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1.  Evaluation of a [13C]-Dextromethorphan Breath Test to Assess CYP2D6 Phenotype 
Journal of clinical pharmacology  2008;48(9):1041-1051.
A [13C]-dextromethorphan ([13C]-DM) breath test was evaluated to assess its feasibility as a rapid, phenotyping assay for CYP2D6 activity. [13C]-DM (0.5 mg/kg) was administered orally with water or potassium bicarbonate-sodium bicarbonate to 30 adult Caucasian volunteers (n = 1 each): CYP2D6 poor metabolizers (2 null alleles; PM-0) and extensive metabolizers with 1 (EM-1) or 2 functional alleles (EM-2). CYP2D6 phenotype was determined by 13CO2 enrichment measured by infrared spectrometry (delta-over-baseline [DOB] value) in expired breath samples collected before and up to 240 minutes after [13C]-DM ingestion and by 4-hour urinary metabolite ratio. The PM-0 group was readily distinguishable from either EM group by both the breath test and urinary metabolite ratio. Using a single point determination of phenotype at 40 minutes and defining PMs as subjects with a DOB ≤ 0.5, the sensitivity of the method was 100%; specificity was 95% with 95% accuracy and resulted in the misclassification of 1 EM-1 individual as a PM. Modification of the initial protocol (timing of potassium bicarbonate-sodium bicarbonate administration relative to dose) yielded comparable results, but there was a tendency toward increased DOB values. Although further development is required, these studies suggest that the [13C]-DM breath test offers promise as a rapid, minimally invasive phenotyping assay for CYP2D6 activity.
doi:10.1177/0091270008319709
PMCID: PMC4791047  PMID: 18728242
CYP2D6; phenotype; dextromethorphan; breath test
2.  Glucocorticoid Genes and the Developmental Origins of Asthma Susceptibility and Treatment Response 
Antenatal corticosteroids enhance lung maturation. However, the importance of glucocorticoid genes on early lung development, asthma susceptibility, and treatment response remains unknown. We investigated whether glucocorticoid genes are important during lung development and their role in asthma susceptibility and treatment response. We identified genes that were differentially expressed by corticosteroids in two of three genomic datasets: lymphoblastoid cell lines of participants in the Childhood Asthma Management Program, a glucocorticoid chromatin immunoprecipitation/RNA sequencing experiment, or a murine model; these genes made up the glucocorticoid gene set (GCGS). Using gene expression profiles from 38 human fetal lungs and C57BL/6J murine fetal lungs, we identified developmental genes that were in the top 5% of genes contributing to the top three principal components (PCs) most highly associated with post-conceptional age. Glucocorticoid genes that were enriched in this set of developmental genes were then included in the developmental glucocorticoid gene set (DGGS). We then investigated whether glucocorticoid genes are important during lung development, and their role in asthma susceptibility and treatment response. A total of 232 genes were included in the GCGS. Analysis of gene expression demonstrated that glucocorticoid genes were enriched in lung development (P = 7.02 × 10−26). The developmental GCGS was enriched for genes that were differentially expressed between subjects with asthma and control subjects (P = 4.26 × 10−3) and were enriched after treatment of subjects with asthma with inhaled corticosteroids (P < 2.72 × 10−4). Our results show that glucocorticoid genes are overrepresented among genes implicated in fetal lung development. These genes influence asthma susceptibility and treatment response, suggesting their involvement in the early ontogeny of asthma.
doi:10.1165/rcmb.2014-0109OC
PMCID: PMC4491138  PMID: 25192440
glucocorticoid genes; lung development; asthma; asthma treatment
3.  Conference Scene 
Pharmacogenomics  2010;11(12):1691-1702.
