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1.  PharmGKB summary: methylene blue pathway 
Pharmacogenetics and genomics  2013;23(9):498-508.
doi:10.1097/FPC.0b013e32836498f4
PMCID: PMC4091817  PMID: 23913015
glucose-6-phosphate dehydrogenase; hemolytic anemia; methemoglobinemia; methylene blue; reduced nicotinamide adenine dinucleotide phosphate; oxidative stress; pentose phosphate pathway; pharmacodynamics; pharmacogenetics; red blood cells
2.  PharmGKB summary: very important pharmacogene information for UGT1A1 
Pharmacogenetics and genomics  2014;24(3):177-183.
doi:10.1097/FPC.0000000000000024
PMCID: PMC4091838  PMID: 24492252
atazanavir; Crigler–Najjar syndrome; Gilbert’s syndrome; indinavir; irinotecan; pharmacogenetics; UGT1A1
3.  PharmGKB summary: abacavir pathway 
Pharmacogenetics and genomics  2014;24(5):276-282.
doi:10.1097/FPC.0000000000000040
PMCID: PMC4074515  PMID: 24625462
abacavir; HIV; HLA-B; HLA-B*57:01; HSP70-HOM; hypersensitivity; pharmacodynamics; pharmacogenetics; pharmacokinetics; PharmGKB
4.  Effect of drug transporter genotypes on pravastatin disposition in European- and African-American participants 
Pharmacogenetics and genomics  2007;17(8):647-656.
Objective
Our aims were to evaluate the effects of polymorphisms in the hepatic drug uptake transporter organic anion transporting polypeptide 1B1 (OATP1B1, SLCO1B1) and efflux transporters multidrug resistance-associated protein 2 (MRP2, ABCC2), bile salt export pump (BSEP, ABCB11), and breast cancer-related protein (BCRP, ABCG2) on single-dose pravastatin pharmacokinetics in healthy European- and African-American participants.
Methods
The pharmacokinetics of a single oral 40mg dose of pravastatin was determined in 107 participants (69 European-Americans and 38 African-Americans). Participants were genotyped for known OATP1B1, MRP2, BSEP, and BCRP polymorphisms. Baseline serum total and unconjugated plasma bilirubin concentrations were also determined.
Results
OATP1B1 genotypes were ethnicity-dependent with a 521C allele frequency of ~15% in European-Americans and ~1% in African-Americans. SLCO1B1 521TC genotype was associated with significantly higher pravastatin area under the curve [AUC(0–5)] (P =0.01) and Cmax values (P< 0.05). When analyzed by diplotype, SLCO1B1*1a/*15 (N =8) participants exhibited 45 and 80% higher AUC values than SLCO1B1*1a/*1a (N=29) (P=0.013) and SLCO1B1*1b/*1b (N=34) (P=0.001) carriers, respectively. SLCO1B1*15/*15 (N=2) participants exhibited 92 and 149% higher AUC values than SLCO1B1*1a/*1a (P=0.017) and SLCO1B1*1b/*1b (P= 0.011) carriers, respectively. European-Americans had significantly higher plasma pravastatin AUC(0–5) (P =0.01) and Cmax values (P=0.009) than African-Americans. Neither ABCC2, ABCB11, nor ABCG2 genotypes were associated with differences in pravastatin pharmacokinetics. We did not observe an effect of SLCO1B1 genotype on baseline total or unconjugated bilirubin levels.
Conclusion
SLCO1B1 genotype, in particular the 521C allele, had a significant effect on the pharmacokinetics of pravastatin. Even when adjusted for the presence of the SLCO1B1 521C or 388G variant allele, European-Americans demonstrated significantly higher pravastatin AUC and Cmax values than African-Americans.
doi:10.1097/FPC.0b013e3280ef698f
PMCID: PMC4063287  PMID: 17622941
ABCB11; ABCC2; ABCG2; BCRP; bilirubin; BSEP; MRP2; OATP1B1; pharmacokinetics; pravastatin; SLCO1B1; transporter
5.  Measuring the Overall Genetic Component of Nevirapine Pharmacokinetics and the Role of Selected Polymorphisms: Towards Addressing the Missing Heritability in Pharmacogenetic Phenotypes? 
Pharmacogenetics and genomics  2013;23(11):591-596.
Objective
Nevirapine is an important component of highly active antiretroviral therapy used in the treatment of human immunodeficiency virus infection. There is considerable variation in the pharmacokinetics of nevirapine and this variation can impact the efficacy and toxicity of nevirapine. While some of this variation can be attributed to environmental factors, the degree to which heritability influences nevirapine pharmacokinetics is unknown. This study aims to estimate how much variation in nevirapine pharmacokinetics is due to genetic factors and to investigate the contribution of selected polymorphisms to this variability.
