Pharmacogenetics and the concept of individualized medicine

Precision medicine activities and opportunities for shaping maternal and neonatal health in Qatar

Precision Medicine (PM) is a transformative clinical medicine strategy that aims to revolutionize healthcare by leveraging biological information and biomarkers. In the context of maternal and neonatal health, PM enables personalized care from preconception through the postnatal period. Qatar has emerged as a key player in PM research, with dedicated programs driving advancements and translating cutting-edge research into clinical applications. This article delves into neonatal and maternal health in Qatar, emphasizing PM programs and initiatives that have been implemented. It also features noteworthy clinical cases that demonstrate the effectiveness of precision interventions. Furthermore, the article highlights the role of pharmacogenomics in addressing various maternal health conditions. The review further explores potential advancements in the application of PM in maternal and neonatal healthcare in Qatar.

Precision Medicine in Parkinson's Disease Using Induced Pluripotent Stem Cells

Parkinson's disease (PD) is one of the most devastating neurological diseases; however, there is no effective cure yet. The availability of human induced pluripotent stem cells (iPSCs) provides unprecedented opportunities to understand the pathogenic mechanism and identification of new therapy for PD. Here a new model system of PD, including 2D human iPSC-derived midbrain dopaminergic (mDA) neurons, 3D iPSC-derived midbrain organoids (MOs) with cellular complexity, and more advanced microphysiological systems (MPS) with 3D organoids, is introduced. It is believed that successful integrations and applications of iPSC, organoid, and MPS technologies can bring new insight on PD's pathogenesis that will lead to more effective treatments for this debilitating disease.

A Study on Associations of Long Noncoding RNA HOTAIR Polymorphisms With Genetic Susceptibility to Chronic Kidney Disease

BACKGROUND

The importance of long noncoding RNAs (lncRNAs) in various biological processes has been increasingly recognized in recent years. This study investigated how gene polymorphism in HOX transcript antisense RNA (HOTAIR) lncRNA affects the predisposition to chronic kidney disease (CKD).

METHODS

This study comprised 150 patients with CKD and 150 healthy controls. A PCR-RFLP and ARMS-PCR techniques were used for genotyping the five target polymorphisms.

RESULTS

According to our findings, rs4759314 confers strong protection against CKD in allelic, dominant, and codominant heterozygote genetic patterns. Furthermore, rs3816153 decreased CKD risk by 78% when TT versus GG, 55% when GG+GT versus TT, and 74% when GT versus TT+GG. In contrast, the CC+CT genotype [odds ratio (OR) = 1.66, 95% confidence intervals (CIs) = 1.05-2.63] and the T allele (OR = 1.50, 95% CI = 1.06-2.11) of rs12826786, as well as the TT genotype (OR = 2.52, 95% CI = 1.06-5.98) of rs3816153 markedly increased the risk of CKD in the Iranian population. Although no linkage disequilibrium was found between the studied variants, the Crs12826786Trs920778Grs1899663Grs4759314Grs3816153 haplotype was associated with a decreased risk of CKD by 86% (OR = 0.14, 95% CI = 0.03-0.66).

CONCLUSION

The rs920778 was not correlated with CKD risk, whereas the HOTAIR rs4759314, rs12826786, rs1899663, and rs3816153 polymorphisms affected the risk of CKD in our population. It seems essential to conduct repeated studies across various ethnic groups to explore the link between HOTAIR variants and their impact on the disease outcome.

Unlocking the Potential of Therapy-Induced Cytokine Responses: Illuminating New Pathways in Cancer Precision Medicine

Precision cancer medicine primarily aims to identify individual patient genomic variations and exploit vulnerabilities in cancer cells to select suitable patients for specific drugs. These genomic features are commonly determined by gene sequencing prior to therapy, to identify individuals who would be most responsive. This precision approach in cancer therapeutics remains a powerful tool that benefits a smaller pool of patients, sparing others from unnecessary treatments. A limitation of this approach is that proteins, not genes, are the ultimate effectors of biological functions, and therefore the targets of therapeutics. An additional dimension in precision medicine that considers an individual's cytokine response to cancer therapeutics is proposed. Cytokine responses to therapy are multifactorial and vary among individuals. Thus, precision is dictated by the nature and magnitude of cytokine responses in the tumor microenvironment exposed to therapy. This review highlights cytokine responses as modules for precision medicine in cancer therapy, including potential challenges. For solid tumors, both detectability of cytokines in tissue fluids and their being amenable to routine sensitive analyses could address the difficulty of specimen collection for diagnosis and monitoring. Therefore, in precision cancer medicine, cytokines offer rational targets that can be utilized to enhance the efficacy of cancer therapy.

Measurement of CYP1A2 and CYP3A4 activity by a simplified Geneva cocktail approach in a cohort of free-living individuals: a pilot study

Introduction: The cytochrome P450 enzyme subfamilies, including CYP3A4 and CYP1A2, have a major role in metabolism of a range of drugs including several anti-cancer treatments. Many factors including environmental exposures, diet, diseaserelated systemic inflammation and certain genetic polymorphisms can impact the activity level of these enzymes. As a result, the net activity of each enzyme subfamily can vary widely between individuals and in the same individual over time. This variability has potential major implications for treatment efficacy and risk of drug toxicity, but currently no assays are available for routine use to guide clinical decision-making. Methods: To address this, a mass spectrometry-based method to measure activities of CYP3A4, CYP1A2 was adapted and tested in free-living participants. The assay results were compared with the predicted activity of each enzyme, based on a self-report tool capturing diet, medication, chronic disease state, and tobacco usage. In addition, a feasibility test was performed using a low-volume dried blood spots (DBS) on two different filter-paper supports, to determine if the same assay could be deployed without the need for repeated standard blood tests. Results: The results confirmed the methodology is safe and feasible to perform in free-living participants using midazolam and caffeine as test substrates for CYP3A4 and CYP1A2 respectively. Furthermore, though similar methods were previously shown to be compatible with the DBS format, the assay can also be performed successfully while incorporating glucuronidase treatment into the DBS approach. The measured CYP3A4 activity score varied 2.6-fold across participants and correlated with predicted activity score obtained with the self-report tool. The measured CYP1A2 activity varied 3.5-fold between participants but no correlation with predicted activity from the self-report tool was found. Discussion: The results confirm the wide variation in CYP activity between individuals and the important role of diet and other exposures in determining CYP3A4 activity. This methodology shows great potential and future cross-sectional and longitudinal studies using DBS are warranted to determine how best to use the assay results to guide drug treatments.

Pharmacogenomic evaluation of CYP2C19 alleles linking low clopidogrel response and the risk of acute coronary syndrome in Indians

BACKGROUND

Clopidogrel is an antiplatelet drug widely prescribed to prevent atherothrombotic events in coronary artery disease patients. However, there is evidence to suggest that the effectiveness of clopidogrel varies owing to genetic diversity in CYP2C19. This heterogeneity in South Asians, who are also known to have high risk of cardiac events than other population groups, highlights the importance of investigating CYP2C19 variants to estimate the risk proportion in the groups.

