The next steps for genomic medicine: challenges and opportunities for the developing world

Improving the computation efficiency of polygenic risk score modeling: faster in Julia

To enable computationally efficient polygenic risk score (PRS) calculations, PRS.jl translates a field standard PRS construction method, PRS-CS, to the Julia programming language.

To enable large-scale application of polygenic risk scores (PRSs) in a computationally efficient manner, we translate a widely used PRS construction method, PRS–continuous shrinkage, to the Julia programming language, PRS.jl. On nine different traits with varying genetic architectures, we demonstrate that PRS.jl maintains accuracy of prediction while decreasing the average runtime by 5.5×. Additional programmatic modifications improve usability and robustness. This freely available software substantially improves work flow and democratizes usage of PRSs by lowering the computational burden of the PRS–continuous shrinkage method.

Family Experiences with Care for Children with Inherited Metabolic Diseases in Canada: A Cross-Sectional Survey

BACKGROUND AND OBJECTIVE

Children with inherited metabolic diseases often require complex and highly specialized care. Patient and family-centered care can improve health outcomes that are important to families. This study aimed to examine experiences of family caregivers (parents/guardians) of children diagnosed with inherited metabolic diseases with healthcare to inform strategies to improve those experiences.

METHODS

A cross-sectional mailed survey was conducted of family caregivers recruited from an ongoing cohort study. Participants rated their healthcare experiences during their child's visits to five types of healthcare settings common for inherited metabolic diseases: the metabolic clinic, the emergency department, hospital inpatient units, the blood laboratory, and the pharmacy. Participants provided narrative descriptions of any memorable negative or positive experiences.

RESULTS

There were 248 respondents (response rate 49%). Caregivers were generally very or somewhat satisfied with the care provided at each care setting. Appropriate treatment, provider knowledge, provider communication, and care coordination were deemed essential aspects of satisfaction with care by the majority of participants across many settings. Memorable negative experiences were reported by 8-22% of participants, varying by setting. Among participants who reported memorable negative experiences, contributing factors included providers' demeanor, lack of communication, lack of involvement of the family, and disregard of an emergency protocol letter provided by the family.

CONCLUSIONS

While caregivers' satisfaction with care for children with inherited metabolic diseases was high, we identified gaps in family-centered care and factors contributing to negative experiences that are important to consider in the future development of strategies to improve pediatric care for inherited metabolic diseases.

Personalized Medicine in Oncology in the Developing World: Barriers and Concepts to Improve Status Quo

Personalized medicine (PM) has revolutionized oncology management in high human development indexed countries. By interrogating both disease and host factors through a variety of tools, oncologists have been able to better target an individual's cancer, leading to improved outcomes. But both the tools used to define these variables, such as next generation sequencing, large immunohistochemical and fluorescence in situ hybridization (FISH) panels, and the weapons employed against each target are extremely expensive. The expenses have to be measured as not only the direct cost to the patient but also the cost to the system to develop and deploy the necessary infrastructure to optimally use them. However, the concepts of predictive, timely prevention and PM have demonstrated improvement in patient's satisfaction and cost effectiveness. In this paper we will summarize the relevant barriers and challenges that limit the implementation of PM in the developing world with an emphasis on the challenges in Nigeria and Nepal.

Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries

In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.

Genomic Interventions in Medicine

Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.

Barriers and Opportunities in Consent and Access Procedures in Low- and Middle-Income Country Biobanks: Meeting Notes from the BCNet Training and General Assembly

As biobanking research in low- and middle-income countries (LMICs) continues to grow, novel legal and policy considerations have arisen. Also, while an expansive literature has developed around these issues, the views and concerns of individual researchers in these contexts have been less actively studied. These meeting notes aim to contribute to the growing literature on biobanking in LMICs by communicating a number of challenges and opportunities identified by biobank researchers themselves. Specifically, we describe concerns that emerge in consent and access policy domains. First, we present a review of the literature on distinct policy and legal concerns faced in LMICs, giving special attention to the general absence of practitioner perspectives. From there, we outline and discuss considerations that were raised by meeting participants at a Biobank and Cohort Building Network (BCNet) Ethical, Legal, and Social Issues training program. We conclude by proposing that the unique perspectives of biobank researchers in LMICs should be given serious attention and further research on these perspectives should be conducted.