Methods
Two doses of immediate-release nevirapine were administered to European (n=11) and African American (n=6) subjects recruited from the Research in Access to Care in the Homeless (REACH) cohort. A repeated drug administration (RDA) method was then used to determine the relative genetic contribution (rGC) to variability in nevirapine AUC0–6h. Nevirapine plasma levels were quantified using LC-MS/MS. Patients were also genotyped for selected polymorphisms in candidate genes that may influence nevirapine pharmacokinetics.
Results
A significant rGC for nevirapine AUC0–6h was found in Europeans (p = 0.02) and African Americans (p = 0.01). A trend towards higher nevirapine AUC0–6h for the CYP2B6 516TT (rs3745274; Q172H) genotype was observed in European Americans (p = 0.19).
Conclusions
This study demonstrates that there is a significant genetic component to variability in nevirapine pharmacokinetics. While genetic variants such as CYP2B6 polymorphisms attributed to some of this variation, these data suggest that there may be additional genetic factors that influence nevirapine pharmacokinetics.
doi:10.1097/FPC.0b013e32836533a5
PMCID: PMC4048019  PMID: 23982262
HIV; Nevirapine; Pharmacogenetics; Pharmacokinetics; CYP2B6
6.  Breast cancer resistance protein (ABCG2) and drug disposition: intestinal expression, polymorphisms and sulfasalazine as an in vivo probe 
Pharmacogenetics and genomics  2008;18(5):439-448.
Breast cancer resistance protein (BCRP) is an efflux transporter expressed in tissues that act as barriers to drug entry. Given that single nucleotide polymorphisms (SNPs) in the ABCG2 gene encoding BCRP are common, the possibility exists that these genetic variants may be a determinant of interindividual variability in drug response. The objective of this study is to confirm the human BCRP-mediated transport of sulfasalazine in vitro, evaluate interindividual variation in BCRP expression in human intestine and to determine the role of ABCG2 SNPs to drug disposition in healthy patients using sulfasalazine as a novel in vivo probe. To evaluate these objectives, pinch biopsies were obtained from 18 patients undergoing esophagogastro–duodenoscopy or colonoscopy for determination of BCRP expression in relation to genotype. Wild-type and variant BCRP were expressed in a heterologous expression system to evaluate the effect of SNPs on cell-surface trafficking. A total of 17 healthy individuals participated in a clinical investigation to determine the effect of BCRP SNPs on sulfasalazine pharmacokinetics. In vitro, the cell surface protein expression of the common BCRP 421 C>A variant was reduced in comparison with the wild-type control. Intestinal biopsy samples revealed that BCRP protein and mRNA expression did not significantly differ between patients with 34GG/421CC versus patients with 34GG/421CA genotypes. Remarkably, in subjects with 34GG/421CA genotype, sulfasalazine area under the concentration-time curve was 2.4-fold greater compared with 34GG/421CC subjects (P<0.05). This study links commonly occurring SNPs in BCRP with significantly increased oral sulfasalazine plasma exposure in humans. Accordingly, sulfasalazine may prove to have utility as in vivo probe for assessing the clinical impact of BCRP for the disposition and efficacy of drugs.
doi:10.1097/FPC.0b013e3282f974dc
PMCID: PMC4043148  PMID: 18408567
breast cancer resistance protein/ATP binding cassette; drug transport; member 2; pharmacogenetics; pharmacokinetics; subfamily G (WHITE); sulfasalazine
7.  Polygenic Heritability Estimates in Pharmacogenetics: Focus on Asthma and Related Phenotypes 
Pharmacogenetics and genomics  2013;23(6):324-328.
While accurate measures of heritability are needed to understand the pharmacogenetic basis of drug treatment response, these are generally not available, since it is unfeasible to give medications to individuals for which treatment is not indicated. Using a polygenic linear mixed modeling approach, we estimated lower-bounds on asthma heritability and the heritability of two related drug-response phenotypes, bronchodilator response and airway hyperreactivity, using genome-wide SNP data from existing asthma cohorts. Our estimate of the heritability for bronchodilator response is 28.5% (se 16%, p = 0.043) and airway hyperresponsiveness is 51.1% (se 34%, p = 0.064), while we estimate asthma genetic liability at 61.5% (se 16%, p < 0.001). Our results agree with previously published estimates of the heritability of these traits, suggesting that the LMM method is useful for computing the heritability of other pharmacogenetic traits. Furthermore, our results indicate that multiple SNP main-effects, including SNPs as yet unidentified by GWAS methods, together explain a sizable portion of the heritability of these traits.
