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Purpose: Irinotecan is an important drug for the treatment of solid tumors. Although genes involved in irinotecan pharmacokinetics have been shown to influence toxicity, there are no data on pharmacodynamic genes. CDC45L, NFKB1, PARP1, TDP1, and XRCC1 have been shown to influence the cytotoxic action of camptothecins, including irinotecan. Polymorphisms in the drug target of camptothecins, topoisomerase I (TOP1), and downstream effectors may influence patient outcomes to irinotecan therapy. We undertook a retrospective candidate gene haplotype association study to investigate this hypothesis.Experimental Design: Haplotype compositions of six candidate genes were constructed in European (n = 93), East Asian (n = 94), and West African (n = 95) populations. Haplotype-tagging single nucleotide polymorphisms (htSNP) were selected based on genealogic relationships between haplotypes. DNA samples from 107 European, advanced colorectal cancer patients treated with irinotecan-based regimens were genotyped for htSNPs as well as three coding region SNPs. Associations between genetic variants and toxicity (grade 3/4 diarrhea and neutropenia) or efficacy (objective response) were assessed.Results:TOP1 and TDP1 htSNPs were related to grade 3/4 neutropenia (P = 0.04) and response (P = 0.04), respectively. Patients homozygous for an XRCC1 haplotype (GGCC-G) were more likely to show an objective response to therapy than other patients (83% versus 30%; P = 0.02). This effect was also seen in a multivariate analysis (odds ratio, 11.9; P = 0.04). No genetic variants were associated with diarrhea.Conclusions: This is the first comprehensive pharmacogenetic investigation of irinotecan pharmacodynamic factors, and our findings suggest that genetic variation in the pharmacodynamic genes may influence the efficacy of irinotecan-containing therapies in advanced colorectal cancer patients.

Supplementary Data from Irinotecan Pharmacogenetics: Influence of Pharmacodynamic Genes

Polymorphisms in miRNA and miRNA pathway genes have been previously associated with cancer risk and outcome, but have not been studied in esophageal adenocarcinoma outcomes. Here, we evaluate candidate miRNA pathway polymorphisms in esophageal adenocarcinoma prognosis and attempt to validate them in an independent cohort of esophageal adenocarcinoma patients. Among 231 esophageal adenocarcinoma patients of all stages/treatment plans, 38 candidate genetic polymorphisms (17 biogenesis, 9 miRNA targets, 5 pri‐miRNA, 7 pre‐miRNA) were genotyped and analyzed. Cox proportional hazard models adjusted for sociodemographic and clinicopathological covariates helped assess the association of genetic polymorphisms with overall survival (OS) and progression‐free survival (PFS). Significantly associated polymorphisms were then evaluated in an independent cohort of 137 esophageal adenocarcinoma patients. Among the 231 discovery cohort patients, 86% were male, median diagnosis age was 64 years, 34% were metastatic at diagnosis, and median OS and PFS were 20 and 12 months, respectively. GEMIN3 rs197412 (aHR = 1.37, 95%CI: [1.04–1.80]; P = 0.02), hsa‐mir‐124‐1 rs531564 (aHR = 0.60, 95% CI: [0.53–0.90]; P = 0.05), and KIAA0423 rs1053667 (aHR = 0.51, 95% CI: [0.28–0.96]; P = 0.04) were found associated with OS. Furthermore, GEMIN3 rs197412 (aHR = 1.33, 95% CI: [1.03–1.74]; P = 0.03) and KRT81 rs3660 (aHR = 1.29, 95% CI: [1.01–1.64]; P = 0.04) were found associated with PFS. Although none of these polymorphisms were significant in the second cohort, hsa‐mir‐124‐1 rs531564 and KIAA0423 rs1053667 had trends in the same direction; when both cohorts were combined together, GEMIN3 rs197412, hsa‐mir‐124‐1 rs531564, and KIAA0423 rs1053667 remained significantly associated with OS. We demonstrate the association of multiple miRNA pathway polymorphisms with esophageal adenocarcinoma prognosis in a discovery cohort of patients, which did not validate in a separate cohort but had consistent associations in the pooled cohort. Larger studies are required to confirm/validate the prognostic value of these polymorphisms in esophageal adenocarcinoma.

Background The drug transporter ABCC2 is upregulated in non-small cell lung cancer (NSCLC) and implicated in platinum resistance. We evaluated the association between germline polymorphisms in the ABCC2 gene and survival outcomes of platinum-treated advanced NSCLC patients. Material and methods Ten candidate and tagging germline polymorphisms in the ABCC2 gene were genotyped in a discovery cohort of 170 platinum-treated stage IV NSCLC patients from the Princess Margaret Cancer Centre. Associations with overall survival were assessed using multivariate Cox proportional hazard models adjusted for prognostic variables. To validate our results, we analyzed the association of the two top polymorphisms in the ABCC2 gene on survival outcomes of 219 stage IIIB-IV NSCLC patients enrolled on the NCIC Clinical Trials Group BR.24 clinical trial. Results Only one polymorphism was validated across both cohorts for an association with overall survival: the A allele of the ABCC2 polymorphism, rs8187710 (4544G>A), was associated with adverse overall survival (adjusted hazard ratio [aHR] 2.22; 95% CI: 1.2–4.0; p =0.009) among our stage IV NSCLC patients. A significant association with overall survival (aHR 1.73; 95% CI: 1.0–2.9; p =0.036) was observed for the same ABCC2 polymorphism in the BR.24 validation cohort. No other ABCC2 polymorphisms were associated with outcome. Conclusion The ABCC2 polymorphism, rs8187710 (4544G>A), is associated with overall survival in platinum-treated advanced NSCLC patients. Additional studies are needed to evaluate the predictive versus prognostic nature of this relationship, and to explore the functional effect of this polymorphism on the pharmacokinetics of platinum drugs.

