PurposeGenotyping CYP2D6 is important for precision drug therapy because it metabolizes approximately 25% of drugs and its activity varies considerably among individuals. Genotype analysis of CYP2D6 is challenging due to its highly polymorphic nature. Over 100 haplotypes (star alleles) have been defined for CYP2D6, some involving a gene conversion with its nearby non-functional but highly homologous paralog CYP2D7. We present Stargazer, a new bioinformatics tool that uses next-generation sequencing (NGS) data to call star alleles for CYP2D6 (https://stargazer.gs.washington.edu/stargazerweb/). Stargazer is currently being extended for other pharmacogenes.MethodsStargazer identifies star alleles from NGS data by detecting single nucleotide variants, insertion-deletion variants, and structural variants. Stargazer detects structural variation including gene deletions, duplications, and conversions by calculating paralog-specific copy number from read depth.ResultsWe applied Stargazer to NGS data of 32 ethnically diverse HapMap trios that were genotyped by TaqMan assays, long-range PCR, quantitative multiplex PCR, High Resolution Melt analysis, and/or Sanger sequencing. CYP2D6 genotyping by Stargazer was 99.0% concordant with data obtained by these methods and showed 28.1% of the samples had structural variation including CYP2D6/CYP2D7 hybrids.ConclusionAccurate genotyping of pharmacogenes with NGS and subsequent allele calling with Stargazer will aid the implementation of precision drug therapy.

Retired star alleles removed *20, *21 Comment "g.12662A>G is likely part of all *2 alleles" was removed *2A, *2C, *2B, *2E, *2F, *2G, *2H, and *2J g.12662A>G was added to allele definition Comments removed *3B, *11, *16, and *30 Other Reassigned to *1.006 *27

The significance of the human multidrug resistance gene (MDR1) G1199A polymorphism, resulting in a Ser400Asn modification in P-glycoprotein (P-gp), remains unclear. We have developed stable recombinant LLC-PK1 epithelial cells expressing either MDR1 wt or MDR1 1199 to evaluate functional consequences of G1199A [N-(4-[2-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-isoquinolinyl)ethyl]-phenyl)-9,10-dihydro-5-methoxy-9-oxo-4-acridine carboxamide]. P-gp activity observed in MDR1 wt and MDR1 1199 cells was completely inhibited in the presence of the specific P-gp inhibitor GF120918. Comparable expression of mRNA and protein in the MDR1-expressed cells and correct localization of P-gp in the apical membrane of recombinant cells was verified. . Therefore, the G1199A polymorphism alters the efflux and transepithelial permeability of a fluorescent substrate and sensitivity to select cytotoxic agents, which may influence drug disposition and therapeutic efficacy of some P-gp substrates.The human multidrug resistance gene (MDR1) encodes a 170-kDa integral membrane protein that mediates ATP-dependent substrate efflux. The protein product, P-glycoprotein (P-gp), a member of the ATP-binding cassette superfamily of transporters, resides in the plasma membrane and functions as an efflux transporter of a variety of natural compounds and lipophilic xenobiotics (for review, see Lin, 2003). Although the contribution of P-gp in multidrug resistance for cancer chemotherapy is well documented, the role of P-gp in drug disposition is not fully understood and has continued to generate significant debate. P-gp mediates the energy-dependent efflux of a broad range of xenobiotics in epithelial tissues throughout the human body, including the intestinal mucosa, liver canalicular membrane, kidney proximal tubules, blood-brain barrier, and placenta (Schinkel, 1997).P-gp efflux may, therefore, act to decrease intestinal absorption, enhance biliary excretion and renal tubular secretion, and limit drug distribution to the fetus and brain. Because P-gp is found in tissues important in drug disposition, variation in expression and function of P-gp due to genetic polymorphisms of MDR1 may influence pharmacokinetics and, in turn, pharmacodynamics.Recent progress has been made in identifying genetic polymorphisms in the MDR1 gene in normal human tissues. The first major screen of the MDR1 gene in 188 healthy Caucasian subjects, identified 15 single nucleotide polymorphisms; however, only one, a C 3 T transition at nucleotide position 3435 (C3435T), was shown to correlate with decreased intestinal P-gp expression and digoxin exposure in vivo (Hoffmeyer et al., 2000). Because the C3435T polymorphism in exon 26 is a synonymous polymorphism that does not modify the amino acid sequence of P-gp, several investigators have searched for clues to the significance of C3435T. Another study reported that C3435T is linked to a nonsynonymous G2677T polymorphism, resulting in an alanine-to-serine transition at amino acid 893, and another synonymous SNP, C1236T (Kim ...

