Recent trends on the role of epigenomics, metabolomics and noncoding RNAs in rationalizing mood stabilizing treatment

Mood stabilizers are the cornerstone in treatment of mood disorders, but their use is characterized by high interindividual variability. This feature has stimulated intensive research to identify predictive biomarkers of response and disentangle the molecular bases of their clinical efficacy. Nevertheless, findings from studies conducted so far have only explained a small proportion of the observed variability, suggesting that factors other than DNA variants could be involved. A growing body of research has been focusing on the role of epigenetics and metabolomics in response to mood stabilizers, especially lithium salts. Studies from these approaches have provided new insights into the molecular networks and processes involved in the mechanism of action of mood stabilizers, promoting a systems-level multiomics synergy. In this article, we reviewed the literature investigating the involvement of epigenetic mechanisms, noncoding RNAs and metabolomic modifications in bipolar disorder and the mechanism of action and clinical efficacy of mood stabilizers.

Genomic variants in the FTO gene are associated with sporadic amyotrophic lateral sclerosis in Greek patients

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a devastating disease whose complex pathology has been associated with a strong genetic component in the context of both familial and sporadic disease. Herein, we adopted a next-generation sequencing approach to Greek patients suffering from sporadic ALS (together with their healthy counterparts) in order to explore further the genetic basis of sporadic ALS (sALS).

RESULTS

Whole-genome sequencing analysis of Greek sALS patients revealed a positive association between FTO and TBC1D1 gene variants and sALS. Further, linkage disequilibrium analyses were suggestive of a specific disease-associated haplotype for FTO gene variants. Genotyping for these variants was performed in Greek, Sardinian, and Turkish sALS patients. A lack of association between FTO and TBC1D1 variants and sALS in patients of Sardinian and Turkish descent may suggest a founder effect in the Greek population. FTO was found to be highly expressed in motor neurons, while in silico analyses predicted an impact on FTO and TBC1D1 mRNA splicing for the genomic variants in question.

CONCLUSIONS

To our knowledge, this is the first study to present a possible association between FTO gene variants and the genetic etiology of sALS. In addition, the next-generation sequencing-based genomics approach coupled with the two-step validation strategy described herein has the potential to be applied to other types of human complex genetic disorders in order to identify variants of clinical significance.

Advancing Global Precision Medicine: An Overview of Genomic Testing and Counseling Services in Malaysia

Precision medicine, genomic and diagnostic services are no longer limited to developed countries. This broadening in geography of biomarker applications and omics diagnostics also demands empirical study of implementation, diagnostic testing, and counseling practices in the field. For example, the Malaysian population has large ethnic diversity and high prevalence of genetic disorders such as hemoglobinopathies and metabolic disorders. Increased morbidity and mortality from such diseases have a direct impact on society and health system sustainability and for this, decision-making becomes of outmost importance. We report here on our findings on the landscape of genomic testing and genetic counseling services in Malaysia. We first defined the framework of all Malaysian stakeholders that offer genomics services and next, we identified the related information gaps, as depicted through the service providers' online websites. Our research framework revealed that there is a very diverse spectrum of genomics services in Malaysia, in which wet- and dry-laboratory services integrate. Moreover, we identify the current gaps and possible remedies to improve the quality of genomic and predictive analytics, not to mention considerations to ensure robust ethics and responsible innovation. To our knowledge, this is the first such study to be performed for a Southeast Asian country. Our genomics and precision medicine services mapping strategy presented in this study may serve as a model for field assessment at regional, national, and international levels as precision medicine is expanding globally and new governance challenges and opportunities continue to emerge for smart implementation science.

Ashkenazi Jewish genomic variants: integrating data from the Israeli National Genetic Database and gnomAD

PURPOSE

The aim of the study was to compare the data for mutations related to clinical disorders reported among Ashkenazi Jewish patients in the Israeli National Genetic Database (INGD) with variants included in the Genome Aggregation Database (gnomAD).