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the world, and it comprises a spectrum of hepatic abnormalities from simple hepatic steatosis to steatohepatitis, fibrosis, cirrhosis, and liver cancer. While the pathogenesis of NAFLD remains incompletely understood, a multihit model has been proposed that accommodates causal factors from a variety of sources, including intestinal and adipose proinflammatory stimuli acting on the liver simultaneously. Prior cellular and molecular studies of patient and animal models have characterized several common pathogenic mechanisms of NAFLD, including proinflammation cytokines, lipotoxicity, oxidative stress, and endoplasmic reticulum stress. In recent years, gut microbiota has gained much attention, and dysbiosis is recognized as a crucial factor in NAFLD. Moreover, several genetic variants have been identified through genome-wide association studies, particularly rs738409 (Ile748Met) inPNPLA3and rs58542926 (Glu167Lys) inTM6SF2, which are critical risk alleles of the disease. Although a high-fat diet and inactive lifestyles are typical risk factors for NAFLD, the interplay between diet, gut microbiota, and genetic background is believed to be more important in the development and progression of NAFLD. This review summarizes the common pathogenic mechanisms, the gut microbiota relevant mechanisms, and the major genetic variants leading to NAFLD and its progression.

There is a growing consensus that the first and most necessary step to improving the efficiency, cost–effectiveness and quality of healthcare systems can be achieved through the implementation of interoperable patient-centric electronic health record (EHR) systems across hospitals and clinics. Targeted therapeutics (including screening, prevention and disease management) through EHR-based clinical decision support delivery may drive both the acceptance and adoption of EHR systems by providing personalized information at the point-of-care. The realization of targeted therapeutics will depend on the resolution of current political, ethical, socioeconomical and technical challenges surrounding EHR implementation efforts. There is a growing need for broad-based consensus initiatives to foster an essential level of standardization for EHRs. The timeliness of these issues is underlined by the rapid emergence of private sector efforts in this potentially lucrative field, from direct-to-consumer testing to Google-, or Microsoft-owned personal health data. This review discusses the potential value for adopting healthcare technology, with a focus on personalized medicine, and highlights the challenges that remain to achieve this.

eHealth is an umbrella term incorporating any area that combines healthcare and technology to improve efficiencies and reduce costs. The ultimate goal of eHealth is to rationalize treatment selection to improve patient safety and outcomes. Telemedicine, first used in the 1920s, is the oldest form of eHealth. The introduction of broadband Internet, followed by wireless technologies, has allowed an explosion of mHealth applications within this field. Wearable technologies, such as smartwatches, are now being used for diagnostics and patient monitoring. Challenges remain to develop reusable Clinical Decision Support systems that will streamline the flow of data from clinical laboratories to point of care. This review explores the history of eHealth, and describes some of the remaining integration and implementation challenges.

Polymorphisms in the vascular endothelial growth factor (VEGF)/angiogenesis pathway have been implicated previously in cancer risk, prognosis and response to therapy including in esophageal adenocarcinoma. Prior esophageal adenocarcinoma studies focused on using candidate polymorphisms, limiting the discovery of novel polymorphisms. Here, we applied the tagSNP (single nucleotide polymorphism) approach to identify new VEGF pathway polymorphisms associated with esophageal adenocarcinoma prognosis and validated them in an independent cohort of esophageal adenocarcinoma patients. In 231 esophageal adenocarcinoma patients of all stages/treatment plans, 58 genetic polymorphisms (18 KDR, 7 VEGFA and 33 FLT1) selected through tagging and assessment of predicted function were genotyped. Cox-proportional hazard models adjusted for important socio-demographic and clinico-pathological factors were applied to assess the association of genetic polymorphisms with overall survival (OS) and progression-free survival (PFS). Significantly associated polymorphisms were then validated in an independent cohort of 137 esophageal adenocarcinoma patients. Among the 231 discovery cohort patients, 86% were male, median diagnosis age was 64 years, 34% were metastatic at diagnosis and median OS and PFS were 20 and 12 months, respectively. KDR rs17709898 was found significantly associated with PFS (adjusted hazard ratio, aHR = 0.69, 95% confidence interval (CI): 0.53-0.90; P = 5.9E-3). FLT1 rs3794405 and rs678714 were significantly associated with OS (aHR = 1.44, 95% CI: 1.04-1.99; P = 0.03 and aHR = 1.50, 95% CI: 1.01-2.24; P = 0.045, respectively). No VEGFA polymorphisms were found significantly associated with either outcome. Upon validation, FLT1 rs3794405 remained strongly associated with OS (aHR = 1.59, 95% CI: 1.04-2.44; P = 0.03). FLT1 rs3794405 is significantly associated with OS in esophageal adenocarcinoma, whereby each variant allele confers a 45-60% increased risk of mortality. Validation and evaluation of this association in other cancer sites are warranted.

Background: Clinically relevant polymorphisms often demonstrate population-specific allele frequencies. Central and South America remain largely uncategorized in the context of pharmacogenomics. Materials & methods: We assessed 15 polymorphisms from 12 genes (ABCB1 3435C>T, ABCG2 Q141K, CYP1B1*3, CYP2C19*2, CYP3A4*1B, CYP3A5*3C, ERCC1 N118N, ERCC2 K751Q, GSTP1 I105V, TPMT 238G>C, TPMT 460G>A, TPMT 719A>G, TYMS TSER, UGT1A1*28 and UGT1A1 -3156G>A) in 81 Peruvian and 95 Mexican individuals. Results: Six polymorphism frequencies differed significantly between the two populations: ABCB1 3435C>T, CYP1B1*3, GSTP1 I105V, TPMT 460G>A, UGT1A1*28 and UGT1A1 -3156G>A. The pattern of observed allele frequencies for all polymorphisms could not be accurately estimated from any single previously studied population. Conclusion: This highlights the need to expand the scope of geographic data for use in pharmacogenomics studies.

Contains fulltext : 140416.pdf (Publisher’s version ) (Closed access) Aim: Fast and frugal decision trees (FFTs) can simplify clinical decision making by providing a heuristic approach to contextual guidance. We wanted to use FFTs for pharmacogenomic knowledge translation at point-of-care. Materials & Methods: The Pharmacogenomics for Every Nation Initiative (PGENI), an international nonprofit organization, collects data on regional polymorphisms as a predictor of metabolism for individual drugs and dosages. We advanced FFTs to work with PGENI pharmacogenomic data to produce medication recommendations that are accurate, transparent and straightforward to automate. Results: By streamlining medication selection processes in the PGENI workflow, information technology applications can now be deployed. Conclusion: We developed a decision tree approach that can translate pharmacogenomic data to provide up-to-date recommended care for populations based on their medication-specific markers. 12 p.