From systems biology to P4 medicine: applications in respiratory medicine

Human health and disease are emergent properties of a complex, nonlinear, dynamic multilevel biological system: the human body. Systems biology is a comprehensive research strategy that has the potential to understand these emergent properties holistically. It stems from advancements in medical diagnostics, “omics” data and bioinformatic computing power. It paves the way forward towards “P4 medicine” (predictive, preventive, personalised and participatory), which seeks to better intervene preventively to preserve health or therapeutically to cure diseases. In this review, we: 1) discuss the principles of systems biology; 2) elaborate on how P4 medicine has the potential to shift healthcare from reactive medicine (treatment of illness) to predict and prevent illness, in a revolution that will be personalised in nature, probabilistic in essence and participatory driven; 3) review the current state of the art of network (systems) medicine in three prevalent respiratory diseases (chronic obstructive pulmonary disease, asthma and lung cancer); and 4) outline current challenges and future goals in the field.

Systems biology and network medicine have the potential to transform medical research and practicehttp://ow.ly/r3jR30hf35x

SLC22A2 - mapping genomic variations within South African indigenous and admixed populations

BACKGROUND

The SLC22A2 gene is a polyspecific transporter that mediates the electrogenic transport of small organic cations with different molecular structures. Furthermore, single-nucleotide polymorphisms (SNPs) of SLC22A2 are clinically significant because they can alter the transport of substrate drugs and may, thus, influence the efficacy and toxicity thereof. Additionally, further studies have reported that SLC22A2 is responsible for 80% of the total metformin clearance. Therefore, loss-of-function variants of SLC22A2 could affect the pharmacokinetic and pharmacodynamic characteristics of metformin. Although it is widely accepted that African populations harbor a greater amount of genomic diversity compared to other populations, limited information is available regarding genetic polymorphisms in SLC genes among African populations, specifically those related to impaired functional activity of hOCT2. Therefore, the aim of this study was to map known impaired function variants in the SLC22A2 gene.

METHODS

Development of multiplex SNaPshot™ genotyping assay for 20 previously reported SLC22A2 nonsynonymous SNPs and the assessment of baseline allele frequencies of these variants in 140 Cape Admixed, 148 Xhosa and 152 Zulu individuals residing in Cape Town, South Africa.

RESULTS

We identified three nonsynonymous SNPs, namely, A270S, R400C and K432Q in the population studied at minor allele frequencies of 6.1%, 3.4% and 0.7%, respectively. The most frequently observed haplotypes across all three populations were CATAATGCGTACGCGCGACG (~85%), CATAATGATTACGCGCGACG (~7%) and CATAATGAGTACGCGCGACG (~4.5%).

CONCLUSIONS

In addition to SNPs, the haplotypes identified in this study can in future also aid in identifying associations between causative genetic variants and drug response. This study contributes in filling the gap that exists with regards to genetic information about important variations in organic cation transporter genes for the indigenous populations of South Africa.

The elusive ideal of inclusiveness: lessons from a worldwide survey of neurologists on the ethical issues raised by whole-genome sequencing

The anticipation of ethical issues that may arise with the clinical use of genomic technologies is crucial to envision their future implementation in a manner sensitive to local contexts. Yet, populations in low- and middle-income countries are underrepresented in studies that aim to explore stakeholders’ perspectives on the use of such technologies. Within the framework of a research project entitled “Personalized medicine in the treatment of epilepsy”, we sought to increase inclusiveness by widening the reach of our survey, inviting neurologists from around the world to share their views and practices regarding the use of whole-genome sequencing in clinical neurology and its associated ethics. We discuss herein the compelling scientific and ethical reasons that led us to attempt to recruit neurologists worldwide, despite the lack, in many low- or middle-income countries, of access to genomic technologies. Recruitment procedures and their results are presented and discussed, as well as the barriers we faced. We conclude that inclusive recruitment remains a challenging, albeit necessary and legitimate, endeavour.

Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013

Background

The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA.

Design

SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis.

Results

The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions.

Conclusions

Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

From big data analysis to personalized medicine for all: challenges and opportunities

Recent advances in high-throughput technologies have led to the emergence of systems biology as a holistic science to achieve more precise modeling of complex diseases. Many predict the emergence of personalized medicine in the near future. We are, however, moving from two-tiered health systems to a two-tiered personalized medicine. Omics facilities are restricted to affluent regions, and personalized medicine is likely to widen the growing gap in health systems between high and low-income countries. This is mirrored by an increasing lag between our ability to generate and analyze big data. Several bottlenecks slow-down the transition from conventional to personalized medicine: generation of cost-effective high-throughput data; hybrid education and multidisciplinary teams; data storage and processing; data integration and interpretation; and individual and global economic relevance. This review provides an update of important developments in the analysis of big data and forward strategies to accelerate the global transition to personalized medicine.