A major challenge for clinicians, pharmaceutical companies and regulatory agencies is to better understand the relative contributions of ontogeny and genetic variation to observed variability in drug disposition and response across the pediatric age spectrum from preterm and term newborns, to infants, children and adolescents. Extrapolation of adult experience with pharmacogenomics and personalized medicine to pediatric patients of different ages and developmental stages, is fraught with many challenges. Compared with adults, pediatric pharmacogenetics and pharmacogenomics involves an added measure of complexity as variability owing to developmental processes, or ontogeny, is superimposed upon genetic variation. Furthermore, some pediatric diseases have no adult correlate or are more prevalent in children compared with adults, and several adverse drug reactions are unique to children, or occur at a higher frequency in children. The primary objective of this conference was to initiate an ongoing series of annual meetings on ‘Pediatric Pharmacogenomics and Personalized Medicine’ organized by the Center for Personalized Medicine and Therapeutic Innovation and Division of Clinical Pharmacology and Medical Therapeutics at Children’s Mercy Hospitals and Clinics in Kansas City, MO, USA. The primary goals of the inaugural meeting were: to bring together clinicians, basic and translational scientists and allied healthcare practitioners, and engage in a multi- and cross-disciplinary dialog aimed at implementing personalized medicine in pediatric settings; to provide a forum for the presentation and the dissemination of research related to the application of pharmacogenomic strategies to investigations of variability of drug disposition and response in children; to explore the ethical, legal and societal implications of pharmacogenomics and personalized medicine that are unique to children; and finally, to create networking opportunities for stimulating discussion, cooperation and collaboration to devise strategies to address the research needs identified.
doi:10.2217/pgs.10.175
PMCID: PMC4610716  PMID: 21142913
4.  Design and Testing of an EHR-Integrated, Busulfan Pharmacokinetic Decision Support Tool for the Point-of-Care Clinician 
Background: Busulfan demonstrates a narrow therapeutic index for which clinicians routinely employ therapeutic drug monitoring (TDM). However, operationalizing TDM can be fraught with inefficiency. We developed and tested software encoding a clinical decision support tool (DST) that is embedded into our electronic health record (EHR) and designed to streamline the TDM process for our oncology partners.
Methods: Our development strategy was modeled based on the features associated with successful DSTs. An initial Requirements Analysis was performed to characterize tasks, information flow, user needs, and system requirements to enable push/pull from the EHR. Back-end development was coded based on the algorithm used when manually performing busulfan TDM. The code was independently validated in MATLAB using 10,000 simulated patient profiles. A 296-item heuristic checklist was used to guide design of the front-end user interface. Content experts and end-users (n = 28) were recruited to participate in traditional usability testing under an IRB approved protocol.
Results: Decision support software was developed to systematically walk the point-of-care clinician through the TDM process. The system is accessed through the EHR which transparently imports all of the requisite patient data. Data are visually inspected and then curve fit using a model-dependent approach. Quantitative goodness-of-fit are converted to single tachometer where “green” alerts the user that the model is strong, “yellow” signals caution and “red” indicates that there may be a problem with the fitting. Override features are embedded to permit application of a model-independent approach where appropriate. Simulations are performed to target a desired exposure or dose as entered by the clinician and the DST pushes the user approved recommendation back into the EHR. Usability testers were highly satisfied with our DST and quickly became proficient with the software.
Conclusions: With early and broad stake-holder engagement we developed a clinical DST for the non-pharmacologist. This tools affords our clinicians the ability to seamlessly transition from patient assessment, to pharmacokinetic modeling and simulation, and subsequent prescription order entry.
doi:10.3389/fphar.2016.00065
PMCID: PMC4811899  PMID: 27065859
software design; decision support; therapeutic drug monitoring; bone marrow transplant; usability testing
5.  CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping 
TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact the performance of PCR-based genotype assays, including TaqMan. Regardless of the test platform used, it is prudent to confirm rare allele calls by an independent method.
doi:10.3389/fphar.2015.00312
PMCID: PMC4709848  PMID: 26793106
CYP2D6; CYP2D7; TaqMan; genotyping; CYP2D6*15; CYP2D6*35; CYP2D6*43
6.  Folate Depletion and Increased Glutamation in Juvenile Idiopathic Arthritis Patients Treated with Methotrexate 
Objective
Folates exist as a fluctuating pool of polyglutamated metabolites that may serve as a clinical marker of MTX activity. This study evaluates circulating folate content and folate polyglutamate distribution in Juvenile Idiopathic Arthritis (JIA) patients and in a cell culture model based on MTX exposure and folate supply.
Methods
Blood, plasma and red blood cell (RBC) measurements of MTX and folates were obtained from previously published data sets and additional sample analysis for JIA patients receiving (n=98) and not receiving (n=78) MTX therapy. Erythroblastoid cells maintained in culture were exposed to MTX and grown under varying levels of folic acid supplementation. Samples were analyzed for cellular folate and MTX content.