METHODS

Given the high prevalence and genetic heterogeneity, the population-based case control was conducted in a cohort of 1191 subjects comprising 645 acute coronary syndrome (ACS) cases (unstable angina, ST-elevation myocardial infarction, and non-ST-elevation myocardial infarction) and 546 healthy controls of South Asian Indian origin. The metabolization status of CYP2C19 was assessed using *2, *3 and *17 variants in the stated cohorts to determine the prevalence of metabolization and its association with phenotypes.

RESULTS

The results suggest a possible genetic association between studied CYP2C19 polymorphisms and ACS, since there was a higher proportion of intermediate and poor metabolizers present in the studied cohorts. The association analyses revealed that the *2 allele of CYP2C19 confers a significant risk for ACS, while the *17 allele provides protection.

CONCLUSIONS

These findings contribute to the understanding of CYP2C19 genetic variants and their impact on clopidogrel response in South Asian Indians. Additionally, they underline the significance of assessing CYP2C19 variations in patients receiving clopidogrel therapy in order to improve therapeutic outcomes.

Virtual Screening of Different Subclasses of Lignans with Anticancer Potential and Based on Genetic Profile

Cancer is a multifactorial disease that continues to increase. Lignans are known to be important anticancer agents. However, due to the structural diversity of lignans, it is difficult to associate anticancer activity with a particular subclass. Therefore, the present study sought to evaluate the association of lignan subclasses with antitumor activity, considering the genetic profile of the variants of the selected targets. To do so, predictive models were built against the targets tyrosine-protein kinase ABL (ABL), epidermal growth factor receptor erbB1 (EGFR), histone deacetylase (HDAC), serine/threonine-protein kinase mTOR (mTOR) and poly [ADP-ribose] polymerase-1 (PARP1). Then, single nucleotide polymorphisms were mapped, target mutations were designed, and molecular docking was performed with the lignans with the best predicted biological activity. The results showed more anticancer activity in the dibenzocyclooctadiene, furofuran and aryltetralin subclasses. The lignans with the best predictive values of biological activity showed varying binding energy results in the presence of certain genetic variants.

Considerations for Embedding Inclusive Research Principles in the Design and Execution of Clinical Trials

There is a growing recognition that the clinical research enterprise has a diversity problem, given that many clinical trials recruit historically marginalized individuals or patients reflective of real-world data at a rate that is far below the incidence and prevalence of the disease for which the investigational therapy or device is targeting. This lack of diversity in clinical research participation can obscure the safety and efficacy of drug therapies and limits our collective ability to develop effective treatments for all patients, leading to even wider health disparities. This review article provides an in-depth analysis of the impact of this bias on public health, along with a description of some of the barriers that prevent historically marginalized populations from participating in clinical research. Some practical solutions that can be employed to increase diversity in clinical trial participation are also discussed, including the crucial role clinical trial sponsors, research organizations, patients, and caregivers need to play in supporting the industry to achieve this ambitious but necessary goal.

Pharmacogenetics of ABCB1, CDA, DCK, GSTT1, GSTM1 and outcomes in a cohort of pediatric acute myeloid leukemia patients from Colombia

BACKGROUND AND AIM

Different studies have shown pharmacogenetic variants related to drug toxicity in acute myeloid leukemia (AML) patients. Our aim was to identify the association between ABCB1, CDA, DCK, GSTT1, and GSTM1 variants with clinical outcomes and toxicity in pediatric patients with AML.

METHODS

Fifty-one confirmed de novo AML pediatric patients were included. A SNaPshot™ assay and conventional PCR were used to evaluate ABCB1, CDA, DCK, GSTT1, and GSTM1 variants. Clinical outcomes and toxicity associations were evaluated using odds ratios and Chi-square analysis.

RESULTS

Patients carrying ABCB1 (1236C > T, rs1128503) GG genotype in had a 6.8 OR (CI 95% 1.08-42.73, p = .044) for cardiotoxicity as compared to patients carrying either AA or GA genotypes 0.14 OR (CI 95% 0.023-0.92, p = .044). For ABCB1 (1236G > A rs1128503/2677C > A/T rs2032582/3435G > A rs1045642) AA/AA/AA combined genotypes had a strong association with death after HSTC OR 13.73 (CI 95% 1.94-97.17, p = .009). Combined genotypes GG/CC/GG with CDA (79A > C, rs2072671) CA genotype or CDA (-451G > A, rs532545) CT genotype, had a 4.11 OR (CI 95% 2.32-725, p = .007) and 3.8 OR (CI 95% 2.23-6.47, p = .027) with MRD >0.1% after first chemotherapy cycle, respectively.

CONCLUSION

Our results highlight the importance of pharmacogenetic analysis in pediatric AML, particularly in populations with a high degree of admixture, and might be useful as a future tool for patient stratification for treatment.

Influence of CYP2B6 and CYP3A4 polymorphisms on the virologic and immunologic responses of patients treated with efavirenz-containing regimen

OBJECTIVES

The main objective of this study was to evaluate the effect of CYP2B6 and CYP3A4 polymorphisms on the virological and immunologic responses of HIV patients. A total of 153 HIV-positive patients were enlisted for the study.

PATIENTS AND METHODS

Viral load and median CD4 T cell counts were evaluated at baseline and month 6 (M6). Samples were identified using TaqMan genotyping assays.

RESULTS

The AG in CYP2B6 rs2279343 was associated with VLS compared to homozygous AA. In the dominant model, the AG/GG genotypes were associated with VLS compared to the AA genotype. Moreover, in overdominant model, the AG genotype was associated with VLS compared to AA/GG. Regarding immunological response, only the AG in SNP rs2279343 CYP2B6 was associated with an increase in CD4 cell count between baseline and M6. In CYP2B6 rs3745274, the CD4 cell count at M6 was higher than that of baseline for GG carriers and for GT carriers. In CYP3A4 rs2740574, the TC carriers showed a higher median CD4 count at M6 compared to that of the baseline count, as well as for CC carriers. The best genotypes combination associated with CD4 cell count improvement were AA/AG in SNP rs2279343 and GG/GT in SNP rs3745274.

CONCLUSION

Our findings support the fact that CYP2B6 rs2279343 could help in the prediction of VLS and both SNPs rs3745274 and rs2279343 in CYP2B6 and CYP3A4 rs2740574 were associated with immune recovery in Malian HIV-positive patients.

Evaluation of the need for pharmacogenomics testing among physicians in the West Bank of Palestine

OBJECTIVES

Pharmacogenomics (PGx) testing optimizes pharmacotherapy and reduces interindividual variation in drug responses. However, it is still not implemented in clinical practice in the West Bank of Palestine (WBP). The aim of this study was to determine the need for PGx education and testing among physicians from different specialties in WBP.

METHODS

This study used a cross-sectional survey that was administered to 381 physicians from different cities in WBP. The questionnaire consisted of 27 closed-ended questions that evaluate the exposure and attitude toward PGx education, the role of PGx testing in clinical practice, and the capabilities of physicians in PGx testing.