Background: Mobile applications (apps) providing clinical decision support (CDS) may show the greatest promise when created by and for frontline clinicians. Our aim was to create a generic model enabling healthcare providers to direct the development of CDS apps. Methods: We combined Change Management with a three-tier information technology architecture to stimulate CDS app development. Results: A Bridging Opportunities Work-frame model was developed. A test case was used to successfully develop an app. Conclusion: Healthcare providers can re-use this globally applicable model to actively create and manage regional decision support applications to translate evidence-based medicine in the use of emerging medication or novel treatment regimens., Medical information needs to be structured in a way that it can be used in a time-constrained environment. This project looked at the process of creating mobile applications (apps), to help medical professionals rapidly apply new knowledge to better treat patients. We developed a novel system that allowed medical professionals to have a leading role in development. With the input from a pharmacist we created an app to deal with pharmacy and patient-related decisions surrounding newly available anticancer pills. Other medical professionals could also use this method to make apps to provide information with relevance to their medical decisions.

Recent studies have made significant advances in understanding the mechanisms of gut microbiota involved in human health and disease [1, 2]. Now the gut microbiota has been recognized as a key player in a broad spectrum of human diseases from obesity associated liver and cardiovascular diseases to mental development and psychiatric diseases [3, 4]. Accordingly, modulations of gut microbial diversity and composition are expected to improve human health and to provide novel therapeutic modalities for human disease. The gut microbial modulators can be simply specific diets and drinks, natural tea and Chinese herbs, or specialized prebiotics and probiotics. In this special issue, authors presented a number of very interesting studies on changes of gut microbiota in digestive diseases. These review and original articles of research and clinical studies cover a range of topics, including the pathogenesis of alcoholic and nonalcoholic fatty liver diseases (NAFLD), the outcome of intestinal bacterial translocation in advanced cirrhosis, the gut microbiota changes in an animal colitis model after treatment with a monoclonal antibody, and fecal microbiota transplantation (FMT) in elderly patients with refractory Clostridium difficile infection. In these articles, authors have described mechanisms of disease development as well as therapeutic effects of specific antibodies, probiotics, and FMT. While we know the simple cause of alcoholic fatty liver disease (AFLD), its pathogenesis is complicated and it involves a wide range of changes in host metabolism and gut microbiota. Certainly, removal of the cause (alcohol abuse) is the first treatment for AFLD, and the use of probiotics can ameliorate its development as shown in recent clinical and animal studies [5–7]. Although sharing many pathological and clinical features with AFLD, NAFLD does not have a simple, single cause. Instead, NAFLD is the result of interactions between gut microbiota, host genetics, and diet. There have been a number of studies evaluating the effects and mechanisms of probiotics [8–10], natural tea [11, 12], and Chinese herbs/recipes [13, 14] on AFLD and NAFLD. These studies reported beneficial effects with promising perspectives for future development of novel therapeutic strategies. However, in light of the nature of gut microbiota being highly diverse and constitutional, built during the early life of individuals, cautious optimism is necessary for any future therapeutic developments aiming at modulations of gut microbiota, as we do not yet know long-term effects from those initial efforts or indeed which of those microbiota and metabolomics changes are contributory, causative, or simply a cofounder in AFLD and NAFLD, or indeed any other condition. Thus far, it is not clear whether the modulations by specific diets and drinks including natural tea, even by probiotics, are able to change the constitutional nature of gut microbiota, although the relative abundance of microbial species is altered upon administrating modulators [12, 13, 15]. Moreover, current analytic strategies on metagenomics data are focused on major changes in gut microbial compositions and have not paid sufficient attention to or have even ignored the changes in minor species with less than 1% abundance. Furthermore, sampling of microbiota in intestinal lumen may not necessarily represent the mucosal portion or the whole population of gut flora [16]. In fact, the true signal and messengers governing the alterations of gut microbiota and host metabolism are largely elusive. Enteric short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate, are fermentation metabolites by intestinal bacteria. Recent studies have suggested a messenger role of SCFAs in several human diseases including metabolic syndrome [17] and autism [4]. In short, careful designs of future studies should take these factors and host genetic background under consideration to discover the real effectors and to discern the true effects of gut microbial modulators in alcoholic and nonalcoholic fatty liver disease and other human diseases. Jinsheng Yu Sharon Marsh Junbo Hu Wenke Feng Chaodong Wu

Breast cancer is a common, life-threatening disease among women. Contemporary hormonal therapy with third-generation aromatase inhibitors for estrogen-receptor-positive breast cancers in postmenopausal women is still facing the challenge of interpatient variability in therapeutic response and intensity of adverse effects.This review highlights up-to-date literature regarding genomic findings in the literature pertaining to anastrozole, exemestane and letrozole metabolism, as well as the drug target aromatase. Genetic polymorphisms in phase I and II aromatase inhibitor metabolizing enzymes that contribute to altered responses among different patient genotypes are discussed. Similarly, aromatase CYP19A1 functional genetic polymorphisms are presented in correlation to altered aromatase activity, disease prognosis and severity of aromatase inhibitor adverse effects.The field of pharmacogenomics has shown remarkable progress over the last few years, notably in cancer. However, large comprehensive genotyping studies, evaluated under clinical settings, are still needed to unravel the potential impact of aromatase inhibitor pharmacogenomics on breast cancer treatment, monitoring and predicting adverse effects.

Typically, chemotherapy selection takes into account patient demographic data, including disease symptoms, family history, environmental factors and concurrent medications. Although validated and approved genomics tests are available for targeted therapeutics, a major challenge facing healthcare is the ability to process the genomic data in the patient’s context and to return clinically interpretable dosing guidance to the physician in a realistic time frame. Delivery of these targeted therapeutics, made possible by clinical decision support systems connected to an electronic health record may help drive both the acceptance and adaptation of an electronic health record system, as well as provide personalized information at point-of-care, as part of the routine workflow. The realization of targeted therapeutics will depend on the concerted efforts of stakeholder groups as they address political, ethical, socioeconomical and technical challenges to achieve personalized medicine adoption through real-world implementation.