Results
Circulating folate levels were lower in JIA patients receiving MTX, with reduced levels of blood, plasma and RBC 5-methyl-tetrahydrofolate (5mTHF) (p<0.0001). Average polyglutamate chain-length (Gluavg) of RBC 5mTHF was elevated in JIA patients receiving MTX (5.63±0.15 vs. 5.54±0.11, p<0.0001) and correlated with both RBC MTX accumulation (p=0.02) and reduced plasma 5mTHF levels (p=0.008). MTX exposure and folate deprivation in erythroblastoid cells resulted in a depletion of bioactive folate species that was associated with a shift to higher Gluavg values for several species, most notably tetrahydrofolate (THF) and 5,10-methylenetetrahydrofolate (CH2-THF). Increased Gluavg resulted from the depletion of short-chain and the accumulation of long-chain glutamate species.
Conclusion
Folate content and polyglutamate distribution are responsive markers of MTX activity and folate supply in vivo and in vitro, and may provide novel clinical markers of pharmacologic activity of MTX.
doi:10.1002/art.38865
PMCID: PMC4376251  PMID: 25186097
7.  Fetal lung and placental methylation is associated with in utero nicotine exposure 
Epigenetics  2014;9(11):1473-1484.
In utero smoke exposure has been shown to have detrimental effects on lung function and to be associated with persistent wheezing and asthma in children. One potential mechanism of IUS effects could be alterations in DNA methylation, which may have life-long implications. The goal of this study was to examine the association between DNA methylation and nicotine exposure in fetal lung and placental tissue in early development; nicotine exposure in this analysis represents a likely surrogate for in-utero smoke. We performed an epigenome-wide analysis of DNA methylation in fetal lung tissue (n = 85, 41 smoke exposed (48%), 44 controls) and the corresponding placental tissue samples (n = 80, 39 smoke exposed (49%), 41 controls) using the Illumina HumanMethylation450 BeadChip array. Differential methylation analyses were conducted to evaluate the variation associated with nicotine exposure. The most significant CpG sites in the fetal lung analysis mapped to the PKP3 (P = 2.94 × 10−03), ANKRD33B (P = 3.12 × 10−03), CNTD2 (P = 4.9 × 10−03) and DPP10 (P = 5.43 × 10−03) genes. In the placental methylome, the most significant CpG sites mapped to the GTF2H2C and GTF2H2D genes (P = 2.87 × 10−06 − 3.48 × 10−05). One hundred and one unique CpG sites with P-values < 0.05 were concordant between lung and placental tissue analyses. Gene Set Enrichment Analysis demonstrated enrichment of specific disorders, such as asthma and immune disorders. Our findings demonstrate an association between in utero nicotine exposure and variable DNA methylation in fetal lung and placental tissues, suggesting a role for DNA methylation variation in the fetal origins of chronic diseases.
doi:10.4161/15592294.2014.971593
PMCID: PMC4623268  PMID: 25482056
asthma; developmental biology; epigenomics; nicotine and DNA methylation; smoking
8.  Detection of an endogenous urinary biomarker associated with CYP2D6 activity using global metabolomics 
Pharmacogenomics  2014;15(16):1947-1962.
Aim
We sought to discover endogenous urinary biomarkers of human CYP2D6 activity.
Patients & methods
Healthy pediatric subjects (n = 189) were phenotyped using dextromethorphan and randomized for candidate biomarker selection and validation. Global urinary metabolomics was performed using liquid chromatography quadrupole time-of-flight mass spectrometry. Candidate biomarkers were tested in adults receiving fluoxetine, a CYP2D6 inhibitor.
Results
A biomarker, M1 (m/z 444.3102) was correlated with CYP2D6 activity in both the pediatric training and validation sets. Poor metabolizers had undetectable levels of M1, whereas it was present in subjects with other phenotypes. In adult subjects, a 9.56-fold decrease in M1 abundance was observed during CYP2D6 inhibition.
