Pharmacogenetics: potential for individualized drug therapy through genetics

Understanding the impact of ABCG2 polymorphisms on drug pharmacokinetics: focus on rosuvastatin and allopurinol

INTRODUCTION

In addition to the well-established understanding of the pharmacogenetics of drug-metabolizing enzymes, there is growing data on the effects of genetic variation in drug transporters, particularly ATP-binding cassette (ABC) transporters. However, the evidence that these genetic variants can be used to predict drug effects and to adjust individual dosing to avoid adverse events is still limited.

AREAS COVERED

This review presents a summary of the current literature from the PubMed database as of February 2024 regarding the impact of genetic variants on ABCG2 function and their relevance to the clinical use of the HMG-CoA reductase inhibitor rosuvastatin and the xanthine oxidase inhibitor allopurinol.

EXPERT OPINION

Although there are pharmacogenetic guidelines for the ABCG2 missense variant Q141K, there is still some conflicting data regarding the clinical benefits of these recommendations. Some caution appears to be warranted in homozygous ABCG2 Q141K carriers when rosuvastatin is administered at higher doses and such information is already included in the drug label. The benefit of dose adaption to lower possible side effects needs to be evaluated in prospective clinical studies.

Pharmacogenomics of Drugs Used in β-Thalassemia and Sickle-Cell Disease: From Basic Research to Clinical Applications

In this short review we have presented and discussed studies on pharmacogenomics (also termed pharmacogenetics) of the drugs employed in the treatment of β-thalassemia or Sickle-cell disease (SCD). This field of investigation is relevant, since it is expected to help clinicians select the appropriate drug and the correct dosage for each patient. We first discussed the search for DNA polymorphisms associated with a high expression of γ-globin genes and identified this using GWAS studies and CRISPR-based gene editing approaches. We then presented validated DNA polymorphisms associated with a high HbF production (including, but not limited to the HBG2 XmnI polymorphism and those related to the BCL11A, MYB, KLF-1, and LYAR genes). The expression of microRNAs involved in the regulation of γ-globin genes was also presented in the context of pharmacomiRNomics. Then, the pharmacogenomics of validated fetal hemoglobin inducers (hydroxyurea, butyrate and butyrate analogues, thalidomide, and sirolimus), of iron chelators, and of analgesics in the pain management of SCD patients were considered. Finally, we discuss current clinical trials, as well as international research networks focusing on clinical issues related to pharmacogenomics in hematological diseases.

Pharmacogenomics in Clinical Practice for Older People

Older people are over-represented among individuals that experience adverse drug reactions (ADR) and adverse drug events (ADE). Furthermore, older people are over-represented among individuals that visit emergency departments and are hospitalized because of ADRs. Moreover, older people are overrepresented among those who suffer ADEs while hospitalized. Finally, older people are among those most likely to have an anaphylactic response to prescription medications. Therefore, older people are prime candidates for efforts aimed at optimizing pharmacotherapeutic outcomes. Pharmacogenomics is an approach of using genetic data to optimize pharmacotherapeutic outcomes. Over the last two decades, pharmacogenomics grew from research initiatives into the current environment of pharmacogenomics implementation. Specifically, implementing pharmacogenomics into clinical settings or within health care systems has proven beneficial in optimizing pharmacotherapeutic outcomes. Therefore, pharmacists focused on optimizing pharmacotherapeutic outcomes for older people should be aware of the approaches to and resources available for implementing pharmacogenomics. KEY WORDS: Drug labeling biomarkers, Genes, Older adults, Pharmacogenomics.

Integrating Multi-Omics Data With EHR for Precision Medicine Using Advanced Artificial Intelligence

With the recent advancement of novel biomedical technologies such as high-throughput sequencing and wearable devices, multi-modal biomedical data ranging from multi-omics molecular data to real-time continuous bio-signals are generated at an unprecedented speed and scale every day. For the first time, these multi-modal biomedical data are able to make precision medicine close to a reality. However, due to data volume and the complexity, making good use of these multi-modal biomedical data requires major effort. Researchers and clinicians are actively developing artificial intelligence (AI) approaches for data-driven knowledge discovery and causal inference using a variety of biomedical data modalities. These AI-based approaches have demonstrated promising results in various biomedical and healthcare applications. In this review paper, we summarize the state-of-the-art AI models for integrating multi-omics data and electronic health records (EHRs) for precision medicine. We discuss the challenges and opportunities in integrating multi-omics data with EHRs and future directions. We hope this review can inspire future research and developing in integrating multi-omics data with EHRs for precision medicine.

TPMT and NUDT15 testing for thiopurine therapy: A major tertiary hospital experience and lessons learned

Variants in thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) are associated with an accumulation of cytotoxic metabolites leading to increased risk of drug-related toxicity with standard doses of thiopurine drugs. We established TPMT and NUDT15 genetic testing for clinical use and evaluated the utilization, service outcomes and potential value of multi-gene PGx testing for 210 patients that underwent pharmacogenetics (PGx) testing for thiopurine therapy with the aim to optimize service delivery for future prescribing. The test was most commonly ordered for Gastroenterology (40.0%) and Neurology (31.4%), with an average turnaround time of 2 days. Following testing, 24.3% patients were identified as intermediate or poor metabolizers, resulting in 51 recommendations for a drug or dose change in thiopurine therapy, which were implemented in 28 (54.9%) patients. In the remaining patients, 14 were not adjusted and 9 had no data available. Focusing on drug gene interactions available for testing in our laboratory, multi-gene PGx results would present opportunities for treatment optimization for at least 33.8% of these patients who were on 2 or more concurrent medications with actionable PGx guidance. However, the use of PGx panel testing in clinical practice will require the development of guidelines and education as revealed by a survey with the test providers. The evaluation demonstrated successful implementation of single gene PGx testing and this experience guides the transition to a pre-emptive multi-gene testing approach that provides the opportunity to improve clinical care.

