Personalized medicine - the promised land: are we there yet?

A tractable physical model for the yeast polarity predicts epistasis and fitness

Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences.

This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.

A Longitudinal Study of the Association between the LEPR Polymorphism and Treatment Response in Patients with Bipolar Disorder

Patients with bipolar disorder (BD) exhibit individual variability in the treatment outcome, and genetic background could contribute to BD itself and the treatment outcome. Leptin levels significantly change in BD patients treated with valproate (VPA), but whether LEPR polymorphisms are associated with treatment response is still unknown. This longitudinal study aimed to investigate the associations between LEPR polymorphisms and VPA treatment response in BD patients who were drug naïve at their first diagnosis of BD. The single-nucleotide polymorphisms (SNPs) of LEPR (rs1137101, rs1137100, rs8179183, and rs12145690) were assayed, and the LEPR polymorphism frequencies of alleles and genotypes were not significantly different between the controls (n = 77) and BD patients (n = 130). In addition, after the 12-week course of VPA treatment in BD patients, the LEPR polymorphisms showed significant effects on changes in disease severity. Moreover, considering the effect of the LEPR haplotype, the frequency of the CAGG haplotype in BD patients was higher than that in the controls (9.3 vs. 2.9%, p = 0.016), and the LEPR CAGG haplotype was associated with a better treatment response than the other haplotypes in BD patients receiving VPA treatment. Therefore, LEPR polymorphisms might serve as mediators involved in the therapeutic action of VPA treatment.

Fast and accurate medication identification

Much of the AI work in healthcare is focused around disease prediction in clinical settings, which is an important application that has yet to deliver in earnest. However, there are other fundamental aspects like helping patients and care teams interact and communicate in efficient and meaningful ways, which could deliver quadruple-aim improvements. After heart disease and cancer, preventable medical errors are the third leading cause of death in the United States. The largest subset of medical errors is medication error. Providing the right treatment plan for patients includes knowledge about their current medications and drug allergies, an often challenging task. The widespread growth of prescribing and consuming medications has increased the need for applications that support medication reconciliation. We show a deep-learning application that can help reduce avoidable errors with their attendant risk, i.e., correctly identifying prescription medication, which is currently a tedious and error-prone task. We demonstrate prescription-pill identification from mobile images in the NIH NLM Pill Image Recognition Challenge dataset. Our application recognizes the correct pill within the top-5 results at 94% accuracy, which compares favorably to the original competition winner at 83.3% for top-5 under comparable, though not identical configurations. The Institute of Medicine claims that better use of information technology can be an important step in reducing medication errors. Therefore, we believe that a more immediate impact of AI in healthcare will occur with a seamless integration of AI into clinical workflows, readily addressing the quadruple aim of healthcare.

Multivariate characterization of white matter heterogeneity in autism spectrum disorder

The complexity and heterogeneity of neuroimaging findings in individuals with autism spectrum disorder has suggested that many of the underlying alterations are subtle and involve many brain regions and networks. The ability to account for multivariate brain features and identify neuroimaging measures that can be used to characterize individual variation have thus become increasingly important for interpreting and understanding the neurobiological mechanisms of autism. In the present study, we utilize the Mahalanobis distance, a multidimensional counterpart of the Euclidean distance, as an informative index to characterize individual brain variation and deviation in autism. Longitudinal diffusion tensor imaging data from 149 participants (92 diagnosed with autism spectrum disorder and 57 typically developing controls) between 3.1 and 36.83 years of age were acquired over a roughly 10-year period and used to construct the Mahalanobis distance from regional measures of white matter microstructure. Mahalanobis distances were significantly greater and more variable in the autistic individuals as compared to control participants, demonstrating increased atypicalities and variation in the group of individuals diagnosed with autism spectrum disorder. Distributions of multivariate measures were also found to provide greater discrimination and more sensitive delineation between autistic and typically developing individuals than conventional univariate measures, while also being significantly associated with observed traits of the autism group. These results help substantiate autism as a truly heterogeneous neurodevelopmental disorder, while also suggesting that collectively considering neuroimaging measures from multiple brain regions provides improved insight into the diversity of brain measures in autism that is not observed when considering the same regions separately. Distinguishing multidimensional brain relationships may thus be informative for identifying neuroimaging-based phenotypes, as well as help elucidate underlying neural mechanisms of brain variation in autism spectrum disorders.

Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision

OBJECTIVE

The objective of this review is to summarize the state of the art of clinical decision support (CDS) circa 1990, review progress in the 25 year interval from that time, and provide a vision of what CDS might look like 25 years hence, or circa 2040.