doi:10.1097/FPC.0b013e3283607acf
PMCID: PMC3767309  PMID: 23532052
Asthma; Pharmacogenetics; Heritability; Bronchodilator Response; Airway Hyperresponsiveness
8.  Valproic acid pathway: pharmacokinetics and pharmacodynamics 
Pharmacogenetics and genomics  2013;23(4):236-241.
doi:10.1097/FPC.0b013e32835ea0b2
PMCID: PMC3696515  PMID: 23407051
pathway; pharmacodynamics; pharmacogenomics; pharmacokinetics; valproic acid
9.  Nomenclature for alleles of the thiopurine methyltransferase gene 
Pharmacogenetics and genomics  2013;23(4):242-248.
The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors’ articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G > A) from TPMT*24 to TPMT*30 and position 611 (T > C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged.
doi:10.1097/FPC.0b013e32835f1cc0
PMCID: PMC3727893  PMID: 23407052
allele; nomenclature; pharmacogenetics; thiopurine methyltransferase
10.  CYP2A6 slow nicotine metabolism is associated with increased quitting by adolescent smokers 
Pharmacogenetics and genomics  2013;23(4):232-235.
Variation in the CYP2A6 gene, that decreases the rate of nicotine metabolic-inactivation, is associated with higher adult smoking cessation rates during clinical trials. We hypothesized that slow metabolism is associated with increased quitting during adolescence. Caucasian adolescent smokers (N=308, aged 12 to 17, 36.3% male) from a cohort study were genotyped for CYP2A6 resulting in 7.8% slow, 14.0% intermediate and 78.2% normal metabolizers. Overall, 144 smokers quit smoking, as indicated by being abstinent for ≥12 months. In logistic regression analyses, the odds ratio for quitting was 2.25 (95% confidence interval 1.05, 4.80; P=0.037) for slow metabolizers relative to normal metabolizers. A linear trend toward increased quitting with decreasing CYP2A6 activity was also observed (odds ratio = 1.44, 95% confidence interval 1.02, 2.01; P=0.034). Thus, CYP2A6 slow metabolism is associated with increased adolescent smoking cessation, indicating that even early in the smoking history genetic variation is influencing smoking cessation.
doi:10.1097/FPC.0b013e32835f834d
PMCID: PMC3744214  PMID: 23462429
adolescent; longitudinal studies; epidemiology; smoking cessation; genetic association studies
11.  PharmGKB Summary: Very Important Pharmacogene Information for Epidermal Growth Factor Receptor (EGFR) 
Pharmacogenetics and genomics  2013;23(11):636-642.
doi:10.1097/FPC.0b013e3283655091
PMCID: PMC3966564  PMID: 23962910
Epidermal growth factor receptor (EGFR); tyrosine kinase inhibitor; erlotinib; gefitinib; pharmacogenomics
12.  Influence of CYP2B6 genetic variants on plasma and urine concentrations of bupropion and metabolites at steady state 
Pharmacogenetics and genomics  2013;23(3):135-141.
Background
Bupropion, an antidepressant and smoking cessation medication, is metabolized to hydroxybupropion (HB), an active metabolite, primarily by CYP2B6.
Objectives
To compare plasma concentrations of bupropion and metabolites at steady state in healthy volunteers with and without CYP2B6 genetic variants.
Methods
In a genotype-guided study of 42 healthy subjects we measured plasma and urine concentrations of bupropion and its metabolites, HB, threohydrobupropion (TB) and erythrohydrobupropion (EB) after 7 days of sustained release bupropion dosing.
Results
CYP2B6*6 and *18 gene variants were associated with approximately 33% reduced concentrations of HB, with no effects on concentrations of bupropion or other metabolites. We could account for 50% of the variation in HB concentrations in a model including genotype and sex.
Conclusions
Since HB is active and steady state concentrations of HB are more than 10 times higher than bupropion, CYP2B6 variants are likely to affect pharmacological activity. Due to the large individual variation within genotype group, the use of therapeutic drug monitoring for dose optimization may be necessary.
doi:10.1097/FPC.0b013e32835d9ab0
PMCID: PMC3763712  PMID: 23344581
13.  A polymorphism in the protein kinase C gene PRKCB is associated with α2-adrenoceptor-mediated vasoconstriction 
Pharmacogenetics and genomics  2013;23(3):127-134.