Personalized Medicine for the Critically Ill Patient: A Narrative Review

Personalized Medicine (PM) is rapidly advancing in everyday medical practice. Technological advances allow researchers to reach patients more than ever with their discoveries. The critically ill patient is probably the most complex of all, and personalized medicine must make serious efforts to fulfill the desire to “treat the individual, not the disease”. The complexity of critically ill pathologies arises from the severe state these patients and from the deranged pathways of their diseases. PM constitutes the integration of basic research into clinical practice; however, to make this possible complex and voluminous data require processing through even more complex mathematical models. The result of processing biodata is a digitized individual, from which fragments of information can be extracted for specific purposes. With this review, we aim to describe the current state of PM technologies and methods and explore its application in critically ill patients, as well as some of the challenges associated with PM in intensive care from the perspective of economic, approval, and ethical issues. This review can help in understanding the complexity of, P.M.; the complex processes needed for its application in critically ill patients, the benefits that make the effort of implementation worthwhile, and the current challenges of PM.

Utilizing a Human-Computer Interaction Approach to Evaluate the Design of Current Pharmacogenomics Clinical Decision Support

A formal assessment of pharmacogenomics clinical decision support (PGx-CDS) by providers is lacking in the literature. The objective of this study was to evaluate the usability of PGx-CDS tools that have been implemented in a healthcare setting. We enrolled ten prescribing healthcare providers and had them complete a 60-min usability session, which included interacting with two PGx-CDS scenarios using the “Think Aloud” technique, as well as completing the Computer System Usability Questionnaire (CSUQ). Providers reported positive comments, negative comments, and suggestions for the two PGx-CDS during the usability testing. Most provider comments were in favor of the current PGx-CDS design, with the exception of how the genotype and phenotype information is displayed. The mean CSUQ score for the PGx-CDS overall satisfaction was 6.3 ± 0.95, with seven strongly agreeing and one strongly disagreeing for overall satisfaction. The implemented PGx-CDS at our institution was well received by prescribing healthcare providers. The feedback collected from the session will guide future PGx-CDS designs for our healthcare system and provide a framework for other institutions implementing PGx-CDS.

Physiologically-Based Pharmacokinetic Modeling for Optimal Dosage Prediction of Quinine Coadministered With Ritonavir-Boosted Lopinavir

The coformulated lopinavir/ritonavir significantly reduces quinine concentration in healthy volunteers due to potential drug-drug interactions (DDIs). However, DDI information in malaria and HIV coinfected patients are lacking. The objective of the study was to apply physiologically-based pharmacokinetic (PBPK) modeling to predict optimal dosage regimens of quinine when coadministered with lopinavir/ritonavir in malaria and HIV coinfected patients with different conditions. The developed model was validated against literature. Model verification was evaluated using the accepted method. The verified PBPK models successfully predicted unbound quinine disposition when coadministered with lopinavir/ritonavir in coinfected patients with different conditions. Suitable dose adjustments to counteract with the DDIs have identified in patients with various situations (i.e., a 7-day course at 1,800 mg t.i.d. in patients with malaria with HIV infection, 648 mg b.i.d. in chronic renal failure, 648 mg t.i.d. in hepatic insufficiency except for severe hepatic insufficiency (324 mg b.i.d.), and 648 mg t.i.d. in CYP3A4 polymorphism).

A pediatric perspective on genomics and prevention in the twenty-first century

We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.

Utilizing a user-centered approach to develop and assess pharmacogenomic clinical decision support for thiopurine methyltransferase

Background

A pharmacogenomic clinical decision support tool (PGx-CDS) for thiopurine medications can help physicians incorporate pharmacogenomic results into prescribing decisions by providing up-to-date, real-time decision support. However, the PGx-CDS user interface may introduce errors and promote alert fatigue. The objective of this study was to develop and evaluate a prototype of a PGx-CDS user interface for thiopurine medications with user-centered design methods.

Methods

This study had two phases: In phase I, we conducted qualitative interviews to assess providers’ information needs. Interview transcripts were analyzed through a combination of inductive and deductive qualitative analysis to develop design requirements for a PGx-CDS user interface. Using these requirements, we developed a user interface prototype and evaluated its usability (phase II).

Results

In total, 14 providers participated: 10 were interviewed in phase I, and seven providers completed usability testing in phase II (3 providers participated in both phases). Most (90%) participants were interested in PGx-CDS systems to help improve medication efficacy and patient safety. Interviews yielded 11 themes sorted into two main categories: 1) health care providers’ views on PGx-CDS and 2) important design features for PGx-CDS. We organized these findings into guidance for PGx-CDS content and display. Usability testing of the PGx-CDS prototype showed high provider satisfaction.

Conclusion

This is one of the first studies to utilize a user-centered design approach to develop and assess a PGx-CDS interface prototype for Thiopurine Methyltransferase (TPMT). This study provides guidance for the development of a PGx-CDS, and particularly for biomarkers such as TPMT.

Implementation of pharmacogenetics in a clozapine treatment resistant patient: a case report

We report the case of a young Caucasian male with disorganized chronic schizophrenia, an active smoker and nonresponder to 400 mg of clozapine/day. Therapeutic clozapine monitoring was analyzed revealing a low clozapine:norclozapine ratio. An additional pharmacogenetic test was carried out showing that the patient carried *1F variant ( CYP1A2 gene), which has been associated with nonresponse to clozapine in smoker patients. A genetic variation in the SLC6A4 gene was also found, which could be related to the poor response to clozapine. The remainder of the genes analyzed ( CYP2D6, ABCB1 and HTR2A) were not directly associated with the patient’s phenotype. The dose of clozapine was increased to 600 mg/day, reaching the therapeutic range. This case shows how pharmacogenetics can help in understanding the value of plasma levels to provide clinical improvement.