Purpose With three available chemotherapy drugs for advanced colorectal cancer (CRC), response rate (RR) and survival outcomes have improved with associated morbidity, accentuating the need for tools to select optimal individualized treatment. Pharmacogenetics identifies the likelihood of adverse events or response based on variants in genes involved in drug transport, metabolism, and cellular targets. Patients and Methods Germline DNA was extracted from 520 patients on the North American Gastrointestinal Intergroup N9741 study. Three study arms were evaluated: IFL (fluorouracil [FU] + irinotecan [IRN]), FOLFOX (FU + oxaliplatin), and IROX (IRN + oxaliplatin). Information on adverse events, response, and disease-free survival was available. Thirty-four variants in 15 candidate genes for analysis based on previous associations with adverse events or outcome were assessed. Genotyping was performed using pyrosequencing. Results All variants were polymorphic. The homozygous UGT1A1*28 allele observed in 9% of patients was associated with risk of grade 4 neutropenia in patients on IROX (55% v 15%; P = .002). Deletion in GSTM1 was associated with grade 4 neutropenia after FOLFOX (28% v 16%; P = .02). Patients with a homozygous variant genotype for GSTP1 were more likely to discontinue FOLFOX because of neurotoxicity (24% v 10%; P = .01). The presence of a CYP3A5 variant was significantly associated with RR on IFL (29% v 60%; P = .0074). Most previously published genotype-toxicity or -efficacy relationships were not validated in this study. Conclusion This study provides a platform to evaluate pharmacogenetic predictors of response or severe adverse events in advanced CRC. Pharmacogenetic studies can be conducted in multicenter trials, and our findings demonstrate that with continued research, clinical application is practical.

It has been well established that the frequencies of genomic variants can vary greatly between the populations of different countries. We sought to quantify the intra-population variability in Ghana to determine the value of genotyping studies done at a nationwide level. Further, we investigated the differences between the Ghanaian and other African populations to determine the quality of genomic representation provided by a small subgroup within the continent with regard to the general population. We genotyped 934 unrelated Ghanaian individuals for 15 single nucleotide polymorphisms (SNPs) from genes defined as clinically relevant based on their reported roles in the transport of, metabolism of, or as targets of the medicines listed in the World Health Organization Essential Medicines list. Populations within Ghana and between nations in Western Africa were genetically cohesive. In contrast, populations in other areas of Africa were genetically divergent. Gene allele frequency also differed significantly between the populations in African nations and the United States for several of the SNPs. These results demonstrate that national populations in similar geographic regions, like Africa, may have widely varying genetic allele frequencies for clinically relevant SNPs. Further genotyping studies of specific populations are necessary to provide the best medical care to all individuals.

The purpose of this study was to evaluate the affinity of docetaxel for 14 transporter proteins and assess the functional significance of 17 variants in five genes involved in drug elimination. Among the transfected models investigated, OATP1B3 (SLCO1B3) was identified as the most efficient influx transporter for docetaxel. None of the observed genotypes (SLCO1B3, ABCB1, and ABCC2) was related with docetaxel clearance in 92 white patients (P > 0.17). However, the simultaneous presence of the CYP3A4*1B and CYP3A5*1A alleles was associated with a 64% increase in docetaxel clearance (P = 0.0015), independent of both sex and CYP3A activity (as determined using the erythromycin breath test). This haplotype was also associated with increased midazolam clearance in another population (P = 0.0198). An analysis of the CYP3A locus among CEPH-HapMap samples revealed that CYP3A4*1B is present exclusively among a subset of CYP3A5 expressors. Therefore, future studies should first stratify the population on the basis of CYP3A5 genotype and then compare CYP3A activity between individuals with and without the CYP3A4*1B allele.

Oxaliplatin, gemcitabine and capecitabine are all active agents against upper gastrointestinal and pancreaticobiliary cancers.Patients with upper gastrointestinal malignancies treated with 0-2 prior chemotherapy regimens received oxaliplatin (85-100 mg/m(2)) as a 2-h i.v. infusion with gemcitabine (800-1000 mg/m(2)) at a constant rate i.v. infusion (CI) of 10 mg/m(2)/min on days 1 and 15 of a 28-day cycle. Capecitabine (600-800 mg/m(2)) was administered orally twice a day on days 1-7 and 15-21. A three per cohort dose escalation schema was used to determine the maximum tolerated dose (MTD) and the dose-limiting toxic effects (DLTs) of this combination regimen.Thirty patients with advanced upper gastrointestinal malignancies were enrolled. The MTD was defined as oxaliplatin 100 mg/m(2) i.v. over 2 h plus gemcitabine 800 mg/m(2) i.v. at a CI of 10 mg/m(2)/min on days 1 and 15 with capecitabine 800 mg/m(2) p.o. b.i.d. days 1-7 and 15-21 of a 29-day cycle. DLTs include grade 3 fatigue and grade 3 dyspnea. One complete and two partial responses were observed.This biweekly schedule of oxaliplatin, gemcitabine and capecitabine is tolerable and warrants further investigation in biliary and pancreatic malignancies.

Oncology pharmacogenomics has seen a great deal of progress in the past 10 years. The release of the Human Genome Project data and the availability of fast, affordable genotyping platforms has allowed the field to expand and has provided invaluable data for pharmacogenomics research. The introduction of US FDA-approved targeted therapy (trastuzumab), package insert changes (irinotecan and tamoxifen) and the initiation of a genotype-guided clinical trial for cancer therapy (TYMS TSER in rectal cancer), along with panels of DNA and expression markers (Roche AmpliChip(®) and Oncotype Dx™ panel) are paving the way towards the integration of pharmacogenomics into clinical practice.