Objectives
α2-Adrenoceptors (α2-AR) mediate both constriction and dilatation of blood vessels. There is substantial inter-individual variability in dorsal hand vein (DHV) constriction responses to α2-AR agonist activation. Genetic factors appear to contribute significantly to this variation. The present study was designed to identify genetic factors contributing to the inter-individual variability in α2-AR-mediated vascular constriction induced by the selective α2-AR agonist dexmedetomidine.
Methods
DHV constriction responses to local infusion of dexmedetomidine were assessed by measuring changes in vein diameter with a linear variable differential transformer. The outcome variable was log-transformed dexmedetomidine ED50 for constriction. A genome-wide association study (GWAS) of 433,378 single nucleotide polymorphisms (SNPs) was performed for the sensitivity of DHV responses in 64 healthy Finnish subjects. 20 SNPs were selected based on the GWAS results and their associations with the ED50 of dexmedetomidine were tested in an independent North American study population of 68 healthy individuals.
Results
In both study populations (GWAS and replication samples), the SNP rs9922316 in the gene for protein kinase C type β was consistently associated with dexmedetomidine ED50 for dorsal hand vein constriction (unadjusted p = 0.00016 for the combined population).
Conclusions
Genetic variation in protein kinase C type β may contribute to the inter-individual variation in dorsal hand vein constriction responses to α2-AR activation by the agonist dexmedetomidine.
doi:10.1097/FPC.0b013e32835d247f
PMCID: PMC3912740  PMID: 23337848
receptors, adrenergic, alpha; dorsal hand vein; GWAS; candidate genes; dexmedetomidine
14.  A compensatory effect upon splicing results in normal function of the CYP2A6*14 allele 
Pharmacogenetics and genomics  2013;23(3):107-116.
A synonymous variant in the first exon of CYP2A6, rs1137115 (51G > A), defines the common reference allele CYP2A6*1A, and is associated with lower mRNA expression and slower in-vivo nicotine metabolism. Another common allele, CYP2A6*14, differs from CYP2A6*1A by a single variant, rs28399435 (86G > A, S29N). However, CYP2A6*14 shows in-vivo activity comparable with that of full-function alleles, and significantly higher than CYP2A6*1A. rs1137115A is predicted to create an exonic splicing suppressor site overlapping an exonic splicing enhancer (ESE) site in the first exon of CYP2A6, whereas rs28399435A is predicted to strengthen another adjacent ESE, potentially compensating for rs1137115A. Using an allelic expression assay to assess cDNAs produced from rs1137115 heterozygous liver biopsy samples, lower expression of the CYP2A6*1A allele is confirmed while CYP2A6*14 expression is found to be indistinguishable from that of rs1137115G alleles. Quantitative PCR assays to determine the relative abundance of spliced and unspliced or partially spliced CYP2A6 mRNAs in liver biopsy samples show that *1A/*1A homozygotes have a significantly lower ratio, due to both a reduction in spliced forms and an increase in unspliced or partially spliced CYP2A6. These results show the importance of common genetic variants that effect exonic splicing suppressor and ESEs to explain human variation regarding clinically-relevant phenotypes.
doi:10.1097/FPC.0b013e32835caf7d
PMCID: PMC3919506  PMID: 23292114
CYP2A6; exonic splice enhancer; exonic splice suppressor; nicotine metabolism; splicing
15.  Association of Common Variants of CYP4A11 and CYP4F2 with Stroke in the Han Chinese Population 
Pharmacogenetics and genomics  2010;20(3):187-194.
20-Hydroxyeicosatetraenoic acid (20-HETE) has been shown to play an important role in cerebral vascular function. We hypothesized that polymorphisms in genes encoding 20-HETE synthesizing enzymes might confer susceptibility to stroke. To test the hypothesis, haplotype tagging SNPs (htSNPs) and potential functional polymorphisms of CYP4A11 and CYP4F2 genes were genotyped in 558 ischemic stroke patients, 221 hemorrhagic stroke patients and 557 controls. The association analyses were performed at both SNP and haplotype levels. We further verified our findings in an independent cohort of 551 ischemic stroke cases and 48 hemorrhagic stroke subjects and 694 unaffected controls. We identified CYP4A11 C-296T and CYP4F2 V433M were associated with significantly increased risk of ischemic stroke (CT+TT vs CC, adjusted odds ratio (OR) 1.50, 95% confidence interval (CI) 1.17–1.93, Pcombined=0.001, Pcorr=0.008; V/M+M/M vs. V/V, OR 1.38, 95% CI, 1.15–1.65, Pcombined=5.6×10−4, Pcorr=0.005, respectively) Interestingly, the effects of CYP4F2 V433M on ischemic stroke in our study was only evident in male subjects. Our results suggest that genetic variation in CYP4A11 and CYP4F2 alters susceptibility to stroke in the Han Chinese population.
doi:10.1097/FPC.0b013e328336eefe
PMCID: PMC3932492  PMID: 20130494
ischemic stroke; Genetics; haplotypes; Han Chinese population
16.  Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment 
Pharmacogenetics and genomics  2013;23(2):69-77.