Pharmacogenetics is a subset of personalized medicine that applies knowledge about genetic variation in gene–drug pairs to help guide optimal dosing. There is a lack of data, however, about pharmacogenetic variation in underserved populations. One strategy for increasing participation of underserved populations in pharmacogenetic research is to include communities in the research process. We have established academic–community partnerships with American Indian and Alaska Native people living in Alaska and Montana to study pharmacogenetics. Key features of the partnership include community oversight of the project, research objectives that address community health priorities, and bidirectional learning that builds capacity in both the community and the research team. Engaging the community as coresearchers can help build trust to advance pharmacogenetic research objectives.

Pharmacogenetic research offers the potential to improve the safety and efficacy of drug prescribing. Assuring that the benefits of this research reach indigenous and other medically underserved people is an important justice concern. First, however, a legacy of mistrust, derived from traditional research practices that disempower communities, must be overcome. Linking pharmacogenetic research to collaborative, power-sharing research partnerships provides a valuable opportunity to develop new and positive precedents for genetic research in indigenous communities.

The human multidrug resistance gene (MDR1), spanning greater than 200 kb, encodes for the ATP-dependent membrane efflux transporter, P-glycoprotein (Pgp). Significant progress has been made in the discovery of MDR1 polymorphisms and the assessment of allelic frequencies. The search for key genetic determinants that predispose individuals to drugs that are substrates or inhibitors of Pgp has just begun. Reports in the literature, particularly focusing on the C3435T polymorphism, have provided discordant results with respect to functional modification in vitro, and Pgp expression and disposition of probe drugs in vivo. Due to the large size of the MDR1 gene, genotyping based on individual single nucleotide polymorphism (SNPs) analysis is not sufficient to predict functional consequences. Strong linkage disequilibrium has been detected between several MDR1 polymorphisms, and discrepancies in the literature may be due to the focus on the influence of single nucleotide variations instead of on linked nucleotide variations. Multiple SNPs found on the same chromosome are assigned to a specific haplotype, and some attempts have been made to determine the role of MDR1 haplotypes in Pgp variability. Most of the data for MDR1 haplotype have been predicted based on computational or mathematical models. However, molecular haplotyping techniques, analysis of linkages on the same chromosome directly by biophysical and biochemical means, may be needed to characterize haplotypes in individuals with a highly polymorphic and large gene like MDR1. Haplotype identification may prove to be vital in identifying the functional significance of MDR1 polymorphisms on disease susceptibility and drug disposition.

The quantitation of F-ara-ATP accumulation in T-lymphocytes provides a novel tool to evaluate patient sensitivity to fludarabine. This tool can be used in future studies to evaluate whether intracellular F-ara-ATP accumulation is associated with efficacy and/or toxicity in patients receiving fludarabine.

Objectives Cytochrome P450 enzymes play a dominant role in drug elimination and variation in these genes is a major source of interindividual differences in drug response. Little is known, however, about pharmacogenetic variation in American Indian and Alaska Native (AI/AN) populations. We have developed a partnership with the Confederated Salish and Kootenai Tribes (CSKT) in northwestern Montana to address this knowledge gap. Methods We resequenced CYP2D6 in 187 CSKT subjects and CYP3A4, CYP3A5, and CYP2C9 in 94 CSKT subjects. Results We identified 67 variants in CYP2D6, 15 in CYP3A4, 10 in CYP3A5, and 41 in CYP2C9. The most common CYP2D6 alleles were CYP2D6*4 and *41 (20.86 and 11.23%, respectively). CYP2D6*3, *5, *6, *9, *10, *17, *28, *33, *35, *49, *1xN, *2xN, and *4xN frequencies were less than 2%. CYP3A5*3, CYP3A4*1G, and *1B were detected with frequencies of 92.47, 26.81, and 2.20%, respectively. Allelic variation in CYP2C9 was low: CYP2C9*2 (5.17%) and *3 (2.69%). In general, allele frequencies in CYP2D6, CYP2C9 and CYP3A5 were similar to those observed in European Americans. There was, however, a marked divergence in CYP3A4 for the CYP3A4*1G allele. We also observed low levels of linkage between CYP3A4*1G and CYP3A5*1 in the CSKT. The combination of nonfunctional CYP3A5*3 and putative reduced function CYP3A4*1G alleles may predict diminished clearance of CYP3A substrates. Conclusions These results highlight the importance of conducting pharmacogenomic research in AI/AN populations and demonstrate that extrapolation from other populations is not appropriate. This information could help to optimize drug therapy for the CSKT population.