Purpose Standard therapy for advanced ovarian cancer consists of a platinum agent in combination with a taxane, which has a 5-year survival rate of approximately 45%. The large individual variability for ovarian cancer patients in both outcome and toxicity risk from chemotherapy makes the identification of pharmacogenetic markers that can be used to screen patients before therapy selection an attractive prospect. Patients and Methods We assessed 27 selected polymorphisms based on previously described associations or putative functional effects in 16 key genes from pathways that may influence cellular sensitivity to taxanes (ABCB1, ABCC1, ABCC2, ABCG2, CDKN1A, CYP1B1, CYP2C8, CYP3A4, CYP3A5, MAPT, and TP53) and platinum (ABCC2, ABCG2, ERCC1, ERCC2, GSTP1, MPO, and XRCC1) using polymerase chain reaction and Pyrosequencing in 914 ovarian cancer patients from the Scottish Randomised Trial in Ovarian Cancer phase III trial who were treated at presentation with carboplatin and taxane regimens after cytoreductive surgery. Results No reproducible significant associations between genotype and outcome or toxicity were found for any of the genes analyzed. Previously reported genotype associations could not be replicated in this large study of a well-defined patient population within one specific clinical trial. Conclusion There are no clear candidates for taxane/platinum pharmacogenetic markers. This study highlights the need for validation of putative genetic markers in large, well-defined clinical sample sets.

Objective: Most drugs are developed based on data from European-derived ‘reference’ populations; however, clinically relevant DNA polymorphisms often demonstrate population-specific patterns of allele frequencies. Given that the knowledge of the frequency distribution of functional polymorphisms in a population may guide national planning for selection of therapeutic options, in the present study we examined the allele frequencies of enzymes responsible for drug disposition in Portugal. Patients & methods: Using PCR- and Pyrosequencing™-based methods, the current study assessed the frequencies of 15 key polymorphisms from genes encoding enzymes involved in Phases I, II and III of drug metabolism, DNA repair and intracellular metabolism in 135 healthy individuals from Portugal. Results: Allele frequencies were derived for cytochrome P450 (CYP)2C9*2 (13.2%), CYP2C9*3 (8%), CYP2C19*2 (14%), CYP3A4*1B (7%), CYP3A5*3C (87.5%), glutathione S-transferase (GST)M1*0 (77.9%), GSTP1 313A>G (33%), inosine triphosphatase 94C>A (7%), UDP-glucuronosyltransferase (UGT)1A1*28 (28%), UGT1A1 -3156G>A (23%), ATP-binding cassette (ABC)B1 1236C>T (46%), ABCB1 2677G>A/T (2 and 42%), ABCG2 421C>A (8%), excision repair cross-complementing rodent repair deficiency 2 2251A>C (3%) and thymidylate synthetase 1494del (31%). Conclusion: Although, on the whole, the frequency distributions among the Portuguese fitted the patterns commonly found in other Europeans well, evidence for some degree of African influence was observed. This is the most comprehensive study on pharmacogenetically relevant variations in Portugal to date, and the baseline of pharmacogenetic data might be important for determining policy guidelines for cancer prevention and drug treatments in the Portuguese population.

The nuclear receptor NR1I2 (also called PXR or SXR) is primarily expressed in mouse and human liver and intestines. Direct activation of NR1I2 occurs in response to a range of xenobiotics, which causes the formation of a heterodimer with the RXR receptor. This heterodimer binds to the nuclear receptor response elements of downstream genes such as ABCB1, CYP2C, and CYP3A. This study determined the extent of NR1I2 variation in three world populations. Variation in NR1I2 was identified by pooled resequencing in African, Asian, and European populations. Validation was performed in European and African populations using PCR and Pyrosequencing technology. RNA expression of NR1I2, ABCB1 and CYP3A4 was assessed using real-time PCR. Of 36 single nucleotide polymorphisms (SNPs) identified, 24 were in the untranslated region, 8 were intronic, and 4 exonic. Thirty-six percent were unique to the African population. In comparison with previously published data, we identified 13 novel polymorphisms. The NR1I2 −566A > C polymorphism was significantly associated with ABCB1 and CYP3A4 RNA expression in colon tumor (P = 0.04 in both cases), however, this polymorphism was not associated with NR1I2 expression. With NR1I2 playing such a large role in the regulation of genes involved in drug metabolism and transport, genetic variation contributing to altered NR1I2 function may have an important clinical impact.

The importance of B-type natriuretic peptide (BNP) as a diagnostic and therapeutic modality in cardiovascular disease is well known. BNP levels correlate clinical and physiologic characteristics, as well as outcomes. We sought to investigate the influence of BNP pathway genetic variation on BNP levels after adjustment for clinical/physiologic factors. DNA was extracted from 147 patients undergoing elective cardiac catheterization. Patients with elevated troponin were excluded. Detailed clinical data was collected including standard demographic, laboratory, echocardiographic and catheterization data. Genotype was determined at 19 loci in five genes relevant to the BNP pathway. Multivariable linear regression models of logBNP, adjusted for clinical variables, were used to assess the incremental influence of the genetic variants. Natriuretic peptide precursor B gene (NPPB) variants incrementally improved models of logBNP after inclusion of clinical/physiologic parameters. The NPPB −381 T > C genotype was significantly associated with logBNP in the model (p = 0.0005), with the model predicting 50% lower BNP levels in otherwise similar T/T vs. C/C subjects. The NPPB 777 G > A (3′ flanking region) genotype was of borderline significance (p = 0.0078). None of the other genotypes examined were significant (all p > 0.2). Genetic variation in NPPB significantly impacts BNP levels after adjustment for clinical/physiologic factors. The full linear regression model predicted up to a 50% relative difference in BNP levels between NPPB −381 T > C genotype groups. This suggests that NPPB sequence variants affect BNP physiology, possibly via transcriptional regulation. Further studies are needed to define whether these variants impact the clinical interpretation of BNP levels.

Breast cancer is the second most common cause of cancer-related death in women in the US and the UK, accounting for 15-17% of all female cancer deaths. Current treatment strategies include hormone therapy, such as anti-estrogens (tamoxifen) and aromatase inhibitors (exemastane, anastrozole, letrozole), as well as cytotoxics, such as the taxanes (paclitaxel, docetaxel). With multiple therapy choices, a method to prospectively screen patients prior to therapy selection is now needed. Pharmacogenetics seeks to develop screening mechanisms to optimise drug therapy. DNA variations in metabolism, transport and drug target genes may contribute to chemotherapy efficacy and toxicities. The status of the identification of genetic markers for breast cancer therapy selection is highlighted in this review.