Pediatric clinical drug trials in low-income countries: key ethical issues

Potential child participants in clinical research trials in low-income countries are often vulnerable because of poverty, high morbidity and mortality, inadequate education, and varied local cultural norms. However, vulnerability by itself must not be accepted as an obstacle blocking children from the health benefits that may accrue as an outcome of sound clinical research. As greater emphasis is placed on evidence-based treatment of children, it should be anticipated that there will be a growing call for agreement on principles to guide clinical investigations in low-income countries. There is now general acceptance of the view that children must be protected from non-evidence-based interventions and from substandard treatments. The questions remaining relate to how best to stimulate clinical research activity that will serve the needs of infants, children, and youth in developing countries and how best to assign priority to ethically sound research that will meet their clinical requirements. In low-income countries, 39 % of citizens are 13 years of age or younger, and consequently it is certain that clinical investigations of some new therapeutic products will be conducted there more frequently. This review offers some suggestions for approaches that will help to achieve more effective ethical consideration, including (1) improving the quality of research ethics boards; (2) fostering collaborative partnerships among important stakeholders; (3) making concerted efforts to build capacity; (4) improving the quality of the consent and waiver process; and (5) developing improved governance for harmonized ethics platforms. Continuing support by international organizations is required to sustain the establishment and maintenance of stronger research ethics boards to protect children enrolled in clinical trials. This review underscores the importance of developing a culture of solidarity and true partnership between developed and low-income country organizations, which will allow all those involved, and especially child patients, to benefit from the advancement of therapeutics.

Human Genomics in Asia

In the past decade, Asia has been actively engaged in human genomic studies and has made great contributions to the field. There is an increase in the number of genomics institutes, consortiums, and initiatives across the continent to study the association between genetic variation and disease. Despite these laudable efforts, Asia faces tremendous challenges in terms of funding, regulation, collaboration, and ethical, legal, and social issues related to genomics. These need to be addressed in the near future to promote the development of genomic medicine.

A call for global governance of biobanks

The progress in genomic research has led to increased sampling and storage of biological samples in biobanks. Most biobanks are located in high-income countries, but the landscape is rapidly changing as low- and middle-income countries develop their own. When establishing a biobank in any setting, researchers have to consider a series of ethical, legal and social issues beyond those in traditional medical research. In addition, many countries may have inadequate legislative structures and governance frameworks to protect research participants and communities from unfair distribution of risks and benefits. International collaborations are frequently being created to support the establishment and proper running of biobanks in low- and middle-income countries. However, these collaborations cause cross-border issues – such as benefit sharing and data access. It is thus necessary to define and implement a fair, equitable and feasible biobank governance framework to ensure a fair balance of risks and benefits among all stakeholders.

Genetic polymorphisms of the organic cation transporter 1 gene (SLC22A1) within the Cape Admixed population of South Africa

Human organic cation transporter 1 (hOCT1) is expressed primarily in hepatocytes and mediate the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for hOCT1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response of individual patients to clinical drugs which are substrates for this transporter. The aim of this study was to investigate the allele and genotype frequencies of single-nucleotide polymorphisms (SNPs) of SLC22A1 in the Cape Admixed population of South Africa. The genotypic and allelic distributions of nineteen nonsynonomous and one intronic SLC22A1 SNPs were determined in 100 healthy Cape Admixed participants, using a SNaPshot(®) multiplex assay. In addition, haplotype structure for SLC22A1 was inferred from the genotypic data. The minor allele frequencies for S14F, P341L, S189L, G220V, V519F, M440I, G465R and the rs622342 intronic variant were 1.0, 0.5, 1.0, 1.0, 1.5, 0.5, 0.5 and 18.0%, respectively. None of the participants carried the variant allele for R61C, C88R, P283L, R287G and G401S. In addition, no variant alleles were observed for A306T, A413V, M420V, I421F, C436F, V501E, and I542V in the population. Twelve haplotypes were inferred from the genotypic data. The frequencies for most common haplotypes CCTCGGCGCGCTAGAGCTGA, CCTCGGCGCGCTAGCGCTGA and CCTCGGCGCGCGAGCGCTGA were 80, 9.9, and 3.5%, respectively.