RESULTS

It was found that exposure to PGx education is low, with most of the respondents (81.1%) answering that PGx was not an integral part of their medical education. The majority (>90%) of the participants agreed that PGx should be included in the medical school curriculum. It was also found that 58.5% of the participants agreed that PGx testing is relevant to their current clinical practice. In addition, most of the participant physicians (>60%) think that they are currently not capable of prescribing and making decisions for pharmacotherapy based on PGx testing.

CONCLUSIONS

It is concluded that there is a high need for PGx education and implementation in clinical practice in WBP. We recommend adding PGx courses to the curricula of medical schools and going forward with the implementation of PGx testing in clinical practice in WBP.

Evaluation of the need for pharmacogenomics testing among physicians in the West Bank of Palestine

OBJECTIVES

Pharmacogenomics (PGx) testing optimizes pharmacotherapy and reduces interindividual variation in drug responses. However, it is still not implemented in clinical practice in the West Bank of Palestine (WBP). The aim of this study was to determine the need for PGx education and testing among physicians from different specialties in WBP.

METHODS

This study used a cross-sectional survey that was administered to 381 physicians from different cities in WBP. The questionnaire consisted of 27 closed-ended questions that evaluate the exposure and attitude toward PGx education, the role of PGx testing in clinical practice, and the capabilities of physicians in PGx testing.

RESULTS

It was found that exposure to PGx education is low, with most of the respondents (81.1%) answering that PGx was not an integral part of their medical education. The majority (>90%) of the participants agreed that PGx should be included in the medical school curriculum. It was also found that 58.5% of the participants agreed that PGx testing is relevant to their current clinical practice. In addition, most of the participant physicians (>60%) think that they are currently not capable of prescribing and making decisions for pharmacotherapy based on PGx testing.

CONCLUSIONS

It is concluded that there is a high need for PGx education and implementation in clinical practice in WBP. We recommend adding PGx courses to the curricula of medical schools and going forward with the implementation of PGx testing in clinical practice in WBP.

Investigations of process parameters during dissolution studies of drug loaded 3D printed tablets

The present research paper attempts to study the effect of different process parameters on the dissolution rate during 3D printed tablets. Three-dimensional printing has the potential of serving tailored made tablets to cater personalized drug delivery systems. Fluorescein loaded PVA filaments through impregnation route was used to fabricate tablets based on Taguchi based design of experimentation using Fused Deposition Modelling (FDM). The effect of print speed, infill percentage and layer thickness were analyzed to study the effect on rate of dissolution. Infill percentage followed by print speed were found to be critical parameters affecting dissolution rate. The data analysis provided an insight into the study of interaction among different 3D printing parameters to develop an empirical relation for percentage release of the drug in human body.

Hot-Melt 3D Extrusion for the Fabrication of Customizable Modified-Release Solid Dosage Forms

In this work, modified-release solid dosage forms were fabricated by adjusting geometrical properties of solid dosage forms through hot-melt 3D extrusion (3D HME). Using a 3D printer with air pressure driving HME system, solid dosage forms containing ibuprofen (IBF), polyvinyl pyrrolidone (PVP), and polyethylene glycol (PEG) were printed by simultaneous HME and 3D deposition. Printed solid dosage forms were evaluated for their physicochemical properties, dissolution rates, and floatable behavior. Results revealed that IBF content in the solid dosage form could be individualized by adjusting the volume of solid dosage form. IBF was dispersed as amorphous state with enhanced solubility and dissolution rate in a polymer solid dosage form matrix. Due to absence of a disintegrant, sustained release of IBF from printed solid dosage forms was observed in phosphate buffer at pH 6.8. The dissolution rate of IBF was dependent on geometric properties of the solid dosage form. The dissolution rate of IBF could be modified by merging two different geometries into one solid dosage form. In this study, the 3D HME process showed high reproducibility and accuracy for preparing dosage forms. API dosage and release profile were found to be customizable by modifying or combining 3D modeling.

Genetic Analysis of Pharmacogenomic VIP Variants of ABCB1, VDR and TPMT Genes in an Ethnically Isolated Population from the North Caucasus Living in Jordan

Background:

Differences in individual responses to the same medications remarkably differ among populations. A number of genes that play integral roles in drug responses have been designated as very important pharmacogenes (VIP), as they are responsible for differences in drug safety, efficacy, and adverse drug reactions among certain ethnic groups. Identifying the polymorphic distribution of VIP in a range of ethnic groups will be conducive to population-based personalized medicine.

Objective:

The aim of the current study is to identify the polymorphic distribution of VIP regarding the Chechen minority group from Jordan and compare their allele frequencies with other populations.

Methods:

A total of 131 unrelated Chechen individuals from Jordan were randomly recruited for blood collection. Identification of allelic and genotypic frequencies of eleven VIP variants within the genes of interest (ABCB1, VDR and TPMT) was carried out by means of the MassARRAY®System (iPLEX GOLD).

Results:

Within ABCB1, we found that the minor allele frequencies of the rs1128503 (A: 0.43), rs2032582 (A: 0.43), rs1045642 (A: 0.43). For VDR, the minor allele frequencies of rs11568820 (T: 0.18), rs1540339 (T: 0.30), rs1544410 (T: 0.41), rs2228570 (T: 0.24), rs3782905 (C: 0.28) and rs7975232 (C: 0.45). Finally, the minor allele frequencies for the TPMT rs1142345 and rs1800460 polymorphisms were found to be (C: 0.02) and (T: 0.01), respectively.

Conclusion:

Significant differences in allelic frequencies of eleven ABCB1, VDR and TPMT VIP variants were found between Jordanian Chechens and other populations. In our study, most populations that are similar to Chechens are those from South Asian, European (Finnish) and European, including: Utah residents with Northern and Western European ancestry, Toscani in Italia, Mexican ancestry in Los Angeles and Circassian from Jordan. The level of similarity between Chechens and those populations means that they might have shared high levels of gene flow in the past. The results obtained in this study will contribute to the worldwide pharmacogenomic databases and provide valuable information for future studies and better individualized treatments.

Pharmacogenomic landscape of VIP genetic variants in Jordanian Arabs and comparison with worldwide populations

The pharmacogenomics has lately become a focal field of research that investigates the influence of genetic variations of drug-metabolizing enzymes and their receptors and downstream proteins on the interindividual variability in response to medications and adverse drug reactions. Therefore, it is significantly important to study and analyze the variations in drug response between different ethnic groups and populations. The current study aimed to detect the distribution of the genotype and allele frequencies in several very important pharmacogenetic (VIP) gene polymorphisms in the Jordanian population of Arab descent. This study involved 500 unrelated Jordanian individuals of Arab descent. A total of 65 VIP variants located within 33 candidate genes were randomly selected from the PharmGKB database and genotyped using the MassARRAY (iPLEX GOLD) system. The chi-square test was used to evaluate the significant differences of minor allele and genotype frequencies between the Jordanian and other populations including CHE, ASW, CEU, CHB, CDX, GIH, GBR, JPT, LWK, MXL, TSI, YRI, CAR, and ACB. This study revealed six variants were not in Hardy Weinberg equilibrium (HWE) (P-value > 0.05) and ten SNPs showed monomorphic features. Most of the remaining forty-nine variant frequencies were significantly different from the compared ethnic groups (P-value < 0.05). The results of this study may be helpful to develop safer treatment by applying the concept of personalized medicine based on the profile of VIP pharmacogene variants of the Jordanian population of Arab descent.