Interindividual pharmacokinetic variability of the anticancer agent irinotecan is high. Life-threatening diarrhea is observed in up to 25% of patients receiving irinotecan and has been related with irinotecan pharmacokinetics and UGT1A1 genotype status. Here, we explore the association of ABCC2 (MRP2) polymorphisms and haplotypes with irinotecan disposition and diarrhea. A cohort of 167 Caucasian cancer patients who were previously assessed for irinotecan pharmacokinetics (90-min infusion given every 21 days), toxicity, and UGT1A1*28 genotype were genotyped for polymorphisms in ABCC2 using Pyrosequencing. Fifteen ABCC2 haplotypes were identified in the studied patients. The haplotype ABCC2*2 was associated with lower irinotecan clearance (28.3 versus 31.6 l/h; P=0.020). In patients who did not carry a UGT1A1*28 allele, a significant reduction of severe diarrhea was noted in patients with the ABCC2*2 haplotype (10 versus 44%; odds ratio, 0.15; 95% confidence interval, 0.04-0.61; P=0.005). This effect was not observed in patients with at least one UGT1A1*28 allele (32 versus 20%; odds ratio, 1.87; 95% confidence interval, 0.49-7.05; P=0.354). This study suggests that the presence of the ABCC2*2 haplotype is associated with less irinotecan-related diarrhea, maybe as a consequence of reduced hepatobiliary secretion of irinotecan. As the association was seen in patients not genetically predisposed at risk for diarrhea due to UGT1A1*28, confirmatory studies of the relationships of ABCC2 genotypes and irinotecan disposition and toxicity are warranted.

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome.

Purpose We conducted a phase II study of carboplatin and irinotecan in patients with advanced non-small cell lung cancer (NSCLC). In addition, we studied the correlation between certain genotypes of enzymes involved in irinotecan metabolism with efficacy and toxicity. Patients and Methods Patients with stage IIIB, IV, or recurrent NSCLC received a combination of irinotecan and carboplatin every 3 weeks at a dose of 200 mg/m2 and area under the curve of 5. Pharmacogenomic analysis was performed on several genes of interest (ABCB1, CYP3A4*1B, ERCC2, GSTP1, UGT1A1*28, and XRCC1). Results Forty-two patients enrolled between December 2001 and January 2004. Six patients achieved partial responses (14%), and 19 (45%) had stable disease. The median progression-free survival was 6.9 months. The median overall survival was 11.7 months, with 1-year overall survival of 42%. The most common toxicities were hematologic; grade 3 or 4 neutropenia was experienced by 26 patients (62%) during treatment, and 15 patients (36%) experienced grade 3 or 4 thrombocytopenia. The homozygous UGT1A1*28 (7/7) genotype was associated with grade 4 neutropenia in three of four patients (75%), but only eight out of 30 (27%) with 6/6 or 6/7 genotypes experienced grade 4 neutropenia ( p = 0.09). None of the 14 patients with the GSTP1 I105V A/A genotype had a partial response, as opposed to five out of 19 (26%) of those with the G/A or G/G genotypes ( p = 0.057). Conclusion The combination of carboplatin and irinotecan is an active combination in NSCLC, with response rates comparable with other platinum-containing doublets. Further studies with irinotecan should incorporate prospective pharmacogenomic analysis to identify markers for response and toxicity.

Background: B-type natriuretic peptide levels are associated with left ventricular enddiastolic pressure (LVEDP) and patient outcomes. There is documented variation in the genetic sequence of natriuretic peptide receptor (NPR)3, which is a primary clearance mechanism for B-type natriuretic peptide (BNP). Methods: DNA was extracted from 147 patients, aged 60 years or over undergoing elective left-heart catheterization for any indication, excluding acute myocardial infarction or severe valvular disease. Genotype was determined at four loci in the NPR3 gene. The logBNP:LVEDP ratio was compared between genotype groups. Linear and logistic regression models of LVEDP were generated. Results: The LogBNP:LVEDP ratio was significantly different among NPR3 IVS2–84 A allele carriers compared with G allele homozygotes (p = 0.008), with the A allele carriers showing a higher BNP level for a given level of LVEDP. The other variants did not alter this relationship (all p > 0.4). When added to the optimal linear regression model for LVEDP, NPR3 IVS2–84 genotype incrementally added to the model (p = 0.024, model r = 0.54). This was also true of the optimal logistic regression model of LVEDP ≥ 20 mmHg (p = 0.026). Conclusions: NPR3 IVS2–84 G>A genotype is associated with altered logBNP:LVEDP ratio and provides incremental value to predictive models of LVEDP. Further studies should address whether this or other variants in the BNP pathway modify the clinical importance of endogenous or exogenous BNP.

With pharmacogenetics comes the promise of individualized therapy selection for many common diseases where multiple treatment options are available. Recent advances including the Human Genome Project, the International HapMap project, advances in throughput and reduction in cost of genetic testing, and the inclusion of genotype-related dosing recommendations into package inserts all point to the integration of pharmacogenetics into clinical practice. However, many countries will not have access to pharmacogenetics resources in the near future. Generation of global genotype profiles will provide a useful, but not perfect resource for incorporating pharmacogenetics into national drug formularies in the form of prioritization or surveillance where individual genotype data would not be attainable. The PharmacoGenetics for Every Nation Initiative is a first step to making pharmacogenetics applicable on a global level.