METHODS

We extracted data for mutations claimed to cause disorders reported among Ashkenazi Jews from the INGD and searched gnomAD for each of them. We compared the allele frequency of each variant in Ashkenazi Jews with that of other delineated populations.

RESULTS

Of the 58 INGD-reported mutations related to autosomal-dominant disorders, 19 were present in gnomAD (32.8%). Of the 309 mutations related to autosomal-recessive disorders, 240 (77.7%) were variants found in gnomAD. Of these variants, 202 (84.2%) were documented among one or more Ashkenazi individuals. At this point in the INGD, there are 168 Ashkenazi assumed founder mutations in 128 different genes corresponding to 111 autosomal-recessive disorders.

CONCLUSION

Integration of information on mutations among Ashkenazi Jews extracted from the INGD with their population frequency recorded in gnomAD is important for effective straightforward molecular diagnosis as well as for targeted carrier screening either for reproductive decision-making or for implementation of disease-modifying behavior.

Allele Drop Out Conferred by a Frequent CYP2D6 Genetic Variation For Commonly Used CYP2D6*3 Genotyping Assays

BACKGROUND/AIM

Accurate genotyping of CYP2D6 is challenging due to its inherent genetic variation, copy number variation (duplications and deletions) and hybrid formation with highly homologous pseudogenes. Because a relatively high percentage (∼25%) of clinically prescribed drugs are substrates for this enzyme, accurate determination of its genotype for phenotype prediction is essential.

METHODS

A cohort of 365 patient samples was genotyped for CYP2D6 using Sanger sequencing (as the gold standard), hydrolysis probe assays or pyrosequencing.

RESULTS

A discrepant result between the three genotyping methods for the loss of function CYP2D6*3 (g.2549delA, rs35742686) genetic variant was found in one of the samples. This sample also contained the CYP2D6 g.2470T>C (rs17002852) variation, which had an allele frequency of 2.47% in our cohort. Redesign of the CYP2D6*3 pyrosequencing and hydrolysis probe assays to avoid CYP2D6 g.2470 corrected the anomaly.

CONCLUSION

To evidence allele drop out and increase the accuracy of genotyping, intra-patient validation of the same genetic variation with at least two separate methods should be considered.

David Bowie and the Art of Slow Innovation: A Fast-Second Winner Strategy for Biotechnology and Precision Medicine Global Development

Original ideas and innovation cannot always be ordered like a courier service and delivered fresh to our desk at 9 am. Yet, most creativity-based organizations, careers, and professions, science and biotechnology innovation included, emphasize the speed as the prevailing ideology. But a narrow focus on speed has several and overlooked shortcomings. For example, it does not offer the opportunity to draw from, and stitch together disparate concepts and practices for truly disruptive innovation. Preventing false starts, learning from others' or our own mistakes, and customizing innovations for local community needs are difficult in a speed-hungry innovation ecosystem. We introduce a new strategy, the Fast-Second Winner, specifically in relation to global development of biotechnologies and precision medicine. This à la carte global development strategy envisions a midstream entry into the innovation ecosystem. Moreover, we draw from the works of the late David Bowie who defied rigid classifications as an artist and prolific innovator, and introduce the concept and practice of slow innovation that bodes well with the Fast-Second Winner strategy. A type of slow innovation, the Fast-Second Winner is actually fast and sustainable in the long term, and efficient by reducing false starts in new precision medicine application contexts and geographies, learning from other innovators' failures, and shaping innovations for the local community needs. The establishment of Centers for Fast-Second Innovation (CFSIs), and their funding, for example, by crowdfunding and other innovative mechanisms, could be timely for omics and precision medicine global development. If precision medicine is about tailoring drug treatments and various health interventions to individuals, we suggest to start from tailoring new ideas, and focus not only on how much we innovate but also what and how we innovate. In principle, the Fast-Second Winner can be applied to omics and other biotechnology responsible development in medical practice or any field of applied innovation.

Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β-type hemoglobinopathy patients

BACKGROUND

Human erythropoiesis is characterized by distinct gene expression profiles at various developmental stages. Previous studies suggest that fetal-to-adult hemoglobin switch is regulated by a complex mechanism, in which many key players still remain unknown. Here, we report our findings from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue.