Electrogenerated chemiluminescence aptasensor for ultrasensitive detection of thrombin incorporating an auxiliary probe

A novel electrogenerated chemiluminescence (ECL) aptasensor for ultrasensitive detection of thrombin incorporating an auxiliary probe was designed by employing specific anti-thrombin aptamer as a capture probe and a ruthenium(II) complex-tagged reporter probe as an ECL probe and an auxiliary probe to assist the ECL probe close to the surface of the electrode. The ECL aptasensor was fabricated by self-assembling a thiolated capture probe on the surface of gold electrode and then hybridizing the ECL probe with the capture probe, and further self-assembling the auxiliary probe. When analyte thrombin was bound with the capture probe, the part of the dehybridized ECL probe was hybridized with the neighboring auxiliary probe, led to the tagged ruthenium(II) complex close to the electrode surface, resulted in great increase in the ECL intensity. The results showed that the increased ECL intensity was directly related to the logarithm of thrombin concentrations in the range from 5.0 × 10(-15)M to 5.0 × 10(-12)M with a detection limit of 2.0 × 10(-15)M. This work demonstrates that employing an auxiliary probe which exists nearby the capture probe can enhance the sensitivity of the ECL aptasensor. This promising strategy will be extended to the design of other biosensors for detection of other proteins and genes.

Cytochrome P450 pharmacogenetics in African populations: implications for public health

INTRODUCTION

Africa harbors a disproportionate burden of disease when taking into account the triple challenge caused by HIV/AIDS, tuberculosis (TB) and malaria, against a backdrop of an increasing burden of noncommunicable diseases. More than 80% of therapeutic drugs used in the management of these diseases/conditions are metabolized by CYP enzymes that exhibit genetic polymorphisms.

AREAS COVERED

There is variability in the expression and activities of CYPs resulting in interindividual differences in the response to standard doses of therapeutic drugs, due to genetic polymorphisms, which exhibit both quantitative and qualitative differences between racial and between ethnic groups. The review aims to evaluate the implications of the genetic variation in CYPs on the public health of Africans. The CYPs reviewed here metabolize most of the commonly used therapeutic drugs and include CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 3A4 and 3A5. Allele frequencies are compared between African ethnic groups and among populations of African, Asian and European origin. Data are obtained from our own studies and literature.

EXPERT OPINION

The variability in the pattern of genetic variation between populations translates into differences in drug response. Understanding CYP variability improves rational drug use and has public health significance.

Biomedical research, a tool to address the health issues that affect African populations

Traditionally, biomedical research endeavors in low to middle resources countries have focused on communicable diseases. However, data collected over the past 20 years by the World Health Organization (WHO) show a significant increase in the number of people suffering from non-communicable diseases (e.g. heart disease, diabetes, cancer and pulmonary diseases). Within the coming years, WHO predicts significant decreases in communicable diseases while non-communicable diseases are expected to double in low and middle income countries in sub-Saharan Africa. The predicted increase in the non-communicable diseases population could be economically burdensome for the basic healthcare infrastructure of countries that lack resources to address this emerging disease burden. Biomedical research could stimulate development of healthcare and biomedical infrastructure. If this development is sustainable, it provides an opportunity to alleviate the burden of both communicable and non-communicable diseases through diagnosis, prevention and treatment. In this paper, we discuss how research using biomedical technology, especially genomics, has produced data that enhances the understanding and treatment of both communicable and non-communicable diseases in sub-Saharan Africa. We further discuss how scientific development can provide opportunities to pursue research areas responsive to the African populations. We limit our discussion to biomedical research in the areas of genomics due to its substantial impact on the scientific community in recent years however, we also recognize that targeted investments in other scientific disciplines could also foster further development in African countries.

Africa: continent of genome contrasts with implications for biomedical research and health

The genomic architecture of African populations is poorly understood and there is considerable variation between ethno-linguistic groups. Genome-wide approaches have been extensively applied to search for genetic associations to complex traits in Europeans, but rarely in Africans. This is largely attributed to lower levels of funding, poor infrastructure and public health systems, and to the small pool of trained scientists. High levels of genetic variation and underlying population structure in Africans present significant challenges, but lower levels of linkage disequilibrium provide an opportunity for more effective localisation of causal variants. High throughput technologies, including dense genotyping arrays, genome sequencing and epigenome studies, together with plummeting costs, are making research more affordable, even for African scientists. Understanding the interactions between genome structure and environmental influences is essential to interpreting their contributions to the increase in infectious diseases and non-communicable diseases, exacerbated by adverse environments and lifestyle choices. The unique genome dynamics in African populations have an important role to play in understanding human health and susceptibility to disease.