Genetic Polymorphisms of Pharmacogenes among the Genetically Isolated Circassian Subpopulation from Jordan

Several genetic variants have been identified that cause variation among different populations and even within individuals of a similar descent. This leads to interindividual variations in the optimal dose of the drug that is required to sustain the treatment efficiency. In this study, 56 single nucleotide polymorphisms (SNPs) within several pharmacogenes were analyzed in 128 unrelated subjects from a genetically isolated group of Circassian people living in Jordan. We also compared these variant distributions to other ethnic groups that are available at two databases (Genome 1000 and eXAC). Our results revealed that the distribution of allele frequencies within genes among Circassians in Jordan showed similarities and disparities when compared to other populations. This study provides a powerful base for clinically relevant SNPs to enhance medical research and future pharmacogenomic studies. Rare variants detected in isolated populations can significantly guide to novel loci involved in the development of clinically relevant traits.

3D-Printed Solid Dispersion Drug Products

With the well-known advantages of additive manufacturing methods such as three-dimensional (3D) printing in drug delivery, it is disappointing that only one product has been successful in achieving regulatory approval in the past few years. Further research and development is required in this area to introduce more 3D printed products into the market. Our study investigates the potential of fixed dose combination solid dispersion drug products generated via 3D printing. Two model drugs-fluorescein sodium (FS) and 5-aminosalicyclic acid (5-ASA)-were impregnated onto a polyvinyl alcohol (PVA) filament, and the influence of solvent choice in optimal drug loading as well as other influences such as the physicochemical and mechanical properties of the resultant filaments were investigated prior to development of the resultant drug products. Key outcomes of this work included the improvement of filament drug loading by one- to threefold due to solvent choice on the basis of its polarity and the generation of a 3D-printed product confirmed to be a solid dispersion fixed dose combination with the two model drugs exhibiting favourable in vitro dissolution characteristics.

Three-Dimensional (3-D) Printing Technology Exploited for the Fabrication of Drug Delivery Systems

BACKGROUND

The conventional dosage forms cannot be administered to all patients because of interindividual variability found among people of different race coupled with different metabolism and cultural necessities. Therefore, to address this global issue there is a growing focus on the fabrication of new drug delivery systems customised to individual needs. Medicinal products printed using 3-D technology are transforming the current medicine business to a plausible alternative of conventional medicines.

METHODS

The PubMed database and Google scholar were browsed by keywords of 3-D printing, drug delivery, and personalised medicine. The data about techniques employed in the manufacturing of 3-D printed medicines and the application of 3-D printing technology in the fabrication of individualised medicine were collected, analysed and discussed.

RESULTS

Numerous techniques can fabricate 3-D printed medicines however, printing-based inkjet, nozzle-based deposition and laser-based writing systems are the most popular 3-D printing methods which have been employed successfully in the development of tablets, polypills, implants, solutions, nanoparticles, targeted and topical dug delivery. In addition, the approval of Spritam® containing levetiracetam by FDA as the primary 3-D printed drug product has boosted its importance. However, some drawbacks such as suitability of manufacturing techniques and the available excipients for 3-D printing need to be addressed to ensure simple, feasible, reliable and reproducible 3-D printed fabrication.

CONCLUSION

3-D printing is a revolutionary in pharmaceutical technology to cater the present and future needs of individualised medicines. Nonetheless, more investigations are required on its manufacturing aspects in terms cost effectiveness, reproducibility and bio-equivalence.

3D Printing Technology in Drug Delivery: Recent Progress and Application

BACKGROUND

3D printing technology is a new chapter in pharmaceutical manufacturing and has gained vast interest in the recent past as it offers significant advantages over traditional pharmaceutical processes. Advances in technologies can lead to the design of suitable 3D printing device capable of producing formulations with intended drug release.

METHODS

This review summarizes the applications of 3D printing technology in various drug delivery systems. The applications are well arranged in different sections like uses in personalized drug dosing, complex drugrelease profiles, personalized topical treatment devices, novel dosage forms and drug delivery devices and 3D printed polypills.

RESULTS

This niche technology seems to be a transformative tool with more flexibility in pharmaceutical manufacturing. Typically, 3D printing is a layer-by-layer process having the ability to fabricate 3D formulations by depositing the product components by digital control. This additive manufacturing process can provide tailored and individualized dosing for treatment of patients different backgrounds with varied customs and metabolism pattern. In addition, this printing technology has the capacity for dispensing low volumes with accuracy along with accurate spatial control for customized drug delivery. After the FDA approval of first 3D printed tablet Spritam, the 3D printing technology is extensively explored in the arena of drug delivery.

CONCLUSION

There is enormous scope for this promising technology in designing various delivery systems and provides customized patient-compatible formulations with polypills. The future of this technology will rely on its prospective to provide 3D printing systems capable of manufacturing personalized doses. In nutshell, the 3D approach is likely to revolutionize drug delivery systems to a new level, though need time to evolve.

Genetic Polymorphisms of Pharmacogenomic VIP Variants in the Circassian Subpopulation from Jordan

BACKGROUND

It has been suggested that genetic variation within candidate pharmacogenes contributes to the differences in drug safety and efficacy as well as risk of adverse drug reactions among different ethnic groups. Illustrating the polymorphic distribution of Very Important Pharmacogenes (VIPs) in various ethnic groups will contribute to the development of personalized medicine for those populations.

OBJECTIVE

The present study aimed to identify the polymorphic distribution of VIPs in the Circassian subpopulation of Jordan and compare their allele frequencies with those of other populations.

METHODS

A total of 130 healthy and unrelated Circassian adults from Jordan were randomly recruited and genotyped for eleven VIP variants within the thiopurine S-methyltransferase (TPMT), ATP-binding cassette, sub-family B, member 1 (ABCB1), and vitamin D receptor (VDR) genes via Sequenom's MassARRAY® genotyping platform (iPLEX GOLD).

RESULTS

Our data on the allelic frequencies of the investigated VIP variants were compared to those of 18 other populations, comprising 11 HapMap populations, 6 Exome Aggregation Consortium populations, and the Chechen- Jordanian population from Jordan. Circassian-Jordanians were found to most resemble the African, Chechen- Jordanian, European (Finnish), European (non-Finnish), and South-Asian populations.

CONCLUSION

Circassians from Jordan significantly differ from other populations in terms of the allelic frequencies of selected VIP variants. The present findings constitute the first set of pharmacogenetic data for Circassian population from Jordan, providing a basis for safe drug administration that may be useful in diagnosing and treating diseases in this ethnic group.