Conclusion
Identification and validation of M1 may provide a noninvasive means of CYP2D6 phenotyping.
doi:10.2217/pgs.14.155
PMCID: PMC4486214  PMID: 25521354
biomarker; clinical; CYP2D6; dextromethorphan; endogenous; fluoxetine; metabolomics; pediatric; phenotype
9.  Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Selective Serotonin Reuptake Inhibitors 
Selective Serotonin Reuptake Inhibitors (SSRIs) are primary treatment options for major depressive and anxiety disorders. CYP2D6 and CYP2C19 polymorphisms can influence the metabolism of SSRIs thereby affecting drug efficacy and safety. We summarize evidence from the published literature supporting these associations and provide dosing recommendations for fluvoxamine, paroxetine, citalopram, escitalopram and sertraline based on CYP2D6 and/or CYP2C19 genotype (updates at www.pharmgkb.org).
doi:10.1002/cpt.147
PMCID: PMC4512908  PMID: 25974703
SSRIs; paroxetine; fluoxetine; fluvoxamine; citalopram; escitalopram; sertraline; pharmacogenomics; personalized medicine; CPIC
10.  Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for CYP3A5 Genotype and Tacrolimus Dosing 
Tacrolimus is the mainstay immunosuppressant drug used after solid organ and hematopoietic stem cell transplantation. Individuals who express CYP3A5 (extensive and intermediate metabolizers) generally have decreased dose-adjusted trough concentrations of tacrolimus as compared to those who are CYP3A5 non-expressers (poor metabolizers), possibly delaying achievement of target blood concentrations. We summarize evidence from the published literature supporting this association and provide dosing recommendations for tacrolimus based on CYP3A5 genotype when known (updates at www.pharmgkb.org).
doi:10.1002/cpt.113
PMCID: PMC4481158  PMID: 25801146
Tacrolimus; CYP3A5; immunosuppressant; pharmacogenetics; pharmacogenomics; transplant
11.  Population Pharmacokinetics of Oral Baclofen in Pediatric Patients with Cerebral Palsy 
The Journal of pediatrics  2014;164(5):1181-1188.e8.
Objective
To characterize the population pharmacokinetics (PK) of oral baclofen and assess impact of patient-specific covariates in children with cerebral palsy (CP) in order to support its clinical use.
Subjects design
Children (2-17 years of age) with CP received a dose of titrated oral baclofen from 2.5 mg 3 times a day to a maximum tolerated dose of up to 20 mg 4 times a day. PK sampling followed titration of 10-12 weeks. Serial R- and S-baclofen plasma concentrations were measured for up to 16 hours in 49 subjects. Population PK modeling was performed using NONMEM 7.1 (ICON PLC; Ellicott City, Maryland).
Results
R- and S-baclofen showed identical concentration-time profiles. Both baclofen enantiomers exhibited linear and dose/kg-proportional PK, and no sex differences were observed. Average baclofen terminal half-life was 4.5 hours. A 2-compartment PK model with linear elimination and transit absorption steps adequately described concentration-time profiles of both baclofen enantiomers. The mean population estimate of apparent clearance/F was 0.273 L/h/kg with 33.4% inter-individual variability (IIV), and the apparent volume of distribution (Vss/F) was 1.16 L/kg with 43.9% IIV. Delayed absorption was expressed by a mean transit time of 0.389 hours with 83.7% IIV. Body weight, a possible genetic factor, and age were determinants of apparent clearance in these children.
Conclusion
The PK of oral baclofen exhibited dose-proportionality and were adequately described by a 2-compartment model. Our population PK findings suggest that baclofen dosage can be based on body weight (2 mg/kg per day) and the current baclofen dose escalation strategy is appropriate in the treatment of children with CP older than 2 years of age.
doi:10.1016/j.jpeds.2014.01.029
PMCID: PMC3992203  PMID: 24607242
12.  SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum 
Scientific Reports  2015;5:9257.
CYP2D6 contributes to the metabolism of many clinically used drugs and is increasingly tested to individualize drug therapy. The CYP2D6 gene is challenging to genotype due to the highly complex nature of its gene locus. TaqMan® technology is widely used in the clinical and research settings for genotype analysis due to assay reliability, low cost, and the availability of commercially available assays. The assay identifying 1023C>T (rs28371706) defining a reduced function (CYP2D6*17) and several nonfunctional alleles, produced a small number of unexpected diplotype calls in three independent sets of samples, i.e. calls suggested the presence of a CYP2D6*4 subvariant containing 1023C>T. Gene resequencing did not reveal any unknown SNPs in the primer or probe binding sites in any of the samples, but all affected samples featured a trio of SNPs on their CYP2D6*4 allele between one of the PCR primer and probe binding sites. While the phenomenon was ultimately overcome by an alternate assay utilizing a PCR primer excluding the SNP trio, the mechanism causing this phenomenon remains elusive. This rare and unexpected event underscores the importance of assay validation in samples representing a variety of genotypes, but also vigilance of assay performance in highly polymorphic genes such as CYP2D6.