Objective
Examine the unique and congruent findings between multiple raters in a genome-wide association studies (GWAS) in the context of understanding individual differences in treatment response during antipsychotic therapy for schizophrenia.
Methods
We performed GWAS to search for genetic variation affecting treatment response. The analysis sample consisted of 738 patients with schizophrenia, successfully genotyped for ~492K SNPs from the Clinical Antipsychotic Trial of Intervention Effectiveness (CATIE). Outcomes included both clinician and patient report of illness severity on global impression scales, the CGI-S and PGI, respectively. Our criterion for genome-wide significance was a pre-specified threshold ensuring that, on average, only 10% of the significant findings are false discoveries.
Results
Thirteen SNPs reached genome-wide significance. The top findings indicated three SNPs in PDE4D, 5q12.1 (p =4.2×10−8, p =1.6×10−7, p =1.8×10−7), mediated the effects of quetiapine on patient reported severity and an additional three SNPs in TJP1, 15q13.1 (p = 2.25×10−7, p = 4.86×10−7, p = 4.91×10−7), mediated the effects of risperidone on patient reported severity. For clinician reported severity, two SNPs in PPA2, 4q24 (p = 3.68×10−7, p = 5.05×10−7), were found to reach genome-wide significance.
Conclusion
We found evidence of both novel and consistent association when examining the results from the patient and clinician ratings suggesting that different raters may capture unique facets of schizophrenia. Although our findings require replication and functional validation, this study demonstrates the potential of GWAS to discover genes that potentially mediate treatment response of antipsychotic medication.
doi:10.1097/FPC.0b013e32835ca260
PMCID: PMC3922978  PMID: 23241943
CATIE; CGI; pharmacogenomics; personalized medicine; schizophrenia; GWAS; single nucleotide polymorphism; PANSS
17.  Nicotinic Acetylcholine Receptor Variation and Response to Smoking Cessation Therapies 
Pharmacogenetics and genomics  2013;23(2):94-103.
Objective
Evaluate nicotinic acetycholine receptor (nAChR) single nucleotide polymorphism (SNP) association with seven day point prevalence abstinence (abstinence) in randomized clinical trials of smoking cessation therapies (RCTs) in individuals grouped by pharmacotherapy randomization to inform the development of personalized smoking cessation therapy.
Methods
We quantified association of four SNPs at three nAChRs with abstinence in eight RCTs. Participants were 2,633 outpatient treatment-seeking, self-identified European ancestry individuals smoking ≥10 cigarettes per day, recruited via advertisement, prescribed pharmacotherapy, and provided with behavioral therapy. Interventions included nicotine replacement therapy (NRT), bupropion, varenicline, placebo or combined NRT and bupropion, and five modes of group and individual behavioral therapy. Outcome measures tested in multivariate logistic regression were end of treatment (EOT) and six month (6MO) abstinence, with demographic, behavioral and genetic covariates.
Results
“Risk” alleles previously associated with smoking heaviness were significantly (P<0.05) associated with reduced abstinence in the placebo pharmacotherapy group (PG) at 6MO [for rs588765 OR (95%CI) 0.41 (0.17–0.99)], and at EOT and at 6MO [for rs1051730, 0.42 (0.19–0.93) and 0.31 (0.12–0.80)], and with increased abstinence in the NRT PG at 6MO [for rs588765 2.07 (1.11–3.87) and for rs1051730 2.54 (1.29–4.99)]. We observed significant heterogeneity in rs1051730 effects (F=2.48, P=0.021) between PGs.
Conclusions
chr15q25.1 nAChR SNP risk alleles for smoking heaviness significantly increase relapse with placebo treatment and significantly increase abstinence with NRT. These SNP-PG associations require replication in independent samples for validation, and testing in larger sample sizes to evaluate whether similar effects occur in other PGs.
doi:10.1097/FPC.0b013e32835cdabd
PMCID: PMC3563676  PMID: 23249876
logistic regression; mediation analysis; nAChR variation; nicotine dependence; pharmacotherapy; randomized clinical trials
18.  Association of sirolimus adverse effects with m-TOR, p70S6K or Raptor polymorphisms in kidney transplant recipients 
Pharmacogenetics and Genomics  2012;22(10):725-732.