[Influence of culture and religion on the treatment of cancer patients]

Religion, which is one of the most important sources of human identity, has so far hardly been taken into account in the clinic. In the largely secularized society of Germany, this has played a highly subordinate role. Currently, however, the development towards a multireligious society is emerging, which will also be reflected in everyday medical care. Disease and mortality in patients can affect different cultural-religious spheres. Although distinction between cultural and religious aspects is possible, it is not necessary for clinical practice. In the situation of oncological therapy, questions may arise which must be answered differently in the religions Christianity, Judaism and Islam and which should be taken into account when selecting therapy. The consideration of cultural-religious rules can intensify the patient's acceptance, but it can also impair it in case of disregard. Such peculiarities can be the separation into male and female spheres or the restriction of certain auxiliary substances or drugs (blood products, narcotics). Kübler-Ross's phase model is suitable for determining where cultural-religious sensitivities should be taken into account in the phases of disease and how cultural-religious offerings can benefit the course of therapy. Due to large individual, regional, cultural and confessional differences, no systematic catalogue of procedures can be provided here. However, knowledge of such differences, more sensitive interaction with patients and their families and cooperation with hospital pastors can strengthen the relationship of trust between doctor and patient and thus improve the conditions for successful oncological therapy. These aspects should not be underestimated when treating people of other faiths in Germany's secular society.

COPD patient education and support - Achieving patient-centredness

BACKGROUND

The art of medicine is undergoing a dramatic shift in focus, evolving to focus on patient involvement as partners in care, transforming the traditional, prescriptive, reactive practice of healthcare into a proactive discipline. The personal and societal burden of chronic diseases is burgeoning and unsustainable in current systems, novel approaches are required to address this.

DISCUSSION

Although considerable progress has been made in the development of diagnostics, therapeutics and care guidelines for patients with chronic obstructive pulmonary disease (COPD), questions remain surrounding the implementation of best practice education and support. Current educational programmes, personal limitations and preferences and patient-clinician communication in modification of coping styles and behaviour are discussed. A novel holistic model, the Kaleidoscope Model of Care is proposed to address the barriers to optimal self-care behaviours.

CONCLUSION AND PRACTICE IMPLICATIONS

Holistic approaches are essential for optimal self-management and improved outcomes. Guidance on personalised goals for patients to help meeting their therapy priorities is needed to aid healthcare professionals (HCPs) and funders to minimise healthcare burden and costs. The novel KALMOD approach may optimise patient empowerment, exploring whole-life factors that impact COPD care and improve interactions between patients and HCPs for optimised outcomes.

Prevalence of the CYP2C19*2 (681 G>A), *3 (636 G>A) and *17 (‑806 C>T) alleles among an Iranian population of different ethnicities

Polymorphisms in the cytochrome P (CYP) 450 family may cause adverse drug responses in individuals. Cytochrome P450 2C19 (CYP2C19) is a member of the CYP family, where the presence of the 681 G>A, 636 G>A and 806 C>T polymorphisms result in the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles, respectively. In the current study, the frequency of the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles in an Iranian population cohort of different ethnicities were examined and then compared with previously published frequencies within other populations. Allelic and genotypic frequencies of the CYP2C19 alleles (*2, *3 and *17) were detected using polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis, PCR-single-strand conformation polymorphism analysis and DNA sequencing from blood samples of 1,229 unrelated healthy individuals from different ethnicities within the Iranian population. The CYP2C19 allele frequencies among the Iranian population were 21.4, 1.7, and 27.1% for the CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles, respectively. The frequency of the homozygous A/A variant of the CYP2C19*2 allele was significantly high and low in the Lur (P<0.001) and Caspian (P<0.001) ethnicities, respectively. However, the frequency of the homozygous A/A variant of the CYP2C19*3 allele was not detected in the Iranian cohort in the current study. The frequency of the heterozygous G/A variant of the CYP2C19*3 allele had the significantly highest and lowest frequency in the Fars (P<0.001) and Lur (P<0.001) groups, respectively. The allele frequency of the homozygous T/T variant of the CYP2C19*17 allele was significantly high in the Caspian (P<0.001) and low in the Kurd (P<0.05) groups. The frequency of the CYP2C19 alleles involved in drug metabolism, may improve the clinical understanding of the ethnic differences in drug responses, resulting in the advancement of the personalized medicine among the different ethnicities within the Iranian population.

Optimization of Antidepressant use with Pharmacogenetic Strategies

BACKGROUND

The response rate in the pharmacological treatment of depression has been estimated to be around 50%, achieving a remission in symptomatology in only one third of the patients. Suboptimal prescription of antidepressants has been proposed as a significant explanatory factor for this therapeutic inefficacy. The use of pharmacogenetic testing might favor the optimization of pharmacotherapy in emotional disorders. However, its implementation in the clinical routine requires studies which prove its efficacy.

OBJECTIVE

The aim is to explore the clinical effects obtained by means of the personalization of antidepressant treatment derived from the pharmacogenetic profile of the individual.

METHOD

A sample of 291 patients under antidepressant treatment was selected, and these patients were genotyped for the most common polymorphisms of the CYP2D6, CYP2C9, CYP2C19 and CYP3A4/5 genes using RT-PCR and TaqMan® technology. 30 of them were subjected to psycho-affective assessment using the HDRS scale before and after a process of individualization of their psychopharmacological treatment in accordance with the genotype obtained.

RESULTS

70% of the individuals treated using the traditional criterion of trial-and-error were not taking the active ingredient most suited to their pharmacogenetic profile. The inclusion of this genetic information in the choice of drug and its dosage entailed a significant, progressive reduction in depressive symptomatology, with an efficacy ratio of 80% and a remission of the pathology in almost 30% of the cases.

CONCLUSION

These results suggest that the prescription of pharmacogenetic profile-based strategies has a positive effect on the therapeutic response to antidepressants.

Personalised 3D Printed Medicines: Which Techniques and Polymers Are More Successful?

The interindividual variability is an increasingly global problem when treating patients from different backgrounds with diverse customs, metabolism, and necessities. Dose adjustment is frequently based on empirical methods, and therefore, the chance of undesirable side effects to occur is high. Three-dimensional (3D) Printed medicines are revolutionsing the pharmaceutical market as potential tools to achieve personalised treatments adapted to the specific requirements of each patient, taking into account their age, weight, comorbidities, pharmacogenetic, and pharmacokinetic characteristics. Additive manufacturing or 3D printing consists of a wide range of techniques classified in many categories but only three of them are mostly used in the 3D printing of medicines: printing-based inkjet systems, nozzle-based deposition systems, and laser-based writing systems. There are several drawbacks when using each technique and also the type of polymers readily available do not always possess the optimal properties for every drug. The aim of this review is to give an overview about the current techniques employed in 3D printing medicines, highlighting their advantages, disadvantages, along with the polymer and drug requirements for a successful printing. The major application of these techniques will be also discussed.