Big data and targeted machine learning in action to assist medical decision in the ICU

Historically, personalised medicine has been synonymous with pharmacogenomics and oncology. We argue for a new framework for personalised medicine analytics that capitalises on more detailed patient-level data and leverages recent advances in causal inference and machine learning tailored towards decision support applicable to critically ill patients. We discuss how advances in data technology and statistics are providing new opportunities for asking more targeted questions regarding patient treatment, and how this can be applied in the intensive care unit to better predict patient-centred outcomes, help in the discovery of new treatment regimens associated with improved outcomes, and ultimately how these rules can be learned in real-time for the patient.

Pharmacogenetic variation influences sensory neuropathy occurrence in Southern Africans treated with stavudine-containing antiretroviral therapy

BACKGROUND

The use of the HIV antiretroviral drug stavudine (d4T), a thymidine analogue, is associated with the development of mitochondrial toxicities such as sensory neuropathy (SN). Genetic variation in genes relating to d4T transport and metabolism, as well as genetic variation in the thymidine synthesis pathway, could influence occurrence of d4T-related toxicity.

METHODS

We examined this hypothesis in a cohort of HIV-positive South African adults exposed to d4T, including 143 cases with SN and 120 controls without SN. Ten SNPs in four genes associated with stavudine transport, and 16 SNPs in seven genes of the thymidine synthesis / phosphorylation pathway were genotyped using Agena mass spectrometry methods. Associations between sensory neuropathy and genetic variants were evaluated using PLINK by univariate and multivariable analyses.

RESULTS

Age and height were significantly associated with SN occurrence. Using logistic regression with age and height as covariates, and uncorrected empirical p-values, genetic variation in SLC28A1, SAMHD1, MTHFR and RRM2B was associated with SN in South Africans using d4T.

CONCLUSION

Variation in genes relating to d4T transport and metabolism, as well as genetic variation in the thymidine synthesis pathway may influence occurrence of d4T-related SN. These data contribute to the characterisation of African pharmacogenetic variation and its role in adverse response to antiretroviral therapy.

CYP2D6 genotype analysis of a Thai population: platform comparison

The highly polymorphic CYP2D6 gene locus leads to a wide range of enzyme activity. Since there are limited data for Thai, the major aim was to investigate CYP2D6 genetic variation in a large Thai population (n = 920). CYP2D6 genotyping was performed using four different platforms. Genotype call rates of the Luminex xTAG® and AmpliChip CYP450 test were 96.5% and 87.4%, respectively. Based on Luminex xTAG® data, the most common alleles and genotypes were *1 0 (49.6%), *1 (24.6%), *2 (10.8%), *5 (6.7%), *41 (6.5%) and *1/*10 (23.9%), *10/*10 (21.5%), *2/*10 (9.4%), *5/*10 (6.9%), *10/*41 (5.7%), respectively. Challenges and limitations of the platforms evaluated are discussed. These data add to our knowledge regarding interethnic variability in CYP2D6 activity and contribute to improving drug therapy in the Thai.

Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure

BACKGROUND

Modern societies are exposed to vast numbers of potentially hazardous chemicals. Despite demonstrated linkages between chemical exposure and severe health effects, there are limited, often conflicting, data on how adverse health effects of exposure differ across individuals.

OBJECTIVES

We tested the hypothesis that population variability in response to certain chemicals could elucidate a role for gene-environment interactions (GxE) in differential susceptibility.

METHODS

High-throughput screening (HTS) data on thousands of chemicals in genetically heterogeneous zebrafish were leveraged to identify a candidate chemical (Abamectin) with response patterns indicative of population susceptibility differences. We tested the prediction by generating genome-wide sequence data for 276 individual zebrafish displaying susceptible (Affected) vs. resistant (Unaffected) phenotypes following identical chemical exposure.

RESULTS

We found GxE associated with differential susceptibility in the sox7 promoter region and then confirmed gene expression differences between phenotypic response classes.

CONCLUSIONS

The results for Abamectin in zebrafish demonstrate that GxE associated with naturally occurring, population genetic variation play a significant role in mediating individual response to chemical exposure. https://doi.org/10.1289/EHP2662.

Pharmacogenetic landscape of Metabolic Syndrome components drug response in Tunisia and comparison with worldwide populations

Genetic variation is an important determinant affecting either drug response or susceptibility to adverse drug reactions. Several studies have highlighted the importance of ethnicity in influencing drug response variability that should be considered during drug development. Our objective is to characterize the genetic variability of some pharmacogenes involved in the response to drugs used for the treatment of Metabolic Syndrome (MetS) in Tunisia and to compare our results to the worldwide populations. A set of 135 Tunisians was genotyped using the Affymetrix Chip 6.0 genotyping array. Variants located in 24 Very Important Pharmacogenes (VIP) involved in MetS drug response were extracted from the genotyping data. Analysis of variant distribution in Tunisian population compared to 20 worldwide populations publicly available was performed using R software packages. Common variants between Tunisians and the 20 investigated populations were extracted from genotyping data. Multidimensional screening showed that Tunisian population is clustered with North African and European populations. The greatest divergence was observed with the African and Asian population. In addition, we performed Inter-ethnic comparison based on the genotype frequencies of five VIP biomarkers. The genotype frequencies of the biomarkers rs3846662, rs1045642, rs7294 and rs12255372 located respectively in HMGCR, ABCB1, VKORC1 and TCF7L2 are similar between Tunisian, Tuscan (TSI) and European (CEU). The genotype frequency of the variant rs776746 located in CYP3A5 gene is similar between Tunisian and African populations and different from CEU and TSI. The present study shows that the genetic make up of the Tunisian population is relatively complex in regard to pharmacogenes and reflects previous historical events. It is important to consider this ethnic difference in drug prescription in order to optimize drug response to avoid serious adverse drug reactions. Taking into account similarities with other neighboring populations, our study has an impact not only on the Tunisian population but also on North African population which are underrepresented in pharmacogenomic studies.