RESULTS

From our in-depth data analysis, pathway analysis, and text mining, we opted to focus on the VEGFA gene, given its gene expression characteristics. Selected VEGFA genomic variants, identified through linkage disequilibrium analysis, were explored further for their association with elevated fetal hemoglobin levels in β-type hemoglobinopathy patients. Our downstream analysis of non-transfusion-dependent β-thalassemia patients, β-thalassemia major patients, compound heterozygous sickle cell disease/β-thalassemia patients receiving hydroxyurea as fetal hemoglobin augmentation treatment, and non-thalassemic individuals indicated that VEGFA genomic variants were associated with disease severity in β-thalassemia patients and hydroxyurea treatment efficacy in SCD/β-thalassemia compound heterozygous patients.

CONCLUSIONS

Our findings suggest that VEGFA may act as a modifier gene of human globin gene expression and, at the same time, serve as a genomic biomarker in β-type hemoglobinopathy disease severity and hydroxyurea treatment efficacy.

Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping

During pregnancy, cell-free DNA (cfDNA) in maternal blood encompasses a small percentage of cell-free fetal DNA (cffDNA), an easily accessible source for determination of fetal disease status in risk families through non-invasive procedures. In case of monogenic heritable disease, background maternal cfDNA prohibits direct observation of the maternally inherited allele. Non-invasive prenatal diagnostics (NIPD) of monogenic diseases therefore relies on parental haplotyping and statistical assessment of inherited alleles from cffDNA, techniques currently unavailable for routine clinical practice. Here, we present monogenic NIPD (MG-NIPD), which requires a blood sample from both parents, for targeted locus amplification (TLA)-based phasing of heterozygous variants selectively at a gene of interest. Capture probes-based targeted sequencing of cfDNA from the pregnant mother and a tailored statistical analysis enables predicting fetal gene inheritance. MG-NIPD was validated for 18 pregnancies, focusing on CFTR, CYP21A2, and HBB. In all cases we could predict the inherited alleles with >98% confidence, even at relatively early stages (8 weeks) of pregnancy. This prediction and the accuracy of parental haplotyping was confirmed by sequencing of fetal material obtained by parallel invasive procedures. MG-NIPD is a robust method that requires standard instrumentation and can be implemented in any clinic to provide families carrying a severe monogenic disease with a prenatal diagnostic test based on a simple blood draw.

Exploring public genomics data for population pharmacogenomics

Racial and ethnic differences in drug responses are now well studied and documented. Pharmacogenomics research seeks to unravel the genetic underpinnings of inter-individual variability with the aim of tailored-made theranostics and therapeutics. Taking into account the differential expression of pharmacogenes coding for key metabolic enzymes and transporters that affect drug pharmacokinetics and pharmacodynamics, we advise that data interpretation and analysis need to occur in light of geographical ancestry, if implications for drug development and global health are to be considered. Herein, we exploit ePGA, a web-based electronic Pharmacogenomics Assistant and publicly available genetic data from the 1000 Genomes Project to explore genotype to phenotype associations among the 1000 Genomes Project populations.

Exosomes: A Cancer Theranostics Road Map

Interindividual variability is yet to be fully characterized, and for this, optimum patient stratification and companion diagnostics are still lacking. Especially when complex disease phenotypes and/or polygenic diseases are considered, patient monitoring and disease management become rather challenging, while acquired resistance to therapy and/or toxicity events are among the unmet needs in the clinic. No doubt, biomarkers are of great importance to disease management and tailor-made theranostics. Microfluidics has gathered great attention lately, mostly due to its low-invasive nature compared to tissue biopsies. Low invasiveness becomes greatly advantageous for microfluidics practices as the latter mirror cell biology revolutionizing cancer diagnostics and management. Recent advances in microfluidics hold the promise of robust clinical diagnostics after they have demonstrated effective exosome separation. We feel that microfluidics-based exosome isolation techniques, if cost-effective, could be implemented in the clinic and/or resource-scarce settings. This article (a) discusses exosomes, (b) comments on the first microfluidic advances in the field of cancer theranostics, (c) presents such advances in exosomes as complementary to liquid biopsies with an emphasis on circulating tumor cells, and (d) proposes a road map for future developments.