Optimization of Antidepressant use with Pharmacogenetic Strategies

Background:

The response rate in the pharmacological treatment of depression has been estimated to be around 50%, achieving a remission in symptomatology in only one third of the patients. Suboptimal prescription of antidepressants has been proposed as a significant explanatory factor for this therapeutic inefficacy. The use of pharmacogenetic testing might favor the optimization of pharmacotherapy in emotional disorders. However, its implementation in the clinical routine requires studies which prove its efficacy.

Objective:

The aim is to explore the clinical effects obtained by means of the personalization of antidepressant treatment derived from the pharmacogenetic profile of the individual.

Method:

A sample of 291 patients under antidepressant treatment was selected, and these patients were genotyped for the most common polymorphisms of the CYP2D6, CYP2C9, CYP2C19 and CYP3A4/5 genes using RT-PCR and TaqMan® technology. 30 of them were subjected to psycho-affective assessment using the HDRS scale before and after a process of individualization of their psychopharmacological treatment in accordance with the genotype obtained.

Results:

70% of the individuals treated using the traditional criterion of trial-and-error were not taking the active ingredient most suited to their pharmacogenetic profile. The inclusion of this genetic information in the choice of drug and its dosage entailed a significant, progressive reduction in depressive symptomatology, with an efficacy ratio of 80% and a remission of the pathology in almost 30% of the cases.

Conclusion:

These results suggest that the prescription of pharmacogenetic profile-based strategies has a positive effect on the therapeutic response to antidepressants.

Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System

The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

Glutathione S-transferases deletions may act as prognosis and therapeutic markers in breast cancer

Breast cancer (BC) is the main worldwide neoplasia in women. The metabolic balance between xenobiotic absorption and elimination rates plays an important role in preventing DNA damage and, consequently, tumor development. The glutathione S-transferases (GSTs), such as GSTM1 and GSTT1, and the NAD(P)H quinone oxidoreductase are important enzymes involved in phase II detoxification reactions. Deletions in GSTM1 and GSTT1, and single-nucleotide polymorphism (SNP) in NQO1 (rs1800655) have been investigated in cancer context, revealing conflicting results. The present study analyzed these genetic polymorphisms in 121 BC patients and 151 BC-free controls in order to verify if they could act as susceptibility modifiers and/or prognostic factors. Binary logistic regressions adjusted by age were performed to assess associations between allelic variants and interactions in polymorphisms combination with BC susceptibility, but no significant association was found. Genotypes distribution was also compared between BC subtypes, but no significant difference was observed (p > 0.05). GSTM1 deletion was significantly associated with histopathological grade, with a greater proportion of patients presenting grade III tumors (p = 0.007). Univariate analysis identified tumor size as the only clinicopathological parameter potentially associated with recurrence risk in patients that received adjuvant chemotherapy (p < 0.1). Thus, logistic regression analysis adjusted by tumor size revealed a positive association between GSTT1 deletion and recurrence risk in general BC (OR 4.25; p = 0.04), while GSTM1 was negatively associated with recurrence risk in ER/PR⁺HER2^- samples (OR 0.07; p = 0.03). In conclusion, the present study indicated that GSTT1 deletion was associated with increased recurrence risk, while GSTM1 correlated with worst prognosis parameters at diagnosis, but was negatively associated with recurrence risk in luminal subtype samples.

Structured academic discussions through an online education-specific platform to improve Pharm.D. students learning outcomes

OBJECTIVE

To facilitate active academic discussions using an online, education-centered platform and reinforce concepts, in order to improve overall course outcomes.

MATERIALS AND METHODS

A third year integrated pharmacotherapy course was enrolled on an online searchable platform, Piazza®, to facilitate academic discussions. Students could ask, answer, and explore content, and build on submitted answers in wiki style in collaboration. Instructor posted learning objectives, endorsed student responses with correct answers and led follow-up discussions. Review sessions were conducted on this platform before all major exams. A student t-test was used to compare class performance with those of previous years.

RESULTS

In a post-activity qualitative survey, most students appreciated the less stressful, online interaction with peers and faculty. For 15 medicinal chemistry course hours, there were 83 posts on Piazza® with 303 total contributions, 107 student responses, and 546min of group discussion time. 94% of questions received student responses and 89% of those were endorsed by the instructor. Students enjoyed pre-exam discussions, organization of the page, and reinforcing material on complex learning objectives. This discussion forum fostered personal exploration of content by the students, which led to better performance on examinations.

CONCLUSIONS

Involving the use of an online, education-centered platform for student discussions was an effective means of increasing class engagement with the course material. Student performance on exams was significantly improved in both cohorts that utilized active learning compared to the cohort without active learning (p=0.001 and p= 0.002 respectively). Piazza® can be utilized for any course and across disciplines.

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption

DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as the gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders of magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.

Time-resolved metabolomics analysis of individual differences during the early stage of lipopolysaccharide-treated rats

Lipopolysaccharide (LPS) can lead to uncontrollable cytokine production and eventually cause fatal sepsis syndrome. Individual toxicity difference of LPS has been widely reported. In our study we observed that two thirds of the rats (24/36) died at a given dose of LPS, while the rest (12/36) survived. Tracking the dynamic metabolic change in survival and non-survival rats in the early stage may reveal new system information to understand the inter-individual variation in response to LPS. As the time-resolved datasets are very complex and no single method can elucidate the problem clearly and comprehensively, the static and dynamic metabolomics methods were employed in combination as cross-validation. Intriguingly, some common results have been observed. Lipids were the main different metabolites between survival and non-survival rats in pre-dose serum and in the early stage of infection with LPS. The LPS treatment led to S-adenosly-methionine and total cysteine individual difference in early stage, and subsequent significant perturbations in energy metabolism and oxidative stress. Furthermore, cytokine profiles were analyzed to identify potential biological associations between cytokines and specific metabolites. Our collective findings may provide some heuristic guidance for elucidating the underlying mechanism of individual difference in LPS-mediated disease.

Patient experiences with pharmacogenetic testing in a primary care setting

AIM

To investigate patient experiences with pharmacogenetic (PGx) testing.

METHODS

Patients were offered PGx testing through a study on pharmacist-assisted delivery of PGx testing and invited to complete pre- and post-testing surveys about their experience.

RESULTS

Of 63 patients tested, 17 completed the baseline survey (27%). Interest in testing was mostly impacted by desire to inform selection of best treatment (n = 13). Seven of 12 patients that completed the follow-up survey indicated that their provider discussed the test result with them. Five patients understood their test result very or somewhat well. All would be likely to have PGx testing again.

CONCLUSION

Patients perceived PGx testing to be useful, though more effort may be needed to improve patient-provider communication of test results.