"The Future of Vulvar Disease: New and Ongoing Challenges": Presidential Lecture - XXIV World Congress 2017, Mendoza, Argentina

The 21st century brought along a number of discoveries and medical advances. With the advances, we can mention the following: target therapies for cancer, genomics and molecular biology, pharmacogenomics, minimally invasive and robotic surgery, immunosuppressive therapies in transplant patients, human papillomavirus in the era of vaccination, and aesthetic vulvovaginal procedures. All of them have greatly influenced medicine. As a scientific society, we have several challenges. In the past, you had to go to a library to get information. Now, we have readily available, accessible information. Thus, here comes the debate; we are facing a change in our educational paradigm, which needs to be approached from an integral and holistic perspective. New historical and cultural circumstances call for a deep reflection on the current social validity of scientific societies. They should be open to new ideas and allow dissent, work in teams, and speak a common language. They must be organized and, in constant communication with its members, support and organize research developing well-designed clinical trials and observational studies. We should work for our patients, recognizing the importance of the whole woman. We all have a great scientific and humanitarian challenge; to succeed, we must not lose sight of who we are working for. We work for them, our patients, and not for us. Our mission is to take care of our them!

Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine

Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

Psychiatric pharmacists' perception on the use of pharmacogenomic testing in the mental health population

AIM

Pharmacogenomics could play a role in improving patient care, reducing adverse drug reactions and overall healthcare costs. However, whether it is utilized may be determined by how it is perceived by healthcare professionals, including pharmacists.

METHODS

A cross-sectional web-based survey evaluated psychiatric pharmacists' use, knowledge and perception of the effectiveness of such testing.

RESULTS

Among participants, 80% worked at sites not offering pharmacogenomic testing, mostly due to a lack of funding. About 36% of pharmacists considered themselves more knowledgeable and 47% considered themselves less knowledgeable about pharmacogenomic testing; however, most agreed on the potential usefulness of testing.

CONCLUSION

Among psychiatric pharmacists, the use of pharmacogenomics appears underappreciated due to factors such as lack of availability and understanding of testing. Original submitted 26 November 2014; Revision submitted 13 February 2015.

Screening for 392 polymorphisms in 141 pharmacogenes

Pharmacogenomics is the study of the association between inter-individual genetic differences and drug responses. Researches in pharmacogenomics have been performed in compliance with the use of several genotyping technologies. In this study, a total of 392 single-nucleotide polymorphisms (SNPs) located in 141 pharmacogenes, including 21 phase I, 13 phase II, 18 transporter and 5 modifier genes, were selected and genotyped in 150 subjects using the GoldenGate assay or the SNaPshot technique. These variants were in Hardy-Weinberg equilibrium (HWE) (P>0.05), except for 22 SNPs. Genotyping of the 392 SNPs revealed that the minor allele frequencies of 47 SNPs were <0.05, 105 SNPs were monomorphic and 22 variants were not in HWE. Also, based on previous studies, we predicted the association between the polymorphisms of certain pharmacogenes, such as cytochrome P450 2D6, cytochrome P450 2C9, vitamin K epoxide reductase complex, subunit 1, cytochrome P450 2C19, human leukocyte antigen, class I, B and thiopurine S-methyltransferase, and drug efficacy. In conclusion, our study demonstrated the allele distribution of SNPs in 141 pharmacogenes as determined by high-throughput screening. Our results may be helpful in developing personalized medicines by using pharmacogene polymorphisms.

Plasmodium falciparum and Plasmodium vivax specific lactate dehydrogenase: genetic polymorphism study from Indian isolates

Control and eradication of malaria is hindered by the acquisition of drug resistance by Plasmodium species. This has necessitated a persistent search for novel drugs and more efficient targets. Plasmodium species specific lactate dehydrogenase is one of the potential therapeutic and diagnostic targets, because of its indispensable role in endoerythrocytic stage of the parasite. A target molecule that is highly conserved in the parasite population can be more effectively used in diagnostics and therapeutics, hence, in the present study polymorphism in PfLDH (Plasmodiumfalciparum specific LDH) and PvLDH (Plasmodiumvivax specific LDH) genes was analyzed using PCR-single strand confirmation polymorphism (PCR-SSCP) and sequencing. Forty-six P. falciparum and thirty-five P. vivax samples were screened from different states of India. Our findings have revealed presence of a single PfLDH genotype and six PvLDH genotypes among the studied samples. Interestingly, along with synonymous substitutions, nonsynonymous substitutions were reported to be present for the first time in the PvLDH genotypes. Further, through amino acid sequence alignment and homology modeling studies we observed that the catalytic residues were conserved in all PvLDH genotypes and the nonsynonymous substitutions have not altered the enzyme structure significantly. Evolutionary genetics studies have confirmed that PfLDH and PvLDH loci are under strong purifying selection. Phylogenetic analysis of the pLDH gene sequences revealed that P. falciparum compared to P. vivax, has recent origin. The study therefore supports PfLDH and PvLDH as suitable therapeutic and diagnostic targets as well as phylogenetic markers to understand the genealogy of malaria species.

Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine

The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.

A systematic review and meta-analysis of trials of treatment of depression from India

BACKGROUND

Antidepressants hold the center stage in the treatment of depression in current clinical practice. However, it is also well-known that the treatment response and dosage requirement are influenced by ethnic variations. Although many efficacy studies have evaluated the efficacy of antidepressants, there is lack of systematic reviews and meta-analysis of the existing literature from India.

OBJECTIVE

To systematically review the efficacy of treatment of depression in the Indian context.

MATERIALS AND METHODS

We searched PubMed, Psychinfo, Medknow and Google scholar to identify studies published in peer-reviewed English language journals. All controlled trials from India evaluating the clinical efficacy of antidepressants, electroconvulsive therapy (ECT), and repetitive transcranial magnetic stimulation (rTMS) for management of depression were evaluated. Data were extracted using standard procedures and risk of bias was evaluated. Effect sizes were computed for the individual studies.