Purpose: The source of the pharmacokinetic variability of 9-nitrocamptothecin (9NC) and its 9-aminocamptothecin (9AC) metabolite is unknown. ATP-binding cassette (ABC) transporters have been reported to modulate camptothecin analogues, are associated with camptothecin resistance, and might also affect 9NC and 9AC pharmacokinetics. The aim of this study was to evaluate the functional consequence of known single nucleotide polymorphisms in the transporter genes ABCB1, ABCC2, and ABCG2 on the pharmacokinetic disposition of 9NC and 9AC. Experimental design: Pharmacokinetic and genotyping studies were performed in 55 patients as part of two phase I studies of 9NC in patients with refractory solid tumors, a phase II study of 9NC in patients with advanced colon cancer, and a study evaluating the disposition of 9NC after administration of a single dose under fasting conditions. DNA was isolated from plasma and analyzed for variants in ABCB1, ABCC2, and ABCG2 genes. The ABCB1 1236C>T (n = 43), ABCB1 2677G>T/A (n = 43), ABCB1 3435C>T (n = 43), ABCC2 3972C>T (n = 39), and ABCG2 421C>A (n = 42) variants were analyzed using Pyrosequencing. Results: The ABCG2 421C>A genotype significantly affected the pharmacokinetics of 9AC. The mean 9AC lactone AUC/dose for wild-type (n = 25) and heterozygous (n = 2) patients were 14.3 ng/mL · h and 51.1 ng/mL. h, respectively (P = 0.032). The mean ± SD 9AC total AUC/dose for wild-type (n = 39) and heterozygous (n = 3) patients were 91.9 ± 78.3 ng/mL · h and 129.0 ± 90.5 ng/mL · h, respectively (P = 0.40). 9NC and 9AC disposition were not significantly influenced by variants in ABCB1, ABCC2, and ABCG2, and ABCB1 and ABCC2, respectively (P>0.05). Conclusion: These findings suggest that inter-individual variability in 9AC disposition, but not 9NC, may be influenced, in part, by ABCG2 genotype. In contrast, there was no evidence for a relationship between ABCG2 and the disposition of 9NC, or for relationships between ABCB1 and ABCC2 genotypes and the disposition of 9NC or 9AC.

Evaluation of: Lee W, St Onge RP, Proctor M et al.: Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet. 1(2), e24 (2005) [2] . Despite intense study, the mechanistic and therapeutic differences in cellular responses to DNA-damaging agents are not fully understood. In order to expand knowledge of DNA damage, the authors of this study assayed the effects of 12 anticancer agents on the complete pool of approximately 4700 homozygous deletion strains of Saccharomyces cerevisiae. The screens identified genes in well-characterized DNA, in addition to genes whose role in DNA-damage-response pathways had not previously been established.

The taxanes paclitaxel and docetaxel exert their anticancer activity by stabilizing microtubules during cell division. There is significant interindividual variability in response and toxicity between paclitaxel and docetaxel. Interpatient variability also exists for response and toxicity from each drug. Variability within genes involved in paclitaxel and/or docetaxel metabolism and transport exists. However, to date there is little evidence to suggest useful markers for the selection of individualized therapy. Epigenetic regulation of taxane pathway genes may play a large role in explaining the variability in toxicity and response.

Introduction: Most cancer pharmacogenetic studies use germline DNA, as tumor tissue is often inaccessible in the advanced disease setting. However, this relies on the assumption that germline DNA is representative of the tumor genotype. To date, there has been little attention paid to defining the relationship between tumor and germline genomes. Materials and methods: This study compared 28 polymorphisms in 13 genes of high importance to cancer pharmacogenetics from ten different chromosome regions, in DNA from normal mucosa and colon tumors in 44 paired samples. Results: 93% of samples had one or fewer genotype discrepancies. 77% of patients had intraindividual genotypes in complete concordance. In addition, although microsatellite instability (MSI) was identified in 20% of tumors, no significant association between MSI and genotype discrepancies was observed (p = 0.672). Conclusions: While this data validates the use of germline DNA pharmacogenetics in colorectal cancer, statistical analysis and modeling of pharmacogenetic data should be employed to incorporate this small, but important, source of error.

Colorectal cancer is one of the most common types of cancer in both men and women. Multiple chemotherapy combinations exist; however, there is currently no strategy for individualised therapy selection prior to treatment. Genetic polymorphisms in genes involved in the metabolism, transport or targets for the commonly used chemotherapy drugs (5-fluorouracil, irinotecan and oxaliplatin) have been described. Many require validation in large prospective trials before they can be used as markers for outcome and/or toxicity. This review describes the data available on polymorphisms in key genes that are associated with chemotherapy toxicity and response in colorectal cancer.

Candidate gene pharmacogenetic studies offer a strategy for the rapid assessment of putative predictive markers. As a first step toward studying the pharmacogenetics of cancer chemotherapy, 51 candidate genes from the pathways of antineoplastic agents were resequenced to identify common genetic polymorphisms that might alter therapeutic response or toxicity. Forty DNA samples were screened from each of three population groups: African-Americans, Asian-Americans and European-Americans. Nearly 378 kb of genomic sequence was obtained from each sample. Nine hundred and four variants were identified, including 139 coding single nucleotide polymorphisms (cSNPs). Three hundred and fifty-six (40%) polymorphisms were common to all three populations and 366 (41%) were population specific. Three hundred and forty-six (38%) variants were novel polymorphisms that were not present in the three public databases that were examined. One hundred and eleven (35%) of the 319 non-synonymous cSNPs that were identified by either resequencing or database mining were predicted by PolyPhen to be either possibly or probably damaging. For the non-synonymous cSNPs identified by resequencing, both the number of cSNPs found and the maximum estimated allele frequency decreased with increasing predicted severity. These results provide experimental validation and estimated allele frequencies for polymorphisms in three common ethnic groups and facilitate applied pharmacogenetic studies of anticancer drugs.

Previous studies have highlighted the use of phenotype generation in immortalized lymphoblastoid cells from the Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees as a powerful means of discovering genes involved in complex biological and pharmacological phenotypes. However, there is no data on how representative CEPH pedigrees are of the general population of European origin for genetic variants of pharmacogenetic significance. A vast amount of data in a population of restricted applicability would be of little value. Genotype and allele frequencies of 28 variants in 15 pharmacogenetically relevant genes were analyzed in germ-line DNA from European- and African-origin blood donors, and CEPH cell lines of European origin. The results demonstrate that allele frequencies for the 28 polymorphisms are highly similar between the CEPH and the European-origin populations. However, genotype frequencies in the CEPH population did not provide a high level of prediction for the African-origin population. These data support the usefulness of the CEPH panel in pharmacogenetic discovery efforts for European-derived populations.