The m-TOR inhibitor sirolimus is an immunosuppressive drug used in kidney transplantation. m-TOR binds with Raptor and phosphorylates p70S6 kinase, a protein involved in numerous cell signalling pathways. We investigated the association of candidate polymorphisms in m-TOR, Raptor and p70S6K, sirolimus dose and exposure, and other time-independent as well as time-dependent covariates, with sirolimus-induced adverse events in kidney transplant recipients. This study included a first group of 113 patients, switched from a calcineurin inhibitor to sirolimus and a validation group of 66 patients from another clinical trial, with the same immunosuppressive regimen. The effects of gene polymorphisms and covariates on total cholesterol, low-density lipoprotein cholesterol, triglycerides, hemoglobin, cutaneous adverse events, oedemas and infections were studied using multilinear regression, or logistic regression imbedded in linear mixed-effect models. An m-TOR variant haplotype was significantly associated with a decrease in hemoglobin levels in the two populations of patients (discovery group: β=−0.82 g/dl, p=0.0076; validation group: β=−1.58 g/dl, p=0.0308). Increased sirolimus trough levels were significantly associated with increased total cholesterol levels (discovery group: β =0.02 g/l, p<0.0001, validation group: β =0.02 g/l, p=0.0002) and triglyceride levels (discovery group: β =0.02 g/l, p=0.0059, validation group: β =0.05 g/l, p=0.0370). Sirolimus trough levels were also associated with an increased risk for cutaneous adverse events (OR=1.97, 95%CI [1.32–1.94], p=0.0009) and oedemas (OR=1.16, 95%CI [1.03–1.30], p=0.01342) in the discovery group, but this was not confirmed in the validation group. These results provide evidence of an association between an m-TOR haplotype and a decrease in hemoglobin in renal transplant recipients.
doi:10.1097/FPC.0b013e328357359d
PMCID: PMC3894420  PMID: 22863900
Adaptor Proteins, Signal Transducing; genetics; Adult; Aged; Female; Follow-Up Studies; Graft Rejection; Haplotypes; Humans; Immunosuppressive Agents; adverse effects; Kidney; drug effects; metabolism; Kidney Transplantation; Logistic Models; Longitudinal Studies; Male; Middle Aged; Ribosomal Protein S6 Kinases, 70-kDa; genetics; Sirolimus; adverse effects; TOR Serine-Threonine Kinases; genetics; sirolimus, adverse event, mammalian target of rapamycin, p70S6 kinase, raptor, pharmacogenetics.
19.  OATP1B1-related drug–drug and drug–gene interactions as potential risk factors for cerivastatin-induced rhabdomyolysis 
Pharmacogenetics and genomics  2013;23(7):355-364.
Objective
Genetic variation in drug metabolizing enzymes and membrane transporters as well as concomitant drug therapy can modulate the beneficial and the deleterious effects of drugs. We investigated whether patients exhibiting rhabdomyolysis who were taking cerivastatin possess functional genetic variants in SLCO1B1 and whether they were on concomitant medications that inhibit OATP1B1, resulting in accumulation of cerivastatin.
Methods
This study had three components: (a) resequencing the SLCO1B1 gene in 122 patients who developed rhabdomyolysis while on cerivastatin; (b) functional evaluation of the identified SLCO1B1 nonsynonymous variants and haplotypes in in-vitro HEK293/FRT cells stably transfected with pcDNA5/FRT empty vector, SLCO1B1 reference, variants, and haplotypes; and (c) in-vitro screening of 15 drugs commonly used among the rhabdomyolysis cases for inhibition of OATP1B1-mediated uptake of cerivastatin in HEK293/FRT cells stably transfected with reference SLCO1B1.
Results
The resequencing of the SLCO1B1 gene identified 54 variants. In-vitro functional analysis of SLCO1B1 nonsynonymous variants and haplotypes showed that the V174A, R57Q, and P155T variants, a novel frameshift insertion, OATP1B1*14 and OATP1B1*15 haplotype were associated with a significant reduction (P<0.001) in cerivastatin uptake (32, 18, 72, 3.4, 2.1 and 5.7% of reference, respectively). Furthermore, clopidogrel and seven other drugs were shown to inhibit OATP1B1-mediated uptake of cerivastatin.