doi:10.1038/srep09257
PMCID: PMC4365394  PMID: 25788121
13.  Common CYP2D6 polymorphisms affecting alternative splicing and transcription: long-range haplotypes with two regulatory variants modulate CYP2D6 activity 
Human Molecular Genetics  2013;23(1):268-278.
Cytochrome P450 2D6 (CYP2D6) is involved in the metabolism of 25% of clinically used drugs. Genetic polymorphisms cause substantial variation in CYP2D6 activity and serve as biomarkers guiding drug therapy. However, genotype–phenotype relationships remain ambiguous except for poor metabolizers carrying null alleles, suggesting the presence of yet unknown genetic variants. Searching for regulatory CYP2D6 polymorphisms, we find that a SNP defining the CYP2D6*2 allele, rs16947 [R296C, 17–60% minor allele frequency (MAF)], previously thought to convey normal activity, alters exon 6 splicing, thereby reducing CYP2D6 expression at least 2-fold. In addition, two completely linked SNPs (rs5758550/rs133333, MAF 13–42%) increase CYP2D6 transcription more than 2-fold, located in a distant downstream enhancer region (>100 kb) that interacts with the CYP2D6 promoter. In high linkage disequilibrium (LD) with each other, rs16947 and the enhancer SNPs form haplotypes that affect CYP2D6 enzyme activity in vivo. In a pediatric cohort of 164 individuals, rs16947 alone (minor haplotype frequency 28%) was associated with reduced CYP2D6 metabolic activity (measured as dextromethorphan/metabolite ratios), whereas rs5758550/rs133333 alone (frequency 3%) resulted in increased CYP2D6 activity, while haplotypes containing both rs16947 and rs5758550/rs133333 were similar to the wild-type. Other alleles used in biomarker panels carrying these variants such as CYP2D6*41 require re-evaluation of independent effects on CYP2D6 activity. The occurrence of two regulatory variants of high frequency and in high LD, residing on a long haplotype, highlights the importance of gene architecture, likely shaped by evolutionary selection pressures, in determining activity of encoded proteins.
doi:10.1093/hmg/ddt417
PMCID: PMC3857955  PMID: 23985325
14.  Reference intervals for urinary renal injury biomarkers KIM-1 and NGAL in healthy children 
Biomarkers in medicine  2014;8(10):1189-1197.
Aim
The aim of this study was to establish reference intervals in healthy children for two novel urinary biomarkers of acute kidney injury, kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL).
Materials & Methods
Urinary biomarkers were determined in samples from children in the UK (n = 120) and the USA (n = 171) using both Meso Scale Discovery (MSD) and Luminex-based analytical approaches.
Results
95% reference intervals for each biomarker in each cohort are presented and stratified by sex or ethnicity where necessary, and age-related variability is explored using quantile regression. We identified consistently higher NGAL concentrations in females than males (p < 0.0001), and lower KIM-1 concentrations in African–Americans than Caucasians (p = 0.02). KIM-1 demonstrated diurnal variation, with higher concentrations in the morning (p < 0.001).
Conclusion
This is the first report of reference intervals for KIM-1 and NGAL using two analytical methods in a healthy pediatric population in both UK and US-based populations.
doi:10.2217/bmm.14.36
PMCID: PMC4076175  PMID: 24661102
KIM-1; nephrotoxicity; pediatric nephrology; proximal tubule
16.  Developmental variations in metabolic capacity of flavin-containing mono-oxygenase 3 in childhood 
AIM
The aim of this study was to investigate intra- and inter-individual variations of functional metabolic capacity of flavin-containing mono-oxygenase (FMO) during childhood using trimethylamine N-oxygenation as a probe reaction.
METHODS
Trimethylamine N-oxygenation functional activity and presence of FMO1 (fetal form), FMO3 (adult form), and FMO5 (endogenous form) were immunochemically determined and compared in human liver microsomes obtained from children at various ages. As a control, the same parameters were studied with recombinant FMO1, FMO3 and FMO5 proteins as enzyme sources. Developmental variation in functional metabolic capacity of FMO was estimated by measuring urinary trimethylamine and its N-oxide in several individuals at different ages and in a group of 77 subjects in childhood.
