PGRNseq: A targeted capture sequencing panel for pharmacogenetic research and implementation

Pharmacogenetics and Genomics

Volumn 26, Issue 4, 2016, Pages 161-168

  Gordon, Adam S ^a   Fulton, Robert S ^c   Qin, Xiang ^b   Mardis, Elaine R ^c   Nickerson, Deborah A ^a   Scherer, Steve ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

pharmacogenomics; rare variation; targeted sequencing

Indexed keywords

11BETA HYDROXYSTEROID DEHYDROGENASE 2; ABC TRANSPORTER A1; ABC TRANSPORTER G1; ADRB1 PROTEIN; ALOX5 PROTEIN; APOA1 PROTEIN; ARID5B PROTEIN; BILE SALT EXPORT PUMP; BRAIN DERIVED NEUROTROPHIC FACTOR; BREAST CANCER RESISTANCE PROTEIN; CACNA1C PROTEIN; CACNA1S PROTEIN; CACNB2 PROTEIN; CATECHOL METHYLTRANSFERASE; CYTOCHROME P450 1A2; CYTOCHROME P450 2A6; CYTOCHROME P450 2B6; CYTOCHROME P450 2C19; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; G PROTEIN COUPLED RECEPTOR KINASE 4; G PROTEIN COUPLED RECEPTOR KINASE 5; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; HLA B ANTIGEN; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 2; MULTIDRUG RESISTANCE PROTEIN 1; PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; COPY NUMBER VARIATION; DRUG RESPONSE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; HUMAN; PHARMACOGENETICS; PHENOTYPE; PRIORITY JOURNAL;

EID: 84953212338     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0000000000000202     Document Type: Article

References (30)

1. Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA, et al. TG and HDLWorking Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med 2014; 371: 22-31
2. O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 2012; 485: 246-250
3. Tammiste A, Jiang T, Fischer K, Mägi R, Krjutškov K, Pettai K, et al. Wholeexome sequencing identifies a polymorphism in the BMP5 gene associated with SSRI treatment response in major depression. J Psychopharmacol 2013; 27: 915-920
4. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 2012; 14: 357-366
5. Kim EH, Lee S, Park J, Lee K, Bhak J, Kim BC. New lung cancer panel for high-Throughput targeted resequencing. Genomics Inform 2014; 12: 50-57
6. Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, et al. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet 2014; 133: 331-345
7. Caudle KE, Klein TE, Hoffman JM, Muller DJ, Whirl-Carrillo M, Gong L, et al. Incorporation of pharmacogenomics into routine clinical practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process. Curr Drug Metab 2014; 15: 209-217
8. Evans WE, Relling MV. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 1999; 286: 487-491
9. Scott SA, Sangkuhl K, Gardner EE, Stein CM, Hulot JS, Johnson JA, et al. Clinical Pharmacogenetics Implementation Consortium guidelines for cytochrome P450-2C19 (CYP2C19) genotype and clopidogrel therapy. Clin Pharmacol Ther 2011; 90: 328-332
10. Liu X, Cheng D, Kuang Q, Liu G, Xu W. Association of UGT1A1 28 polymorphisms with irinotecan-induced toxicities in colorectal cancer: a meta-Analysis in Caucasians. Pharmacogenomics J 2014; 14: 120-129
11. Johnson JA, Gong L, Whirl-Carrillo M, Gage BF, Scott SA, Stein CM, et al. Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther 2011; 90: 625-629
12. Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, et al. NHLBI GO Exome Sequencing Project. Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a largescale exome dataset. Hum Mol Genet 2014; 23: 1957-1963
13. Ramsey LB, Bruun GH, Yang W, Treviño LR, Vattathil S, Scheet P, et al. Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition. Genome Res 2012; 22: 1-8
14. Ramirez AH, Shaffer CM, Delaney JT, Sexton DP, Levy SE, Rieder MJ, et al. Novel rare variants in congenital cardiac arrhythmia genes are frequent in drug-induced torsades de pointes. Pharmacogenomics J 2013; 13: 325-329
15. Wang D, Chen H, Momary KM, Cavallari LH, Johnson JA, Sadée W. Regulatory polymorphism in vitamin K epoxide reductase complex subunit 1 (VKORC1) affects gene expression and warfarin dose requirement. Blood 2008; 112: 1013-1021
16. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, et al. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 2011; 7: e1002078
17. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 2013; 11: 11.10.1-11.10.33
18. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, et al. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 2012; 13: 8
19. Major E, Rigó K, Hague T, Bérces A, Juhos S. HLA typing from 1000 genomes whole genome and whole exome illumina data. PLoS One 2013; 8: e78410
20. Hicks JK, Swen JJ, Gaedigk A. Challenges in CYP2D6 phenotype assignment from genotype data: a critical assessment and call for standardization. Curr Drug Metab 2014; 15: 218-232
21. Mwenifumbo JC, Tyndale RF. Genetic variability in CYP2A6 and the pharmacokinetics of nicotine. Pharmacogenomics 2007; 8: 1385-1402
22. The International HapMap Consortium. The International HapMap Project. Nature 2003; 426: 789-796
23. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1, 092 human genomes. Nature 2012; 491: 56-65
24. Nickerson DA, Rieder MJ, Crawford DC. An Overview of the Environmental Genome Project, Essays on the Future of Environmental Health Research. 2005; 42-53
25. Kim JH, Jarvik GP, Browning BL, Rajagopalan R, Gordon AS, Rieder MJ, et al. Exome sequencing reveals novel rare variants in the ryanodine receptor and calcium channel genes in malignant hyperthermia families. Anesthesiology 2013; 119: 1054-1065
26. Wilke RA, Ramsey LB, Johnson SG, Maxwell WD, McLeod HL, Voora D, et al. The clinical pharmacogenomics implementation consortium: CPIC guideline for SLCO1B1 and simvastatin-induced myopathy. Clin Pharmacol Ther 2012; 92: 112-117
27. Budnitz DS, Pollock DA, Weidenbach KN, Mendelsohn AB, Schroeder TJ, Annest JL. National surveillance of emergency department visits for outpatient adverse drug events. JAMA 2006; 296: 1858-1866
28. Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, et al. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems. Clin Pharmacol Ther 2014; 96: 482-489
29. Gaedigk A. Complexities of CYP2D6 gene analysis and interpretation. Int Rev Psychiatry 2013; 25: 534-553
30. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 2006; 38: 1166-1172