Medical education in pharmacogenomics-results from a survey on pharmacogenetic knowledge in healthcare professionals within the European pharmacogenomics clinical implementation project Ubiquitous Pharmacogenomics (U-PGx)

Purpose

Due to the diversity within Europe, the implementation of pharmacogenomic testing in clinical practice faces specific challenges. In the context of the European pharmacogenomics implementation project “Ubiquitous Pharmacogenomics” (U-PGx; funded by the European Commission), we studied the current educational background.

Methods

We developed a questionnaire including 29 questions. It was spread out to healthcare professionals working at the future implementation sites (in Austria, Greece, Italy, Netherlands, Slovenia, Spain and Great Britain) of the U-PGx project in preparation of an educational programme. Aim of the survey was to analyse the current educational situation at the implementation sites.

Results

In total, 70 healthcare professionals participated in the survey. Of participants, 84.3% found pharmacogenomics relevant to their current practice, but experience was still rare. More than two-thirds (65.7%) did not order nor recommend a pharmacogenomic test in the past year. This was mainly attributed to not having enough knowledge on pharmacogenomics (40.0%). Needs were identified in application of pharmacogenomics (identifying drugs 41.4%, interpreting test results 37.2%) as well as in underlining mechanisms (better knowledge on drug metabolism 67.1%, better knowledge on basic principles of pharmacogenomics 60.0%).

Conclusions

This study analysed the specific attitudes, experience and education on pharmacogenomics of future users. There was a general positive attitude and interest towards pharmacogenomic testing. However, the grade of own experience, and knowledge about application and interpretation of pharmacogenomics caused uncertainty. Thus, education and training programmes may be helpful for implementation of pharmacogenomics at a homogenous level within Europe.

Electronic supplementary material

The online version of this article (doi:10.1007/s00228-017-2292-5) contains supplementary material, which is available to authorized users.

Key Pharmacogenomic Considerations for Sickle Cell Disease Patients

Sickle cell disease (SCD), although a monogenic disease, exhibits a complex clinical phenotype that hampers optimum patient stratification and disease management, especially on hydroxyurea treatment. Moreover, theranostics, the combination of diagnostics to individualize and optimize therapeutic interventions, has not been firmly on the forefront of SCD research and clinical management to date. We suggest that if tailor-made theranostics in SCD is envisaged, pharmacogenomics is anticipated to be the way forward. Herein, we present the current key pharmacogenomic opportunities and challenges in SCD, considering population variation, ethics, and socioeconomic aspects. We focus on pharmacogenomics and pain management, genethics, and cost-effectiveness in SCD. We searched for and synthesized data from PubMed and Google Scholar, and the references from relevant articles, using the keywords "pharmacogenomics," "sickle cell disease," "hydroxyurea," "ethics," "pain management," "morphine metabolism," "opioids," "pharmacogenomics and chronic pain," "cost-effectiveness," and "economic evaluation." Only articles published in English were included. So far, when pharmacogenomics in SCD has been considered, interindividual variability in hydroxyurea response/toxicity has been of primary interest. We underscore the need to extend pharmacogenomic considerations on other therapeutic interventions currently present using a holistic patient-centric approach, and taking disease complications into account as well. Furthermore, we raise awareness toward socioeconomic, ethical, and population differences in the way sickle cell pharmacogenomics might unfold in the future. If pharmacogenomics in SCD is to be used in the clinic in an evidence-based manner, cost-effectiveness and population-specific empirical ethics data are urgently needed.

