENE; THERAPY; DESIGN; UGT1A1; DRUG;

D O I：

10.2217/pgs-2019-0057

中图分类号：

R9 [药学];

学科分类号：

1007 ;

摘要：

Aim: This study assesses the technical performance and cost of a targeted next-generation sequencing (NGS) multigene pharmacogenetic (PGx) test. Materials & methods: A genetic test was developed for 21 PGx genes using molecular inversion probes to generate library fragments for NGS. Performance of this test was assessed using 53 unique reference control cell lines from the Genetic Testing Reference Materials Coordination Program (GeT-RM). Results: 93.7% of variants were successfully called and the repeatability rate was 99.9%. Reference calls were available for 78.4% of diplotype calls resulting from PGx testing, and concordance for the test was 85.7%. Cost per sample was $32-$56. Conclusion: A targeted NGS assay using molecular inversion probe technology is able to characterize the pharmacogenome efficiently.

引用

页码：1005 / 1019

页数：15

共 59 条

[1] Advancing Pharmacogenomics Education in the Core PharmD Curriculum through Student Personal Genomic Testing [J].

Adams, Solomon M. ;

Anderson, Kacey B. ;

Coons, James C. ;

Smith, Randall B. ;

Meyer, Susan M. ;

Parker, Lisa S. ;

Empey, Philip E. .

AMERICAN JOURNAL OF PHARMACEUTICAL EDUCATION, 2016, 80 (01)

[2] A global reference for human genetic variation [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Wang, Jun ;

Wilson, Richard K. ;

Boerwinkle, Eric ;

Doddapaneni, Harsha ;

Han, Yi ;

Korchina, Viktoriya ;

Kovar, Christie ;

Lee, Sandra ;

Muzny, Donna ;

Reid, Jeffrey G. ;

Zhu, Yiming ;

Chang, Yuqi ;

Feng, Qiang ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Lan, Tianming ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Liu, Shengmao ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Tang, Meifang ;

Wang, Bo .

NATURE, 2015, 526 (7571) :68-+

[3] Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 Genotype and Use of Ondansetron and Tropisetron [J].

Bell, G. C. ;

Caudle, K. E. ;

Whirl-Carrillo, M. ;

Gordon, R. J. ;

Hikino, K. ;

Prows, C. A. ;

Gaedigk, A. ;

Agundez, J. A. G. ;

Sadhasivam, S. ;

Klein, T. E. ;

Schwab, M. .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2017, 102 (02) :213-218

[4] Preemptive Genotyping for Personalized Medicine: Design of the Right Drug, Right Dose, Right Time-Using Genomic Data to Individualize Treatment Protocol [J].

Bielinski, Suzette J. ;

Olson, Janet E. ;

Pathak, Jyotishman ;

Weinshilboum, Richard M. ;

Wang, Liewei ;

Lyke, Kelly J. ;

Ryu, Euijung ;

Targonski, Paul V. ;

Van Norstrand, Michael D. ;

Hathcock, Matthew A. ;

Takahashi, Paul Y. ;

McCormick, Jennifer B. ;

Johnson, Kiley J. ;

Maschke, Karen J. ;

Vitek, Carolyn R. Rohrer ;

Ellingson, Marissa S. ;

Wieben, Eric D. ;

Farrugia, Gianrico ;

Morrisette, Jody A. ;

Kruckeberg, Keri J. ;

Bruflat, Jamie K. ;

Peterson, Lisa M. ;

Blommel, Joseph H. ;

Skierka, Jennifer M. ;

Ferber, Matthew J. ;

Black, John L. ;

Baudhuin, Linnea M. ;

Klee, Eric W. ;

Ross, Jason L. ;

Veldhuizen, Tamra L. ;

Schultz, Cloann G. ;

Caraballo, Pedro J. ;

Freimuth, Robert R. ;

Chute, Christopher G. ;

Kullo, Iftikhar J. .

MAYO CLINIC PROCEEDINGS, 2014, 89 (01) :25-33

[5] Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for CYP3A5 Genotype and Tacrolimus Dosing [J].

Birdwell, K. A. ;

Decker, B. ;

Barbarino, J. M. ;

Peterson, J. F. ;

Stein, C. M. ;

Sadee, W. ;

Wang, D. ;

Vinks, A. A. ;

He, Y. ;

Swen, J. J. ;

Leeder, J. S. ;

van Schaik, R. H. N. ;

Thummel, K. E. ;

Klein, T. E. ;

Caudle, K. E. ;

MacPhee, I. A. M. .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2015, 98 (01) :19-24

[6] MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing [J].

Boyle, Evan A. ;

O'Roak, Brian J. ;

Martin, Beth K. ;

Kumar, Akash ;

Shendure, Jay .

BIOINFORMATICS, 2014, 30 (18) :2670-2672

[7]

Bushnell B., 2019, BBMAP SHORT READ ALI

[8] Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and HLA-B Genotypes and Phenytoin Dosing [J].

Caudle, K. E. ;

Rettie, A. E. ;

Whirl-Carrillo, M. ;

Smith, L. H. ;

Mintzer, S. ;

Lee, M. T. M. ;

Klein, T. E. ;

Callaghan, J. T. .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2014, 96 (05) :542-548

[9] Clinical Pharmacogenetics Implementation Consortium Guidelines for Dihydropyrimidine Dehydrogenase Genotype and Fluoropyrimidine Dosing [J].

Caudle, K. E. ;

Thorn, C. F. ;

Klein, T. E. ;

Swen, J. J. ;

McLeod, H. L. ;

Diasio, R. B. ;

Schwab, M. .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2013, 94 (06) :640-645

[10] The HLA system: Genetics, immunology, clinical testing, and clinical implications [J].

Choo, Sung Yoon .

YONSEI MEDICAL JOURNAL, 2007, 48 (01) :11-23

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