RESULTS

Effect sizes were computed from 35 clinical trials. Overall, medications were superior to placebo for treatment of depression (mean effect size (ES) of 0.87, confidence intervals (CI of 0.71-1.02). The effect was greatest for tricyclic antidepressants (ES of 1.00, CI of 0.80-1.21) followed by monoamine oxidase inhibitors (ES 0.54, CI of 0.40-0.67). ECT was superior to antidepressants (ES 0.32, CI of - 0.21 to 0.86) and active rTMS was found to be superior to sham rTMS with mean effect size of 0.74 (CI 0.39-1.08). Risk of bias was found to be considerable. However, the review literature suggests that most of the studies have not been powered adequately and have been limited to small sample sizes.

CONCLUSIONS

Although there is some data from India with respect to efficacy of antidepressants, most of the trials have been of shorter duration have been inadequately powered. The available data support the superiority of antidepressants over placebo and that of ECT over antidepressants.

Genetic variations in stem cell-related genes and colorectal cancer prognosis

BACKGROUND

Many properties of cancer cells are reminiscent of those in normal stem cells. Genes important to stem cell development have been significantly implicated in the etiology and clinical outcome of colorectal cancer (CRC). However, the associations of genetic variations in these genes with CRC prognosis have not yet been elucidated.

METHODS

We analyzed the effects of eight potentially functional single nucleotide polymorphisms (SNPs) in six stem cell-related genes on the prognosis of a well-characterized population of 380 Chinese CRC patients diagnosed from February 2006 to January 2010.

RESULTS

The most significant finding was related to rs879882, a variant in the 5' region of POU5F1 gene which encodes a protein essential for embryonic stem cell self-renewal and pluripotency, and induced pluripotent stem cell reprogramming. The variant-containing genotypes of rs879882 were associated with an increased risk of recurrence (hazard ratio [HR] = 2.10, 95% confidence interval [CI] 1.17-3.76, P = 0.01). In chemotherapy-stratified analysis, the association remained borderline significant in patients receiving chemotherapy (HR = 1.97, 95% CI 0.89-4.34, P = 0.09). In addition, a nonsynonymous SNP of APC gene was also significantly associated with recurrence risk in chemotherapy-treated patients (HR = 2.63, 95% CI 1.14-6.06 P = 0.02). Further analyses showed a combined effect of the two SNPs in predicting CRC recurrence in patients receiving chemotherapy (P = 0.04) but not in those without chemotherapy (P = 0.43). Moreover, an exploratory multivariate assessment model indicated that these two variants enhanced the power to predict recurrence after chemotherapy.

CONCLUSION

We presented one of the first epidemiologic studies showing that stem cell-related genetic variants may impact CRC clinical outcomes, especially in chemotherapy-treated patients.

Personalized approach of medication by indirect anticoagulants tailored to the patient-Russian context: what are the prospects?

Indirect anticoagulants such as warfarin are the ‘gold standard’ for prevention and treatment of thromboembolic complications in patients at risk (in atrial fibrillation of valvular and nonvalvular etiology, the presence of artificial heart valves, orthopedic and trauma interventions, and other pathological conditions). A wide range of doses required to achieve a therapeutic effect indicates the need for a personalized approach to the appointment of warfarin. In addition to the dependence on the patient's clinical characteristics (sex, age, smoking status, diagnosis), there is a clear association between the warfarin dose and the carriage of certain allelic variants of key genes that makes it possible to apply molecular genetic testing for individual dose adjustment. This provides a more rapid target anticoagulant effect and also reduces the risk of bleeding associated with a possible overdose of warfarin. Implementation of this approach will allow more wide and safe application of indirect anticoagulants in Russia for needy patients.

Functional polymorphisms of circadian positive feedback regulation genes and clinical outcome of Chinese patients with resected colorectal cancer

BACKGROUND

Previous studies have demonstrated that circadian genes play a role in the development and progression of many cancers. This study aims to assess the effects of single nucleotide polymorphisms (SNPs) in circadian genes on recurrence and survival of colorectal cancer (CRC) patients.

METHODS

Nine functional SNPs in 3 genes (CLOCK, NPAS2, and BMAL1) on the circadian positive feedback loop were selected and genotyped using the Sequenom iPLEX genotyping system in a cohort of 411 resected Chinese CRC patients. Multivariate Cox proportional hazards model and Kaplan-Meier curve were used for the prognosis analysis.

RESULTS

The authors identified 2 SNPs in the CLOCK gene to be significantly associated with CRC overall survival. SNP rs3749474 exhibited a significant association with survival of CRC patients in the additive model (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.37-0.81; P = .003). In addition, patients carrying the heterozygous variant of rs1801260 had significantly increased overall survival compared with those carrying homozygous wild-type genotype (HR, 0.31; 95% CI, 0.11-0.88; P = .03). Findings from functional assay provided further biological support for these significant associations. Stratified analysis found no modifying effect of chemotherapy on the prognostic significance of both SNPs. Moreover, we observed cumulative effects of these 2 SNPs on CRC overall survival (P for trend = .01). Compared with patients carrying no unfavorable genotypes, those carrying 2 unfavorable genotypes had a 2.92-fold increased risk of death (P = .03).

CONCLUSIONS

The results suggest for the first time that CLOCK gene polymorphisms may serve as an independent prognostic marker for CRC patients.

Fatal methanol poisoning

Methanol poisoning has become a considerable problem in Iran. Liver can show some features of poisoning after methanol ingestion. Therefore, our concern was to examine liver tissue histopathology in fatal methanol poisoning cases in Iranian population. In this study, 44 cases of fatal methanol poisoning were identified in a year. The histological changes of the liver were reviewed. The most striking features of liver damage by light microscopy were micro-vesicular steatosis, macro-vesicular steatosis, focal hepatocyte necrosis, mild intra-hepatocyte bile stasis, feathery degeneration and hydropic degeneration. Blood and vitreous humor methanol concentrations were examined to confirm the proposed history of methanol poisoning. The majority of cases were men (86.36%). In conclusion, methanol poisoning can cause histological changes in liver tissues. Most importantly in cases with mean blood and vitreous humor methanol levels greater than 127 ± 38.9 mg/dL more than one pathologic features were detected.