Conclusion
Reduced function of OATP1B1 related to genetic variation and drug–drug interactions likely contributed to cerivastatin-induced rhabdomyolysis. Although cerivastatin is no longer in clinical use, these findings may translate to related statins and other substrates of OATP1B1.
doi:10.1097/FPC.0b013e3283620c3b
PMCID: PMC3894639  PMID: 23652407
cerivastatin; clopidogrel; OATP1B1; rhabdomyolysis
20.  The relationship of polymorphisms in ABCC2 and SLCO1B3 with docetaxel pharmacokinetics and neutropenia: CALGB 60805 (Alliance) 
Pharmacogenetics and genomics  2013;23(1):29-33.
Docetaxel-related neutropenia was associated with polymorphisms in the drug transporters ABCC2 and SLCO1B3 in Japanese cancer patients. We hypothesized that this association is because of reduced docetaxel clearance, associated with polymorphisms in those genes. We studied 64 US cancer patients who received a single cycle of 75 mg/m2 of docetaxel monotherapy. We found that the ABCC2 polymorphism at rs-12762549 trended to show a relationship with reduced docetaxel clearance (P = 0.048), but not with neutropenia. There was no significant association of the SLCO1B3 polymorphisms with docetaxel clearance or neutropenia. We conclude that the relationship between docetaxel-associated neutropenia and polymorphisms in drug transporters identified in Japanese patients was not confirmed in this cohort of US cancer patients.
doi:10.1097/FPC.0b013e32835b16d8
PMCID: PMC3647228  PMID: 23188068
ABCC2 (pharmacogenetics); docetaxel; neutropenia; pharmacokinetics; SLCO1B3
21.  Preclinical discovery of candidate genes to guide pharmacogenetics during phase I development: the example of the novel anticancer agent ABT-751 
Pharmacogenetics and genomics  2013;23(7):10.1097/FPC.0b013e3283623e81.
Objective
ABT-751, a novel orally available antitubulin agent, is mainly eliminated as inactive glucuronide (ABT-751G) and sulfate (ABT-751S) conjugates. We performed a pharmacogenetic investigation of ABT-751 pharmacokinetics using in-vitro data to guide the selection of genes for genotyping in a phase I trial of ABT-751.
Methods
UDP-glucuronosyltransferase (UGT) and sulfotransferase (SULT) enzymes were screened for ABT-751 metabolite formation in vitro. Forty-seven cancer patients treated with ABT-751 were genotyped for 21 variants in these genes.
Results
UGT1A1, UGT1A4, UGT1A8, UGT2B7, and SULT1A1 were found to be involved in the formation of inactive ABT-751 glucuronide (ABT-751G) and sulfate (ABT-751S). SULT1A1 copy number (> 2) was associated with an average 34% increase in ABT-751 clearance (P= 0.044), an 18% reduction in ABT-751 AUC (P = 0.045), and a 50% increase in sulfation metabolic ratios (P=0.025). UGT1A8 rs6431558 was associated with a 28% increase in glucuronidation metabolic ratios (P =0.022), and UGT1A4*2 was associated with a 65% decrease in ABT-751 Ctrough (P = 0.009).
Conclusion
These results might represent the first example of a clinical pharmacokinetic effect of the SULT1A1 copy number variant on the clearance of a SULT1A1 substrate. A-priori selection of candidate genes guided by in-vitro metabolic screening enhanced our ability to identify genetic determinants of interpatient pharmacokinetic variability.
doi:10.1097/FPC.0b013e3283623e81
PMCID: PMC3858967  PMID: 23670235
ABT-751; drug development; drug metabolism; pharmacogenetics; phase I; sulfotransferase; UDP-glucuronosyltransferase
22.  Genome-wide association study of plasma efavirenz pharmacokinetics in AIDS Clinical Trials Group protocols implicates several CYP2B6 variants 
Pharmacogenetics and genomics  2012;22(12):858-867.
Objectives
Prior candidate gene studies have associated CYP2B6 516G→T [rs3745274] and 983T→C [rs28399499] with increased plasma efavirenz exposure. We sought to identify novel variants associated with efavirenz pharmacokinetics.
Materials and methods
Antiretroviral therapy-naive AIDS Clinical Trials Group studies A5202, A5095, and ACTG 384 included plasma sampling for efavirenz pharmacokinetics. Log-transformed trough efavirenz concentrations (Cmin) were previously estimated by population pharmacokinetic modeling. Stored DNA was genotyped with Illumina HumanHap 650Y or 1MDuo platforms, complemented by additional targeted genotyping of CYP2B6 and CYP2A6 with MassARRAY iPLEX Gold. Associations were identified by linear regression, which included principal component vectors to adjust for genetic ancestry.