RESULTS
There was a significant correlation between trimethylamine N-oxygenation functional activity and FMO3 expression levels in human liver microsomes (r = 0.71, P < 0.05, n = 9). Trimethylamine N-oxygenation was catalyzed largely by FMO3 and not by FMO1 or FMO5. On the basis of analysis of intra-individual observations and collective urine samples under daily dietary conditions it was possible that neonates or infants harbouring at least one non-inactive-allele of the FMO3 gene could have developmental FMO3 metabolic capacity in childhood.
CONCLUSIONS
Developmental variations in functional metabolic capacity of FMO3 in childhood were shown both on the basis of in vivo phenotyping tests and in in vitro liver microsomal determinations.
doi:10.1111/j.1365-2125.2010.03876.x
PMCID: PMC3080647  PMID: 21395651
FMO3; infant; neonate; trimethylamine; trimethylaminuria
17.  Fluticasone Propionate Pharmacogenetics: CYP3A4*22 Polymorphism and Pediatric Asthma Control 
The Journal of pediatrics  2013;162(6):1222-1227.e2.
Objective
To determine the relationship between allelic variations in genes involved in fluticasone propionate (FP) metabolism and asthma control among children with asthma managed with inhaled FP.
Study design
The relationship between variability in asthma control scores and genetic variation in drug metabolism was assessed by genotyping nine single nucleotide polymorphisms (SNPs) in CYP3A4, CYP3A5, and CYP3A7. Genotype information was compared with asthma control scores (0 = well-controlled to 15 = poorly-controlled), determined by using a questionnaire modified from the National Heart Lung and Blood Institute Expert Panel 3 guidelines.
Results
Our study cohort was comprised of 734 children with asthma (mean age 8.8 ± 4.3 years), who were predominantly male (61%) and non-Hispanic Whites (53%); 413 children (56%) were receiving inhaled glucocorticoids daily, of which FP was prescribed most frequently (65%). Among the children receiving daily FP, SNPs in the genes CYP3A5 and CYP3A7 were not associated with asthma control scores. In contrast, asthma control scores were significantly improved among 20 (7%) children with the CYP3A4*22 allele (median 3, range 0-6), as compared with the 201 patients without the CYP3A4*22 allele (median 4, range 0-15) (P=0.02). The presence of CYP3A4*22 was associated with improved asthma control scores by 2.1 points (95% CI: 0.5-3.8).
Conclusions
The presence of CYP3A4*22, which is associated with decreased hepatic CYP3A4 expression and activity, was accompanied by improved asthma control among FP treated children. Decreased CYP3A4 activity may improve asthma control with inhaled FP.
doi:10.1016/j.jpeds.2012.11.031
PMCID: PMC3620714  PMID: 23290512
asthma; fluticasone; inhaled glucocorticoids; corticosteroids; children; pharmacogenetics
18.  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
19.  High-resolution melt analysis to detect sequence variations in highly homologous gene regions: application to CYP2B6 
Pharmacogenomics  2013;14(8):10.2217/pgs.13.66.
High-resolution melt (HRM) analysis using ‘release-on-demand’ dyes, such as EvaGreen® has the potential to resolve complex genotypes in situations where genotype interpretation is complicated by the presence of pseudogenes or allelic variants in close proximity to the locus of interest. We explored the utility of HRM to genotype a SNP (785A>G, K262R, rs2279343) that is located within exon 5 of the CYP2B6 gene, which contributes to the metabolism of a number of clinically used drugs. Testing of 785A>G is challenging, but crucial for accurate genotype determination. This SNP is part of multiple known CYP2B6 haplotypes and located in a region that is identical to CYP2B7, a nonfunctional pseudogene. Because small CYP2B6-specific PCR amplicons bracketing 785A>G cannot be generated, we simultaneously amplified both genes. A panel of 235 liver tissue DNAs and five Coriell samples were assessed. Eight CYP2B6/CYP2B7 diplotype combinations were found and a novel variant 769G>A (D257N) was discovered. The frequency of 785G corresponded to those reported for Caucasians and African–Americans. Assay performance was confirmed by CYP2B6 and/or CYP2B7 sequence analysis in a subset of samples, using a preamplified CYP2B6-specific long-range-PCR amplicon as HRM template. Inclusion rather than exclusion of a homologous pseudogene allowed us to devise a sensitive, reliable and affordable assay to test this CYP2B6 SNP. This assay design may be utilized to overcome the challenges and limitations of other methods. Owing to the flexibility of HRM, this assay design can easily be adapted to other gene loci of interest.