Fatal methanol poisoning: features of liver histopathology

Methanol poisoning has become a considerable problem in Iran. Liver can show some features of poisoning after methanol ingestion. Therefore, our concern was to examine liver tissue histopathology in fatal methanol poisoning cases in Iranian population. In this study, 44 cases of fatal methanol poisoning were identified in a year. The histological changes of the liver were reviewed. The most striking features of liver damage by light microscopy were micro-vesicular steatosis, macro-vesicular steatosis, focal hepatocyte necrosis, mild intra-hepatocyte bile stasis, feathery degeneration and hydropic degeneration. Blood and vitreous humor methanol concentrations were examined to confirm the proposed history of methanol poisoning. The majority of cases were men (86.36%). In conclusion, methanol poisoning can cause histological changes in liver tissues. Most importantly in cases with mean blood and vitreous humor methanol levels greater than 127 ± 38.9 mg/dL more than one pathologic features were detected.

Functional mapping of drug response with pharmacodynamic-pharmacokinetic principles

Recent research in pharmacogenomics has inspired our hope to predict drug response by linking it with DNA information extracted from the human genome. However, many genetic models of drug response do not incorporate biochemical principles of host-drug interactions, limiting the effectiveness of the predictive models. We argue that functional mapping, a computational tool aimed at identifying genes and genetic networks that control dynamic traits, can help explain the detailed genetic architecture of drug response by incorporating pharmacokinetic and pharmacodynamic processes. Functional mapping is particularly powerful in determining the genetic commonality and differences of drug efficacy vs. drug toxicity and drug sensitivity vs. drug resistance. We pinpoint several future directions in which functional mapping can be coupled with systems biology to unravel the genetic and metabolic machinery of drug response.

Bioethics and the reinforcement of socio-technical expectations

Over the past few years, considerable interest has been paid to the way in which social expectations (hopes, hypes, fears) about new genomic technologies help shape, and in themselves are shaped by, emerging technologies, regulatory regimes and social concerns. In comparison, little attention has been paid to the role of expectations in related, but non-scientific discourses, such as bioethics. Drawing on a review of publications addressing the ethical issues associated with pharmacogenetics, this paper presents a detailed critique of bioethicists' contribution to these debates. The review highlights how, almost a decade after bioethical debate around pharmacogenetics started, and in contrast to the profession's self-perception as a form of regulator, bioethicists still largely restrict themselves to reviews of possible ethical issues raised by this technology, rather than critiquing others' positions and arguing for specific points of view. In addition the paper argues that bioethicists tend to: accept unquestioningly scientists' expectations about the development and ethical issues raised by pharmacogenetics; ignore contributions from bioethicists who do question these expectations; and engage in an ethical debate, the boundaries of which have been laid down and defined by academic and industry scientists. The paper concludes by offering some possible explanations for why the bioethical discourse has taken this form.

[Biomarkers: "Found in translation"]

Despite continued increase in global Pharma R & D expenditure, the number of innovative drugs obtaining market approval has declined since 1994. The pharmaceutical industry is now entering a crucial juncture where increasing rates of attrition in clinical drug development as well as increasing development timelines are impacted by external factors such as intense regulatory pricing and safety pressures, increasing sales erosion due to generics, as well as exponential increases in the costs of bringing a drug to market. Despite these difficulties, numerous opportunities exist such as multiple unmet medical needs, the increasing incidence of certain diseases such as Alzheimer's disease, cancer, diabetes and obesity due to demographic changes, as well as the emergence of evolving markets such as China, India, and Eastern Europe. Consequently, Pharma is now responding to this challenge by improving both the productivity and the innovation in its drug discovery and development pipelines. In this regard, the advent of new technologies and expertise such as genomics, proteomics, structural biology, and molecular informatics in an integrated systems biology approach also provides a powerful opportunity for Pharma to address some of these difficulties. The key features behind this new strategy imply a discovery process based on an improved understanding of the molecular mechanism of diseases and drugs, translational research that places the patient at the center of the research process, and the application of biomarkers throughout the discovery and development phases. Moreover, new paradigms are required to improve target validation and develop more predictive cellular and animal models of human pathologies, a greater capacity in informatics-based analysis, and, consequently, a greater access to the vast sources of accumulating biological data and its integrated analysis. In the present review, we will address some of these issues and in particular emphasize how the application of biomarkers could potentially lead to improved productivity, quality, and innovation in drug discovery and ultimately better and safer medicines with improved therapeutic efficacy in specific pathologies for targeted patients.

Pharmacogenetic treatments for drug addiction: cocaine, amphetamine and methamphetamine

BACKGROUND

Pharmacogenetics uses genetic variation to predict individual differences in response to medications and holds much promise to improve treatment of addictive disorders.

OBJECTIVES

To review how genetic variation affects responses to cocaine, amphetamine, and methamphetamine and how this information may guide pharmacotherapy.

METHODS

We performed a cross-referenced literature search on pharmacogenetics, cocaine, amphetamine, and methamphetamine.

RESULTS

We describe functional genetic variants for enzymes dopamine-beta-hydroxylase (DbetaH), catechol-O-methyltransferase (COMT), and dopamine transporter (DAT1), dopamine D4 receptor, and brain-derived neurotrophic factor (BDNF). A single nucleotide polymorphism (SNP; C-1021T) in the DbetaH gene is relevant to paranoia associated with disulfiram pharmacotherapy for cocaine addiction. Individuals with variable number tandem repeats (VNTR) of the SLC6A3 gene 3'-untranslated region polymorphism of DAT1 have altered responses to drugs. The 10/10 repeat respond poorly to methylphenidate pharmacotherapy and the 9/9 DAT1 variant show blunted euphoria and physiological response to amphetamine. COMT, D4 receptor, and BDNF polymorphisms are linked to methamphetamine abuse and psychosis.