Pharmacogenomics in pediatric acute lymphoblastic leukemia: promises and limitations

Despite the significant advances achieved in pediatric acute lymphocytic leukemia (ALL) treatment, adverse side effects of drugs remain a challenging issue. Numerous ALL pharmacogenomic studies have been conducted to elucidate the predisposing genetic factors for their development. Plausible pharmacogenomic data are available for the osteonecrosis associated with glucocorticoids, the neurotoxicity associated with vincristine and the cardiotoxicity related to anthracyclines. However, these data have not been fully translated into the clinic due to several limitations, most importantly the lack of reliable evidence. The most robust pharmacogenomics data are those for thiopurines and methotrexate use, with evidence-based preemptive testing recommendations for the former. Pharmacogenomics has a significant potential utility in pediatric ALL treatment regimens. In this review, gaps and limitations in this field are emphasized, which may provide a useful guide for future research design.

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine

This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine. Notably, the concept of culturomics expands on that of phenomics and allows a reintroduction of the culture-based phenotypic characterization into the 21st century research repertoire, bolstered by robust technology for automated and massive execution, but its potential is largely unappreciated at present; the few available references show unenthusiastic pursuit and in narrow applications. This has not to be so: depending on the specific brand of culturomics, the scope of applications may extend to medicine, agriculture, environmental sciences, pharmacomicrobiomics, and biotechnology innovation. Moreover, culturomics may produce Big Data. This calls for a new generation of data scientists and innovative ways of harnessing and valorizing Big Data beyond classical genomics. Much more detailed and objective classification and identification of microbiota may soon be at hand through culturomics, thus enabling precision diagnosis toward truly personalized medicine. Culturomics may both widen the scope of microbiology and improve its contributions to diagnostics and personalized medicine, characterizing microbes and determining their associations with health and disease dynamics.

The Israeli National Genetic database: a 10-year experience

Background

The Israeli National and Ethnic Mutation database (http://server.goldenhelix.org/israeli) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar) and ExAC (http://exac.broadinstitute.org) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources.

Results

In September 2016, there were 2444 entries in the database, 890 among Jews, 1376 among Israeli Arabs, and 178 entries among Palestinian Arabs, corresponding to an ~4× data content increase compared to when originally launched. While the Israeli Arab population is much smaller than the Jewish population, the number of pathogenic variants causing recessive disorders reported in the database is higher among Arabs (934) than among Jews (648). Nevertheless, the number of pathogenic variants classified as founder mutations in the database is smaller among Arabs (175) than among Jews (192). In 2016, the entire database content was compared to that of other databases such as ClinVar and ExAC. We show that a significant difference in the percentage of pathogenic variants from the Israeli genetic database that were present in ExAC was observed between the Jewish population (31.8%) and the Israeli Arab population (20.6%).

Conclusions

The Israeli genetic database was launched in 2006 on the ETHNOS software and is available online ever since. It allows querying the database according to the disorder and the ethnicity; however, many other features are not available, in particular the possibility to search according to the name of the gene. In addition, due to the technical limitations of the previous ETHNOS software, new features and data are not included in the present online version of the database and upgrade is currently ongoing.

Performance Ratio Based Resource Allocation Decision-Making in Genomic Medicine

In modern healthcare systems, the available resources may influence the morbidity, mortality, and-consequently-the level of healthcare provided in every country. This is of particular interest in developing countries where the resources are limited and must be spent wisely to address social justice and the right for equal access in healthcare services by all the citizens in economically viable terms. In this light, the current allocation is, in practice, inefficient and rests mostly on each country's individual political and historical context and, thus, does not always incorporate decision-making enabled by economic models. In this study, we present a new economic model, specifically for resource allocation for genomic medicine, based on performance ratio, with potential applications in diverse healthcare sectors, which are particularly appealing for developing countries and low-resource environments. The model proposes a new method for resource allocation taking into account (1) the size of innovation of a new technology, (2) the relative effectiveness in comparison with social preferences, and (3) the cost of the technology, which permits the measurement of effectiveness to be determined differently in the context of a specific disease and then to be expressed in a relative form using a common performance ratio. The present work expands on previous work for innovation in economic models pertaining to genomic medicine and supports translational science.