'Personalized medicine' to identify genetic risks for type 2 diabetes and focus prevention: can it fulfill its promise?

Public health measures are required to address the worldwide increase in type 2 diabetes. Proponents of personalized medicine predict a future in which disease treatment and, more important, prevention will be tailored to high-risk individuals rather than populations and will be based on genetic and other new biomarker tests. Accurate biomarker tests to identify people at risk for diabetes could allow more-targeted and perhaps individualized prevention efforts. DNA variants conferring higher risk for type 2 diabetes have been identified. However, these account for only a small fraction of genetic risk, which limits their practical predictive value. Nor has identification of these variants yet led to new, individualized prevention methods. Further research is needed to identify genomic and other types of biomarkers that could accurately predict risk and facilitate targeted prevention.

Pharmacogenetics and rational drug use around the world

The WHO embraces evidence-based medicine to formulate an essential medicines list (EML) considering disease prevalence, drug efficacy, drug safety and cost-effectiveness. The EML is used by developing countries to build a national formulary. As pharmacogenetics in developed countries evolves, the Pharmacogenetics for Every Nation Initiative (PGENI) convened with representatives from China, Mexico, Ghana and South Africa in August 2009 to evaluate the use of human pharmacogenetics to enhance global drug use policy. The diseases causing mortality, the lack of integration of pharmacovigilance at the national formulary level, the pharmacogenetics research agenda and pharmacogenetics clinician education did not differ greatly among the countries. While there are many unanswered questions, systematically incorporating pharmacogenetics at the national formulary level promises to improve global drug use.

Africa: the next frontier for human disease gene discovery?

The populations of Africa harbour the greatest human genetic diversity following an evolutionary history tracing its beginnings on the continent to time before the emergence of Homo sapiens. Signatures of selection are detectable as responses to ancient environments and cultural practices, modulated by more recent events including infectious epidemics, migrations, admixture and, of course, chance. The age of high-throughput biology is not passing Africa by. African-based cohort studies and networks with an African footprint are ideal springboards for disease-related genetic and genomic studies. Initiatives like HapMap, the 1000 Genomes Project, MalariaGEN, the INDEPTH network and Human Heredity and Health in Africa are catalysts to exploring African genetic diversity and its role in the spectrum from health to disease. The challenges are abundant in dissecting biological questions in the light of linguistic, cultural, geographic and political boundaries and their respective roles in shaping health-related profiles. Will studies based on African populations lead to a new wave of discovery of genetic contributors to disease?

Can pharmacogenomics improve malaria drug policy?

Coordinated global efforts to prevent and control malaria have been a tour-de-force for public health, but success appears to have reached a plateau in many parts of the world. While this is a multifaceted problem, policy strategies have largely ignored genetic variations in humans as a factor that influences both selection and dosing of antimalarial drugs. This includes attempts to decrease toxicity, increase effectiveness and reduce the development of drug resistance, thereby lowering health care costs. We review the potential hurdles to developing and implementing pharmacogenetic-guided policies at a national or regional scale for the treatment of uncomplicated falciparum malaria. We also consider current knowledge on some component drugs of artemisinin combination therapies and ways to increase our understanding of host genetics, with the goal of guiding policy decisions for drug selection.

Health biotechnology innovation on a global stage

There is much to be gained for the biotechnology sector from collaborations between developing countries and developed countries. Thorsteinsdóttir and colleagues describe the benefits of such collaborations and the hurdles that they must overcome in order to succeed.

With increasing globalization, infectious diseases are spreading faster than ever before, creating an urgent need for international collaboration. The rise of emerging economies has changed the traditional collaborative landscape and provided opportunities for more diverse models of collaboration involving developing countries, including North–South, South–South and North–South–South partnerships. Here, we discuss how developing countries can partner with other nations to address their shared health problems and to promote innovation. We look specifically at what drives collaborations and at the challenges that exist for them, and we propose actions that can strengthen these partnerships.