CONCLUSIONS

Disulfiram and methylphenidate pharmacotherapies for cocaine addiction are optimized by considering polymorphisms affecting DbetaH and DAT1 respectively. Altered subjective effects for amphetamine in DAT1 VNTR variants suggest a 'protected' phenotype.

SCIENTIFIC SIGNIFICANCE

Pharmacogenetic-based treatments for psychostimulant addiction are critical for successful treatment.

Pharmacogenetic treatments for drug addiction: alcohol and opiates

AIMS

Psychiatric pharmacogenetics involves the use of genetic tests that can predict the effectiveness of treatments for individual patients with mental illness such as drug dependence. This review aims to cover these developments in the pharmacotherapy of alcohol and opiates, two addictive drugs for which we have the majority of our FDA approved pharmacotherapies.

METHODS

We conducted a literature review using Medline searching terms related to these two drugs and their pharmacotherapies crossed with related genetic studies.

RESULTS

Alcohol's physiological and subjective effects are associated with enhanced beta-endorphin release. Naltrexone increases baseline beta-endorphin release blocking further release by alcohol. Naltrexone's action as an alcohol pharmacotherapy is facilitated by a putative functional single nucleotide polymorphism (SNP) in the opioid mu receptor gene (Al18G) which alters receptor function. Patients with this SNP have significantly lower relapse rates to alcoholism when treated with naltrexone. Caucasians with various forms of the CYP2D6 enzyme results in a 'poor metabolizer' phenotype and appear to be protected from developing opioid dependence. Others with a "ultra-rapid metabolizer" phenotype do poorly on methadone maintenance and have frequent withdrawal symptoms. These patients can do well using buprenorphine because it is not significantly metabolized by CYP2D6.

CONCLUSIONS

Pharmacogenetics has great potential for improving treatment outcome as we identify gene variants that affect pharmacodynamic and pharmacokinetic factors. These mutations guide pharmacotherapeutic agent choice for optimum treatment of alcohol and opiate abuse and subsequent relapse.

Pharmacogenetics of glucose-lowering drug treatment: a systematic review

Intensive blood glucose lowering can significantly reduce the risk of micro- and macrovascular complications in patients with diabetes mellitus. However, 30% of all treated patients do not achieve optimal blood glucose levels. Genetic factors may influence the response to glucose-lowering medication. A search of MEDLINE-indexed literature published between January 1966 and July 2007 revealed 37 studies reporting data on genetic polymorphisms and response to glucose-lowering drugs. Most studies involving cytochrome P450 (CYP) genes had small sample sizes (21 studies <50 subjects) and were among healthy volunteers. Multiple studies indicated that the CYP2C9 *3 allele (Ile359Leu polymorphism) was associated with decreased clearance of sulfonylurea drugs. Supporting this, one study reported an increased insulin secretion in CYP2C9*3 allele carriers when using the sulfonylurea agent glyburide. The CYP2C9*3 allele was also associated with a decreased clearance of meglitinides, whereas the CYP2C8*3 (Arg139Lys; Lys399Arg) variant increased the clearance of meglitinides. Polymorphisms in genes encoding the inwardly rectifying potassium channel Kir6.2 (KCNJ11) and the insulin receptor substrate-1 (IRS1) were reported to be associated with an increased risk of (secondary) failure to respond to sulfonylurea therapy. A significant decrease in fasting plasma glucose and hemoglobin A(1c) (HbA(1c)) in response to rosiglitazone was seen in subjects carrying the Pro12Ala polymorphism of the peroxisome proliferator-activated receptor-gamma (PPARG) gene. Conversely, carriers of this polymorphism also had a higher conversion to diabetes mellitus when treated with acarbose; this effect was also seen in adiponectin (ADIPOQ) gene polymorphism carriers. Future studies with adequate sample sizes in which several SNPs in multiple candidate genes are genotyped in patients with diabetes should provide reliable information on genetic variants and response to glucose-lowering drugs.

Pharmacogenetics of major depression: insights from level 1 of the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial

Major depression is a serious mental illness frequently associated with devastating consequences for those affected. Suicide rates are significantly elevated, creating a sense of urgency to identify effective yet safe treatment options. A plethora of antidepressants are available on the market today, designed to act on different neurotransmitter systems in the brain, providing the clinician with several treatment strategies. There is, however, very little guidance as to which antidepressant may be most successful in a certain individual. Biomarkers that can predict treatment outcome would thus be of great value, shortening the time until remission and reducing costs for the healthcare system by reducing unsuccessful treatment attempts. The proven contribution of heredity to major depression risk suggests that genetic markers may be good biomarkers for treatment outcome.The Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study and a large ancillary pharmacogenetic study in 1953 STAR*D participants constitute the largest effort to date to identify genetic predictors of antidepressant treatment outcome. In this review, the results of candidate gene studies carried out so far are summarized and discussed, and some future directions are proposed.

From evidence-based medicine to genomic medicine

The concept of 'evidence-based medicine' dates back to mid-19th century or even earlier. It remains pivotal in planning, funding and in delivering the health care. Clinicians, public health practitioners, health commissioners/purchasers, health planners, politicians and public seek formal 'evidence' in approving any form of health care provision. Essentially 'evidence-based medicine' aims at the conscientious, explicit and judicious use of the current best evidence in making decisions about the care of individual patients. It is in fact the 'personalised medicine' in practice. Since the completion of the human genome project and the rapid accumulation of huge amount of data, scientists and physicians alike are excited on the prospect of 'personalised health care' based on individual's genotype and phenotype. The first decade of the new millennium now witnesses the transition from 'evidence-based medicine' to the 'genomic medicine'. The practice of medicine, including health promotion and prevention of disease, stands now at a wide-open road as the scientific and medical community embraces itself with the rapidly expanding and revolutionising field of genomic medicine. This article reviews the rapid transformation of modern medicine from the 'evidence-based medicine' to 'genomic medicine'.