CYP2C9, CYPC19 and CYP2D6 gene profiles and gene susceptibility to drug response and toxicity in Turkish population

Pharmacogenetics is a vast field covering drug discovery research, the genetic basis of pharmacokinetics and dynamics, genetic testing and clinical management in diseases. Pharmacogenetic approach usually focuses on variations of drug transporters, drug targets, drug metabolizing enzymes and other biomarker genes. Cytochrome P450 (CYP) enzymes, an essential source of variability in drug-response, play role in not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds such as steroids, vitamins and fatty acids. CYP2C9, CYP2C19 and CYP2D6 enzymes being highly polymorphic are responsible for metabolism of a variety of drug groups. In the study, it was determined the genotype and allele frequency of CYP2C9∗2, CYP2C19∗3, CYP2C19∗2, CYP2C19∗3, CYP2C19∗17, CYP2D6∗9 and CYP2D6∗41, very common and functional single-nucleotide polymorphisms (SNPs), in healthy volunteers. The genotype distributions were consistent with the Hardy-Weinberg equilibrium in the population (p > 0.05). It is believed that the determination of polymorphisms in the enzymes may be beneficial in order to prevention or reduction in adverse effects and death. The recessive allele frequencies of CYP2C9∗2, CYP2C19∗3, CYP2C19∗2, CYP2C19∗3, CYP2C19∗17, CYP2D6∗9 and CYP2D6∗41 were 11, 13, 12, 13, 25, 4 and 15%, respectively. According to the obtained results, the carriers of CYP2D6∗9 variant allele should be received higher doses of the drugs metabolizing with this enzyme in Turkish population, while the carriers of other variant alleles do not generally have any requirement of dose regimen.

The genetic profiles of CYP1A1, CYP1A2 and CYP2E1 enzymes as susceptibility factor in xenobiotic toxicity in Turkish population

Evaluation and sequencing of heritable alterations in the human genome and the large-scale identification of gene polymorphism for understanding the genetic background of individuals in response to potential toxicants are provided by toxicogenetics. Cytochrome P450 (CYP) enzymes play role not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds. CYP1A1, CYP1A2 and CYP2E1 enzymes, which are in phase I enzymes, are responsible for metabolic activation and detoxification of several chemical compounds. In the present study, it was determined the genotype and allele frequency of CYP1A1∗2A, CYP1A2∗1C, CYP1A2∗1F, CYP2E1 and CYP2E1∗6, very common and functional single-nucleotide polymorphisms (SNPs), in Turkish healthy volunteers. It is believed that the determination of polymorphisms in the enzymes may be beneficial to prevent and reduce and adverse effects and death in response to drugs. The allele frequencies of these genes were 24%, 9%, 33%, 42%, and 12%, respectively. In the present study, the genotype profile of Turkish population was determined about critical enzymes for xenobiotic metabolism. It is suggested that the obtained results might be beneficial in order to dose adjustment of drugs and prevention of adverse reactions, and further investigation about mentioned enzymes and their polymorphisms.

Variants in CDA and ABCB1 are predictors of capecitabine-related adverse reactions in colorectal cancer

Adverse reactions to capecitabine-based chemotherapy limit full administration of cytotoxic agents. Likewise, genetic variations associated with capecitabine-related adverse reactions are associated with controversial results and a low predictive value. Thus, more evidence on the role of these variations is needed. We evaluated the association between nine polymorphisms in MTHFR, CDA, TYMS, ABCB1, and ENOSF1 and adverse reactions, dose reductions, treatment delays, and overall toxicity in 239 colorectal cancer patients treated with capecitabine-based regimens. The ABCB1*1 haplotype was associated with a high risk of delay in administration or reduction in the dose of capecitabine, diarrhea, and overall toxicity. CDA rs2072671 A was associated with a high risk of overall toxicity. TYMS rs45445694 was associated with a high risk of delay in administration or reduction in the dose of capecitabine, HFS >1 and HFS >2. Finally, ENOSF1 rs2612091 was associated with HFS >1, but was a poorer predictor than TYMS rs45445694. A score based on ABCB1-CDA polymorphisms efficiently predicts patients at high risk of severe overall toxicity (PPV, 54%; sensitivity, 43%) in colorectal cancer patients treated with regimens containing capecitabine. Polymorphisms in ABCB1, CDA, ENOSF1,and TYMS could help to predict specific and overall severe adverse reactions to capecitabine.

The population genetics of pharmacogenomics VIP variants in the Sherpa population

Polymorphic distributions of pharmacogenes among some ethnicities are under-represented in current pharmacogenetic research. Particularly, there is a paucity of pharmacogenetic information in the Sherpa population in Tibet. We used the Sequenom MassARRAY single nucleotide polymorphism (SNP) genotyping technology to detect 86 very important pharmacogene (VIP) variants in Sherpas and compared the genotypic frequencies of these variants with HapMap populations. Overall, 59 of the 60 previously reported variants in the HapMap populations were found in our study. We found minimal differences between populations of Sherpas and Chinese Han in Beijing (CHB), Chinese in Metropolitan Denver, Colorado (CHD), Japanese in Tokyo, Japan (JPT), and Mexicans in Los Angeles, California (MEX) after a strict Bonferroni correction. Only 8, 4, 5, 4 VIP genotypes, respectively, were different in these groups. Additionally, pairwise FST values and clustering analyses showed that the VIP variants in the Sherpa population exhibited a close genetic affinity with the CHB and JPT populations, but they were most similar to the CHD population. Our results contribute to a better understanding of the molecular basis underlying ethnic differences in drug response, which may potentially benefit the development of personalized medicine for the Sherpa population.

Prepubertal male rats with high rates of germ-cell apoptosis present exacerbated rates of germ-cell apoptosis after serotonin depletion

Male germ-cell apoptosis occurs naturally and can be increased by exposure to drugs and toxic chemicals. Individuals may have different rates of apoptosis and are likely to also exhibit differential sensitivity to outside influences. Previously, we reported that p-chloroamphetamine (pCA), a substance that inhibits serotonin synthesis, induced germ-cell apoptosis in prepubertal male rats. Here, we identified prepubertal rats with naturally high or low rates of germ-cell apoptosis and evaluated gene expression in both groups. Bax and Shbg mRNA levels were higher in rats with high rates of germ-cell apoptosis. Rats were then treated with pCA and the neuro-hormonal response and gene expression were evaluated. Treatment with pCA induced a reduction in serotonin concentrations but levels of sex hormones and gonadotrophins were not changed. Rats with initially high rates of germ-cell apoptosis had even higher rates of germ-cell apoptosis after treatment with pCA. In rats with high rates of germ-cell apoptosis Bax mRNA expression remained high after treatment with pCA. On the basis of category, an inverse relationship between mRNA expression of Bax and Bcl2, Bax and AR and Bax and Hsd3b2 was found. Here we provide evidence that innate levels of germ-cell apoptosis could be explained by the level of mRNA expression of genes involved with apoptosis and spermatogenesis.

gammaMAXT: a fast multiple-testing correction algorithm

BACKGROUND

The purpose of the MaxT algorithm is to provide a significance test algorithm that controls the family-wise error rate (FWER) during simultaneous hypothesis testing. However, the requirements in terms of computing time and memory of this procedure are proportional to the number of investigated hypotheses. The memory issue has been solved in 2013 by Van Lishout's implementation of MaxT, which makes the memory usage independent from the size of the dataset. This algorithm is implemented in MBMDR-3.0.3, a software that is able to identify genetic interactions, for a variety of SNP-SNP based epistasis models effectively. On the other hand, that implementation turned out to be less suitable for genome-wide interaction analysis studies, due to the prohibitive computational burden.