Improved sensitivity for the electrochemical biosensor with an adjunct probe

Despite their promising applications in the biomedical research, the development of electrochemical biosensors with improved sensitivity and low detection limit has remained a great challenge. Here, we demonstrate a new approach to improve the sensitivity of the electrochemical biosensor by simply introducing an adjunct probe into its construction. This signal-on biosensor consists of a thiol-functionalized capture probe attached on the gold electrode surface, an electrochemical sign (methyl blue, MB)-modified reporter probe which is complementary to the capture probe, and an adjunct probe attached nearby the capture probe. The adjunct probe functions as a fixer to immobilize the element of reporter probe which is displaced by the target DNA and protein, increasing the chance of the dissociative reporter probe to collide with the electrode surface and facilitating the electron transfer. The biosensor with an adjunct probe exhibits improved sensitivity and a large dynamic range for DNA and the thrombin assay and can even distinguish 1-base mismatched target DNA. Importantly, the use of this biosensor is not limited to such and is viable for sensitive detection of numerous biomolecules, including RNA, proteins, and small molecules such as cocaine.

Toward point-of-care microchip profiling of proteins

Profiling of protein biomarkers is powerful for the analysis of complex proteomes altered during the progression of diseases. Lab-on-a-chip technologies can potentially provide the throughput and efficiency required for point-of-care and clinical applications. While initial studies utilized 1D microchip separation techniques, researchers have recently developed novel 2D microchip separation platforms with the ability to profile thousands of proteins more effectively. Despite advancements in lab-on-a-chip technologies, very few reports have demonstrated a point-of-care microchip-based profiling of proteins. In this review, recent progress in 1D and 2D microchip profiling of protein mixtures of a biological sample with potential point-of-care applications are discussed. A selection of recent microchip immunoassay-based techniques is also highlighted.

Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico

Mexico is developing the basis for genomic medicine to improve healthcare of its population. The extensive study of genetic diversity and linkage disequilibrium structure of different populations has made it possible to develop tagging and imputation strategies to comprehensively analyze common genetic variation in association studies of complex diseases. We assessed the benefit of a Mexican haplotype map to improve identification of genes related to common diseases in the Mexican population. We evaluated genetic diversity, linkage disequilibrium patterns, and extent of haplotype sharing using genomewide data from Mexican Mestizos from regions with different histories of admixture and particular population dynamics. Ancestry was evaluated by including 1 Mexican Amerindian group and data from the HapMap. Our results provide evidence of genetic differences between Mexican subpopulations that should be considered in the design and analysis of association studies of complex diseases. In addition, these results support the notion that a haplotype map of the Mexican Mestizo population can reduce the number of tag SNPs required to characterize common genetic variation in this population. This is one of the first genomewide genotyping efforts of a recently admixed population in Latin America.

Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking

BACKGROUND

Integrative analysis between dynamical modeling of metabolic networks and data obtained from high throughput technology represents a worthy effort toward a holistic understanding of the link among phenotype and dynamical response. Even though the theoretical foundation for modeling metabolic network has been extensively treated elsewhere, the lack of kinetic information has limited the analysis in most of the cases. To overcome this constraint, we present and illustrate a new statistical approach that has two purposes: integrate high throughput data and survey the general dynamical mechanisms emerging for a slightly perturbed metabolic network.

METHODOLOGY/PRINCIPAL FINDINGS

This paper presents a statistic framework capable to study how and how fast the metabolites participating in a perturbed metabolic network reach a steady-state. Instead of requiring accurate kinetic information, this approach uses high throughput metabolome technology to define a feasible kinetic library, which constitutes the base for identifying, statistical and dynamical properties during the relaxation. For the sake of illustration we have applied this approach to the human Red blood cell metabolism (hRBC) and its capacity to predict temporal phenomena was evaluated. Remarkable, the main dynamical properties obtained from a detailed kinetic model in hRBC were recovered by our statistical approach. Furthermore, robust properties in time scale and metabolite organization were identify and one concluded that they are a consequence of the combined performance of redundancies and variability in metabolite participation.

CONCLUSIONS/SIGNIFICANCE

In this work we present an approach that integrates high throughput metabolome data to define the dynamic behavior of a slightly perturbed metabolic network where kinetic information is lacking. Having information of metabolite concentrations at steady-state, this method has significant relevance due its potential scope to analyze others genome scale metabolic reconstructions. Thus, I expect this approach will significantly contribute to explore the relationship between dynamic and physiology in other metabolic reconstructions, particularly those whose kinetic information is practically nulls. For instances, I envisage that this approach can be useful in genomic medicine or pharmacogenomics, where the estimation of time scales and the identification of metabolite organization may be crucial to characterize and identify (dis)functional stages.