Validation of a CYP2D6 Genotyping Panel on the NanoChip Molecular Biology Workstation

Background: CYP2D6 is a highly polymorphic phase I enzyme that metabolizes 20%–25% of clinically used drugs. The objective of this study was to validate a CYP2D6 genotyping assay with the NanoChip® Molecular Biology Workstation.

Methods: We genotyped 200 anonymized human DNA samples with the Pyrosequencing® platform at the Medical College of Wisconsin and with the NanoChip platform at Dartmouth Medical School. We compared CYP2D6 genotypes and resolved samples with genotypic discrepancies with the Jurilab CYP2D6 duplication/deletion assay or with traditional DNA sequencing. The Jurilab assay is a long-range PCR assay used to evaluate sequence structures 3′ of the CYP2D7 and CYP2D6 coding regions. For the NanoChip platform, we performed multipad addressing and duplicate runs to test the intra- and intercartridge precision, within- and between-run precision, and reproducibility of the defined genotypes.

Results: We used both platforms to genotype all 200 DNA samples for CYP2D6*3, *4, *5, *6, *7, *8, and gene duplication. The 2 methods showed 99.4% concordance in the genotyping results; we found only 8 discrepant genotypes among 1400 DNA analyses. Confirmatory molecular analysis of the discrepant genotypes revealed that the NanoChip assay showed better agreement. The imprecision of the NanoChip method (CV) was 8.9%–17.7%.

Conclusions: This validation study of the NanoChip electronic microarray–based CYP2D6 genotyping assay revealed a CV &lt;20% and good concordance with the Pyrosequencing method and a confirmatory sequencing method.

Common laboratory methods in pharmacogenomics studies

PURPOSE

Common laboratory methods used in pharmacogenomics studies are described.

SUMMARY

The reliable and accurate determination of a person's genetic makeup at a particular locus in the DNA molecule, or genotype, is fundamental to pharmacogenomics. Whole blood cells and buccal cells are commonly collected to obtain a DNA sample. Once DNA is collected, the genomic DNA must be isolated from other cellular material. Next, a specific region of interest must be identified and amplified, performed via polymerase chain reaction (PCR). Gel electrophoresis is often performed after PCR to verify that PCR was successful and that the amplified target sequence is the correct size. Numerous methods are available to determine a person's genotype and differ based on allele discrimination and detection. PCR coupled with restriction fragment length polymorphism (RFLP) analysis, a conventional genotyping method, does not rely on automated technology and is practical for laboratories that genotype a limited number of samples. Pyrosequencing is an automated genotyping method in which the principal allele discrimination method is a primer extension reaction coupled with a luciferase-based enzyme reaction. TaqMan relies on the use of fluorescencelabeled probes, in addition to PCR primers, in the reaction mixture, enabling PCR amplification and allele discrimination in the same step. Mass spectrometry differentiates DNA molecules using a defined mass. Denaturing high-performance liquid chromatography (DHPLC) uses a reverse-phase ion-pair column to discriminate between variant and nonvariant alleles.

CONCLUSION

An understanding of the common genotyping methods used in pharmacogenomics studies, including PCR-RFLP analysis, pyrosequencing, TaqMan, mass spectrometry, and DHPLC, will aid pharmacy practitioners and students when interpreting the methods sections of such studies.

Nutrigenomics: integrating genomic approaches into nutrition research

It has been suggested that the supermarket of today will be the pharmacy of tomorrow. Such statements have been derived from recognition of our increasing ability to optimize nutrition, and maintain a state of good health through longer periods of life. The new field of nutrigenomics, which focuses on the interaction between bioactive dietary components and the genome, recognizes that current nutritional guidelines may be ideal for only a relatively small proportion of the population. There is good evidence that nutrition has significant influences on the expression of genes, and, likewise, genetic variation can have a significant effect on food intake, metabolic response to food, individual nutrient requirements, food safety, and the efficacy of disease-protective dietary factors. For example, a significant number of human studies in various areas are increasing the evidence for interactions between single nucleotide polymorphisms (SNPs) in various genes and the metabolic response to diet, including the risk of obesity. Many of the same genetic polymorphisms and dietary patterns that influence obesity or cardiovascular disease also affect cancer, since overweight individuals are at increased risk of cancer development. The control of food intake is profoundly affected by polymorphisms either in genes encoding taste receptors or in genes encoding a number of peripheral signaling peptides such as insulin, leptin, ghrelin, cholecystokinin, and corresponding receptors. Total dietary intake, and the satiety value of various foods, will profoundly influence the effects of these genes. Identifying key SNPs that are likely to influence the health of an individual provides an approach to understanding and, ultimately, to optimizing nutrition at the population or individual level. Traditional methods for identification of SNPs may involve consideration of individual variants, using methodologies such as restriction fragment length polymorphisms or quantitative real-time PCR assays. New developments allow identification of up to 500,000 SNPs in an individual, and with increasingly lowered pricings these developments may explode the population-level potential for dietary optimization based on nutrigenomic approaches.

Status of clinical gene sequencing data reporting and associated risks for information loss

Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict risks from toxin exposures, and inform nutritional needs. Despite the significance of sequencing, methods for reporting results are problematic. Frequent use of paper and infrequent use of naming standards impede data exchange and make incorporation into the electronic medical record difficult. Reports often describe only variations found, rather than all data (all patient bases sequenced). Also, reports frequently do not describe reference data used to define variations. These practices create risks for loss of both data and information. Standardized electronic reporting of all data (all bases sequenced and all reference data) and electronic record systems capable of storing these results would both prevent data loss and simplify the preservation of information those data provide.