Results
Among 856 individuals, CYP2B6 516G→T was associated with efavirenz estimated Cmin (P = 8.5 × 10−41). After adjusting for CYP2B6 516G→T, CYP2B6 983T→C was associated (P = 9.9 × 10−11). After adjusting for both CYP2B6 516G→T and 983T→C, a CYP2B6 variant (rs4803419) in intron 3 was associated (P = 4.4 × 10−15). After adjusting for all the three variants, non-CYP2B6 polymorphisms were associated at P-value less than 5× 10−8. In a separate cohort of 240 individuals, only the three CYP2B6 polymorphisms replicated. These three polymorphisms explained 34% of interindividual variability in efavirenz estimated Cmin. The extensive metabolizer phenotype was best defined by the absence of all three polymorphisms.
Conclusion
Three CYP2B6 polymorphisms were independently associated with efavirenz estimated Cmin at genome-wide significance, and explained one-third of interindividual variability. These data will inform continued efforts to translate pharmacogenomic knowledge into optimal efavirenz utilization.
doi:10.1097/FPC.0b013e32835a450b
PMCID: PMC3614365  PMID: 23080225
CYP2B6; efavirenz; HIV; pharmacogenomics; pharmacokinetics
23.  PharmGKB summary: zidovudine pathway 
Pharmacogenetics and genomics  2012;22(12):891-894.
doi:10.1097/FPC.0b013e32835879a8
PMCID: PMC3696524  PMID: 22960662
ABCC4; ABCB1; HIV infection; UGT2B7; zidovudine
24.  Multiple genetic variants predict steady-state nevirapine clearance in HIV-infected Cambodians 
Pharmacogenetics and genomics  2012;22(12):868-876.
Objective
In a previous analysis involving protocol ANRS 12154, interindividual variability in steady-state nevirapine clearance among HIV-infected Cambodians was partially explained by CYP2B6 516G→T (CYP2B6*6). Here, we examine whether additional genetic variants predict nevirapine clearance in this cohort.
Methods
Analyses included Phnom Penh ESTHER (Ensemble pour une Solidarité Thérapeutique Hospitalière en Réseau) cohort participants who had consented for genetic testing. All participants were receiving nevirapine plus two nucleoside analogs. The mean individual nevirapine clearance estimates were derived from a population model developed on nevirapine concentrations at 18 and 36 months of therapy. Polymorphisms were assayed in ABCB1, CYP2A6, CYP2B6, CYP2C19, CYP3A4, CYP3A5, and NR1I2.
Results
Of 198 assayed loci, 130 were polymorphic. Among 129 individuals with evaluable genetic data, nevirapine clearance ranged from 1.06 to 5.00 l/h in 128 individuals and was 7.81 l/h in one individual. In bivariate linear regression, CYP2B6 516G→T (CYP2B6*6) was associated with lower nevirapine clearances (P = 3.5 × 10–6). In a multivariate linear regression model conditioned on CYP2B6 516G→T, independent associations were identified with CYP2B6 rs7251950, CYP2B6 rs2279343, and CYP3A4 rs2687116. The CYP3A4 association disappeared after censoring the outlier clearance value. A model that included CYP2B6 516G→T (P = 1.0 × 10–9), rs7251950 (P = 4.8 × 10–5), and rs2279343 (P = 7.1 × 10–5) explained 11% of interindividual variability in nevirapine clearance.
Conclusion
Among HIV-infected Cambodians, several CYP2B6 polymorphisms were associated independently with steady-state nevirapine clearance. The prediction of nevirapine clearance was improved by considering several polymorphisms in combination.
doi:10.1097/FPC.0b013e32835a5af2
PMCID: PMC3586376  PMID: 23104099
Cambodia; CYP2B6; nevirapine pharmacokinetics; pharmacogenetics; population approach
25.  Metformin pathways: pharmacokinetics and pharmacodynamics 
Pharmacogenetics and genomics  2012;22(11):820-827.
doi:10.1097/FPC.0b013e3283559b22
PMCID: PMC3651676  PMID: 22722338
AMP-activated protein kinase; diabetes mellitus; metformin; multidrug and toxin extrusion 1; OCT1; OCT2; pathway; pharmacodynamics; pharmacogenomic; pharmacokinetics; type 2 diabetes

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