RESULTS

In this work we introduce gammaMAXT, a novel implementation of the maxT algorithm for multiple testing correction. The algorithm was implemented in software MBMDR-4.2.2, as part of the MB-MDR framework to screen for SNP-SNP, SNP-environment or SNP-SNP-environment interactions at a genome-wide level. We show that, in the absence of interaction effects, test-statistics produced by the MB-MDR methodology follow a mixture distribution with a point mass at zero and a shifted gamma distribution for the top 10 % of the strictly positive values. We show that the gammaMAXT algorithm has a power comparable to MaxT and maintains FWER, but requires less computational resources and time. We analyze a dataset composed of 10(6) SNPs and 1000 individuals within one day on a 256-core computer cluster. The same analysis would take about 10(4) times longer with MBMDR-3.0.3.

CONCLUSIONS

These results are promising for future GWAIs. However, the proposed gammaMAXT algorithm offers a general significance assessment and multiple testing approach, applicable to any context that requires performing hundreds of thousands of tests. It offers new perspectives for fast and efficient permutation-based significance assessment in large-scale (integrated) omics studies.

Molecular Dynamics: New Frontier in Personalized Medicine

The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.

Pharmacogenomics of preterm birth prevention and treatment

Pharmacogenomics and personalised medicine incorporate genetic factors, historical data, and environmental exposures to predict individual variation in response to medications. The study of pharmacology and pharmacogenomics is challenging in obstetrics, and our knowledge in this area lags behind other disciplines of medicine. Some preliminary data, however, suggest that some of the interindividual variation seen in response to medications given for the prevention (progesterone) and the treatment (nifedipine, terbutaline, and others) of preterm labour may be caused by pharmacogenomic effects. A comprehensive approach, integrating clinical data, environmental factors, including concomitant medications and genotype, to optimise the prevention and treatment strategies for preterm birth, is urgently needed.

TWEETABLE ABSTRACT

Some of the variation to meds for prematurity prevention/treatment may arise from pharmacogenomic effects.

Model-Based Individualized Treatment of Chemotherapeutics: Bayesian Population Modeling and Dose Optimization

6-Mercaptopurine (6-MP) is one of the key drugs in the treatment of many pediatric cancers, auto immune diseases and inflammatory bowel disease. 6-MP is a prodrug, converted to an active metabolite 6-thioguanine nucleotide (6-TGN) through enzymatic reaction involving thiopurine methyltransferase (TPMT). Pharmacogenomic variation observed in the TPMT enzyme produces a significant variation in drug response among the patient population. Despite 6-MP's widespread use and observed variation in treatment response, efforts at quantitative optimization of dose regimens for individual patients are limited. In addition, research efforts devoted on pharmacogenomics to predict clinical responses are proving far from ideal. In this work, we present a Bayesian population modeling approach to develop a pharmacological model for 6-MP metabolism in humans. In the face of scarcity of data in clinical settings, a global sensitivity analysis based model reduction approach is used to minimize the parameter space. For accurate estimation of sensitive parameters, robust optimal experimental design based on D-optimality criteria was exploited. With the patient-specific model, a model predictive control algorithm is used to optimize the dose scheduling with the objective of maintaining the 6-TGN concentration within its therapeutic window. More importantly, for the first time, we show how the incorporation of information from different levels of biological chain-of response (i.e. gene expression-enzyme phenotype-drug phenotype) plays a critical role in determining the uncertainty in predicting therapeutic target. The model and the control approach can be utilized in the clinical setting to individualize 6-MP dosing based on the patient's ability to metabolize the drug instead of the traditional standard-dose-for-all approach.

The obesity-risk variant of FTO is inversely related with the So-Eum constitutional type: genome-wide association and replication analyses

Background

Body constitutional types described in the traditional Korean medicine system, Sasang constitutional medicine, are heritable, as has been revealed by twin and family studies. Thus, individuals with the same constitution type usually have similar pathophysiological and psychological traits. In several recent genome-wide association (GWA) analyses performed to identify constitution-associated variants, the association signals were not replicated due to small sample size and dissimilar, non-objective methods for classification of the constitutional types.

Methods

We conducted GWA analysis and followed replication analysis in two large populations (5,490 subjects: 3,810 subjects at discovery stage and 1,680 subjects at replication stage) to identify the replicable constitution-associated variants, wherein subjects with the highest tertile of constitution probability values versus the reference with the lowest tertile of the values obtained from a recently developed constitution analysis tool were compared.

Results

We found that the obesity-risk variant in intron 1 of the fat mass and obesity–associated (FTO) gene was replicably inversely associated with the So-Eum (SE) type, characterized by reduced appetite, slim body, and cautious personality (rs7193144 in combined samples: odds ratio = 0.729, p = 1.47 × 10⁻⁷), and substantial association signal remained after controlling for body mass index (BMI). In contrast, the association of the variant with the Tae-Eum type, characterized by high body mass, disappeared after controlling BMI.

Conclusions

In summary, the obesity-risk variant in FTO intron 1 was inversely associated with the SE type, independent of BMI, which corresponded well with the characteristics of the SE type, such as the lowest body mass and lowest susceptibility to metabolic disorders among the constitutional types. Therefore, the obesity-risk variant of FTO associated with body mass increase might be involved in the determination of body constitution type.

Electronic supplementary material

The online version of this article (doi:10.1186/s12906-015-0609-4) contains supplementary material, which is available to authorized users.

An index of barriers for the implementation of personalised medicine and pharmacogenomics in Europe

BACKGROUND

Personalised medicine (PM) is an innovative way to produce better patient outcomes by using an individualised or stratified approach to disease and treatment rather than a collective treatment approach for patients. Despite its tangible advantages, the complex process to translate PM into the member states and European healthcare systems has delayed its uptake. The aim of this study is to identify relevant barriers represented by an index to summarise challenging areas for the implementation of PM in Europe.

METHODS

A systematic literature review was conducted, and a gaps-and-needs assessment together with a strengths-weaknesses-opportunities-and-threats analysis were applied to review strategic reports and conduct interviews with key stakeholders. Furthermore, surveys were sent out to representatives of stakeholder groups. The index was constructed based on the priorisation of relevant factors by stakeholders.

RESULTS

A need for stakeholder-agreed standards at all levels of implementation of PM exists, from validating biomarkers to definitions of 'informed consent'. The barriers to implement PM are identified in 7 areas, namely, stakeholder involvement, standardisation, interoperable infrastructure, European-level policy making, funding, data and research, and healthcare systems.

CONCLUSIONS

Challenges in the above-mentioned areas can and must be successfully tackled if we are to create a healthier Europe through PM. In order to create an environment in which PM can thrive for the patients' best outcomes, there is an urgent need for systematic actions to remove as many barriers as possible.