doi:10.2217/pgs.13.66
PMCID: PMC3866959  PMID: 23746185
CYP2B6; CYP2B7; genotyping; high-resolution melt analysis; HRM; SNPs
20.  A modified generalized Fisher method for combining probabilities from dependent tests 
Rapid developments in molecular technology have yielded a large amount of high throughput genetic data to understand the mechanism for complex traits. The increase of genetic variants requires hundreds and thousands of statistical tests to be performed simultaneously in analysis, which poses a challenge to control the overall Type I error rate. Combining p-values from multiple hypothesis testing has shown promise for aggregating effects in high-dimensional genetic data analysis. Several p-value combining methods have been developed and applied to genetic data; see Dai et al. (2012b) for a comprehensive review. However, there is a lack of investigations conducted for dependent genetic data, especially for weighted p-value combining methods. Single nucleotide polymorphisms (SNPs) are often correlated due to linkage disequilibrium (LD). Other genetic data, including variants from next generation sequencing, gene expression levels measured by microarray, protein and DNA methylation data, etc. also contain complex correlation structures. Ignoring correlation structures among genetic variants may lead to severe inflation of Type I error rates for omnibus testing of p-values. In this work, we propose modifications to the Lancaster procedure by taking the correlation structure among p-values into account. The weight function in the Lancaster procedure allows meaningful biological information to be incorporated into the statistical analysis, which can increase the power of the statistical testing and/or remove the bias in the process. Extensive empirical assessments demonstrate that the modified Lancaster procedure largely reduces the Type I error rates due to correlation among p-values, and retains considerable power to detect signals among p-values. We applied our method to reassess published renal transplant data, and identified a novel association between B cell pathways and allograft tolerance.
doi:10.3389/fgene.2014.00032
PMCID: PMC3929847  PMID: 24600471
generalized Fisher method (Lancaster procedure); weight function; correlated p-values; multiple hypothesis testing; high dimensional genetic data
21.  Trends in Adverse Reactions to Trimethoprim-Sulfamethoxazole 
Pediatrics  2013;131(1):e103-e108.
OBJECTIVE:
To examine temporal trends of adverse drug reactions (ADRs) associated with trimethoprim-sulfamethoxazole (TMP-SMX) use in children.
METHODS:
We performed a retrospective observational study to characterize TMP-SMX ADRs in children between 2000 and 2009. We completed a chart review at our institution by identifying children diagnosed with TMP-SMX ADRs. To compare local trends to comparable institutions, we estimated the frequency of hospitalizations for TMP-SMX ADRs at 25 tertiary pediatric hospitals utilizing the Pediatric Health Information System database. To determine whether changes in outpatient prescribing rates occurred, we used the National Ambulatory Medical Care Survey/National Hospital Ambulatory Medical Care Survey.
RESULTS:
At our institution, 109 children were diagnosed with a TMP-SMX ADR (5 cases from 2000 to 2004 as compared with 104 cases from 2005 to 2009). Fifty-eight percent had been treated for a skin and soft tissue infection (SSTI). A similar trend was observed nationally, where the incidence of TMP-SMX ADRs more than doubled from 2004 to 2009 at comparable pediatric hospitals (P < .001). Although national outpatient data revealed no change in overall TMP-SMX prescribing, the percentage of children prescribed TMP-SMX for SSTI sharply increased during the study period (0%–2% [2000-2004]; 9%–17% [2005–2009]).
CONCLUSIONS:
The majority of TMP-SMX ADRs at our institution occurred in conjunction with SSTI treatment. TMP-SMX ADRs have occurred more frequently coincident with increased prescribing for SSTI. Increased usage alone may explain the increasing trend of TMP-SMX ADRs in children; however drug–disease interaction may play a role and requires further investigation.
doi:10.1542/peds.2012-1619
PMCID: PMC3529952  PMID: 23209098
adverse drug reaction; trimethoprim-sulfamethoxazole; skin and soft tissue infections; pediatrics; physician practice patterns
22.  Genetic Determinants of Variable Metabolism Have Little Impact on the Clinical Use of Leading Antipsychotics in the CATIE study 
Purpose
To evaluate systematically in real clinical settings whether functional genetic variations in drug metabolizing enzymes influence optimized doses, efficacy, and safety of antipsychotic medications.