To determine the relationship between CYP3A5 polymorphism and cyclosporine pharmacokinetic parameters among healthy volunteers, an oral cyclosporine (CsA) pharmacokinetic study was performed in 16 healthy subjects. Blood CsA concentrations were measured by high-performance liquid chromatography. Concentration-versus-time data were analyzed by a noncompartmental method using WinNonLin, and the blood samples were genotyped for the CYP3A5 using the polymerase chain reaction and pyrosequencing. CsA pharmacokinetic parameters were dichotomized and compared using the 1-way ANOVA test according to the CYP3A5*3C genotype. There were 6 homozygous A/A (wild type), 6 homozygous G/G (variant), and 4 heterozygous A/G genotypes for CYP3A5*3 C in these 16 healthy volunteers. All whites were G/G group, and all African Americans except 1 were either A/A or A/G group. The mean AUC (ng x h/mL) of CsA for the 3 genotype groups were 4962 +/- 1074 (A/A), 6677 +/- 1153 (G/G), and 5416 +/- 1817 (A/G), (A/A versus G/G, P = 0.03), and the mean CL/F (mL/min/kg) were 15.6 +/- 3.1 (A/A), 12.0 +/- 2.3 (G/G), and 14.7 +/- 5.9 (A/G), (A/A versus G/G, P = 0.04). None of the other parameters were significantly different among the 3 genotypes. In conclusion, the CYP3A5*3C polymorphism appears to affect AUC and CL/F of oral CsA significantly in healthy subjects, which may partly explain some of the differences of pharmacokinetics in CsA between African Americans and whites.

Irinotecan is an anticancer drug approved in combination therapy for advanced colorectal cancer. Severe, life-threatening toxicities can occur from irinotecan treatment. Although multiple genes may play a role in irinotecan activity, the UDP glycuronosyltransferase 1 family, polypeptide A1 (UGT1A1) enzyme has been strongly associated with toxicity. A common dinucleotide repeat polymorphism in the UGT1A1 promoter region (UGT1A1*28) has been correlated with severe toxicity in cancer patients receiving irinotecan-containing therapy. Prospective screening of patients prior to chemotherapy selection may reduce the frequency of severe toxicities by allowing alternate therapy selections for patients carrying the UGT1A1*28 polymorphism.

Purpose: The ATP-binding cassette transporter ABCG2 (breast cancer resistance protein) is an efflux protein that plays a role in host detoxification of various xenobiotic substrates, including the irinotecan metabolite 7- ethyl-10-hydroxycamptothecin (SN-38). The ABCG2 421C>A polymorphism has been associated with reduced protein expression and altered function in vitro. The aim of this study was to evaluate the ethnic distribution and potential functional consequence of the ABCG2 421C>A genotype in cancer patients treated with irinotecan. Experimental Design: ABCG2 genotyping was performed using Pyrosequencing on DNA from 88 American Caucasians, 94 African Americans, 938 Africans, and 95 Han Chinese, as well as in 84 European Caucasian patients treated with irinotecan undergoing additional blood sampling for pharmacokinetic studies. Results: Significant differences in allele frequencies were observed between the given world populations (P < 0.001), the variant allele being most common in the Han Chinese population with a frequency as high as 34%. The mean area under the curve of irinotecan and SN-38 were 19,851 and 639 ng × hour/mL, respectively. The frequency of the variant allele (10.7%) was in line with results in American Caucasians. No significant changes in irinotecan pharmacokinetics were observed in relation to the ABCG2 421C>A genotype, although one of two homozygous variant allele carriers showed extensive accumulation of SN-38 and SN-38 glucuronide. Conclusions: The ABCG2 421C>A polymorphism appears to play a limited role in the disposition of irinotecan in European Caucasians. It is likely that the contribution of this genetic variant is obscured by a functional role of other polymorphic proteins.

Objective The adenosine triphosphate–binding cassette transporter ABCG2 (breast cancer resistance protein [BCRP]) functions as an efflux transporter for many drugs, including the topoisomerase I inhibitor diflomotecan, and is expressed at high levels in the intestine and liver. We performed an exploratory analysis to evaluate the effects of the natural allelic variant ABCG2 421C>A on the pharmacokinetics of diflomotecan. Methods The drug was administered to 22 adult white patients with cancer as a 20–minute infusion (dose, 0.10–0.27 mg), followed 2 weeks later by an oral solution (dose, 0.10–0.35 mg). Results The ABCG2 421C>A genotype significantly affected the pharmacokinetics of diflomotecan; in 5 patients heterozygous for this allele, plasma levels after intravenous drug administration were 299% (P = .015) of those in 15 patients with wild–type alleles, at mean values of 138 ng · h/mL · mg−1 (95% confidence interval, 11.3–264 ng · h/mL · mg−1) versus 46.1 ng · h/mL · mg−1 (95% confidence interval, 25.6–66.7 ng · h/mL · mg−1), respectively. Diflomotecan levels were not significantly influenced by 11 known variants in the ABCB1, ABCC2, cytochrome P450 (CYP) 3A4, and CYP3A5 genes. Conclusion These findings provide the first evidence linking variant ABCG2 alleles to altered drug exposure and suggest that interindividual variability in substrate drug effects might be influenced, in part, by ABCG2 genotype. Clinical Pharmacology & Therapeutics (2004) 76, 38–44; doi: 10.1016/j.clpt.2004.03.003

Methotrexate (MTX) is a commonly used disease-modifying antirheumatic drug in rheumatoid arthritis (RA). Polymorphisms occur in several genes encoding key enzymes in the folic acid pathway, which is influenced by MTX, but have not been evaluated in patients with RA. The effect of race on allele frequency has also not been evaluated. In this study, the allele frequencies of polymorphisms in six key enzymes in the MTX–folate pathway in patients with RA and healthy controls, including several common racial groups were studied. European– and African–American patients with RA and European and African healthy controls were genotyped for 22 genetic loci in six genes in the MTX cellular pathway. Differences in genotype distributions between the different racial groups were evaluated using χ2 tests. Allele frequencies were significantly different (p < 0.001) for eight single nucleotide polymorphisms between the European and African controls. The allele frequencies of two polymorphisms showed significant differences (p < 0.001) between the African– and European–American patients with RA. Thus, racial differences exist between the allele frequencies of several polymorphisms in enzymes in the MTX-folate pathway in patients with RA and healthy controls. Whether such differences contribute to a differential response to MTX in patients with RA deserves to be investigated.