Methods
DNA was collected from 750 patients with chronic schizophrenia treated with five antipsychotic drugs (olanzapine, quetiapine, risperidone, ziprasidone and perphenazine) as part of the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) study. Doses for each of the medicines were optimized to 1, 2, 3, or 4x units in identically-appearing capsules in a double blind design. We analyzed 25 known functional genetic variants in the major and minor metabolizing enzymes for each medication. These variants were tested for association with optimized dose and other relevant clinical outcomes.
Results
None of the tested variants showed a nominally significant main effect in association with any of the tested phenotypes in European-Americans, African-Americans or all patients. Even after accounting for potential covariates no genetic variant was found to be associated with dosing, efficacy, overall tolerability, or tardive dyskinesia.
Conclusion
There are no strong associations between common functional genetic variants in drug metabolizing enzymes and dosing, safety or efficacy of leading antipsychotics, strongly suggesting merely modest effects on the use of these medicines in most patients in typical clinical settings.
doi:10.1097/GIM.0b013e3181863239
PMCID: PMC3697113  PMID: 18813134
Pharmacogenetics; CYP 450; Drug Metabolizing Enzymes; Antipsychotics; Personalized Medicine
23.  Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction 
BioData Mining  2013;6:1.
Background
Multifactor Dimensionality Reduction (MDR) has been widely applied to detect gene-gene (GxG) interactions associated with complex diseases. Existing MDR methods summarize disease risk by a dichotomous predisposing model (high-risk/low-risk) from one optimal GxG interaction, which does not take the accumulated effects from multiple GxG interactions into account.
Results
We propose an Aggregated-Multifactor Dimensionality Reduction (A-MDR) method that exhaustively searches for and detects significant GxG interactions to generate an epistasis enriched gene network. An aggregated epistasis enriched risk score, which takes into account multiple GxG interactions simultaneously, replaces the dichotomous predisposing risk variable and provides higher resolution in the quantification of disease susceptibility. We evaluate this new A-MDR approach in a broad range of simulations. Also, we present the results of an application of the A-MDR method to a data set derived from Juvenile Idiopathic Arthritis patients treated with methotrexate (MTX) that revealed several GxG interactions in the folate pathway that were associated with treatment response. The epistasis enriched risk score that pooled information from 82 significant GxG interactions distinguished MTX responders from non-responders with 82% accuracy.
Conclusions
The proposed A-MDR is innovative in the MDR framework to investigate aggregated effects among GxG interactions. New measures (pOR, pRR and pChi) are proposed to detect multiple GxG interactions.
doi:10.1186/1756-0381-6-1
PMCID: PMC3560267  PMID: 23294634
A-MDR; Epistasis enriched risk score; Epistasis enriched gene network; pRR; pOR; pChi
24.  PharmGKB summary: carbamazepine pathway 
Pharmacogenetics and Genomics  2011;21(12):906-910.
doi:10.1097/FPC.0b013e328348c6f2
PMCID: PMC3349991  PMID: 21738081
carbamazepine; cytochrome P450 metabolizing enzymes; HLA-B; pharmacogenomics; pharmacokinetics
25.  Development of biomarkers to optimize pediatric patient management: what makes children different? 
Biomarkers in Medicine  2011;5(6):781-794.
Despite the frequent utilization of biomarkers in medical practice, there is a relative paucity of information regarding validated pediatric biomarkers. Frequently, biomarkers found to be efficacious in adults are extrapolated to the pediatric clinical setting without considering that the pathogenesis of many diseases is distinctly different in children, and ontogeny directly influences disease evolution and therapeutic response in children. New and innovative approaches are necessary to provide reliable, validated biomarkers that can be used to improve and advance pediatric medical care.
doi:10.2217/bmm.11.96
PMCID: PMC3321646  PMID: 22103612
biomarker; children; development; genomics; ontogeny; pediatrics; pharmacogenomics

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