METHOD

Informal review of the medical literature with iterative review and discussion among the authors to arrive at six axes (data, knowledge, inference, architecture and technology, implementation and integration, and users) to frame the review and discussion of selected barriers and facilitators to the effective use of CDS.

RESULT

In each of the six axes, significant progress has been made. Key advances in structuring and encoding standardized data with an increased availability of data, development of knowledge bases for CDS, and improvement of capabilities to share knowledge artifacts, explosion of methods analyzing and inferring from clinical data, evolution of information technologies and architectures to facilitate the broad application of CDS, improvement of methods to implement CDS and integrate CDS into the clinical workflow, and increasing sophistication of the end-user, all have played a role in improving the effective use of CDS in healthcare delivery.

CONCLUSION

CDS has evolved dramatically over the past 25 years and will likely evolve just as dramatically or more so over the next 25 years. Increasingly, the clinical encounter between a clinician and a patient will be supported by a wide variety of cognitive aides to support diagnosis, treatment, care-coordination, surveillance and prevention, and health maintenance or wellness.

Personalized medicine and genome-based treatments: Why personalized medicine ≠ individualized treatments

The sequencing of the human genome and decreasing costs of sequencing technology have led to the notion of ‘personalized medicine’. This has been taken by some authors to indicate that personalized medicine will provide individualized treatments solely based on one’s DNA sequence. We argue this is overly optimistic and misconstrues the notion of personalization. Such interpretations fail to account for economic, policy and structural constraints on the delivery of healthcare. Furthermore, notions of individualization based on genomic data potentially take us down the road of genetic reductionism obscuring the role of environmental factors in disease and ill health. We propose that one should see personalized medicine as a way of using personal genomic information to stratify individuals into subpopulations and suggest that personalized medicine be seen within a broader idea of personalized healthcare, reflecting healthcare that integrates personal genomic data into cultural, environmental and personal contexts.

Benefits and burdens of newborn screening: public understanding and decision-making

In this article we review the literature regarding the public understanding of the potential benefits and burdens of expanded newborn bloodspot screening. We draw attention to broadened notions of benefit that go beyond early identification of asymptomatic individuals and interventions to reduce morbidity or mortality, and include benefits gained by families through knowledge that may facilitate life choices, as well as gains generated by avoiding diagnostic delays. We also reflect on burdens such as increasing false-positive results and parental anxiety, together with risks of overdiagnosis when the natural history of a condition is poorly understood. We conclude that expanded notions of benefit and burden bring with them implications for parental consent and confidentiality and the secondary use of bloodspots.

Comparison of commercial genetic-testing services in Korea with 23andMe service

INTRODUCTION

Genetic testing services for disease prediction, drug responses, and traits are commercially available by several companies in Korea. However, there has been no evaluation study for the accuracy and usefulness of these services. We aimed to compare two genetic testing services popular in Korea with 23andMe service in the United States.

MATERIALS AND METHODS

We compared the results of two persons (one man and one woman) serviced by Hellogene Platinum (Theragen Bio Institute), DNAGPS Optimus (DNAlink), and 23andMe service.

RESULTS

Among 3 services, there were differences in the estimation of relative risks for the same disease. For lung cancer, the range of relative risk was from 0.9 to 2.09. These differences were thought to be due to the differences of applied single nucleotide polymorphisms (SNPs) in each service for the calculation of risk. Also, the algorithm and population database would have influence on the estimation of relative disease risks. The concordance rate of SNP calls between DNAGPS Optimus and 23andMe services was 100% (30/30). conclusions: Our study showed differences in disease risk estimations among three services, although they gave good concordance rate for SNP calls. We realized that the genetic services need further evaluation and standardization, especially in disease risk estimation algorithm.

Personalized medicine, availability, and group disparity: an inquiry into how physicians perceive and rate the elements and barriers of personalized medicine

BACKGROUND

The success of personalized medicine depends on factors influencing the availability and implementation of its new tools to individualize clinical care. However, little is known about physicians' views of the availability of personalized medicine across racial/ethnic groups and the relationship between perceived availability and clinical implementation. This study examines physicians' perceptions of key elements/tools and potential barriers to personalized medicine in connection with their perceptions of the availability of the latter across subpopulations.

METHODS

Study subjects consisted of physicians recruited from Cincinnati Children's Hospital Medical Center and UC Health. An electronic survey conducted from September 2012 to November 2012 recruited 104 physicians. Wilcoxon rank sum analysis compared groups.

RESULTS

Physicians were divided about whether personalized medicine contributes to health equality, as 37.4% of them believe that personalized medicine is currently available only for some subpopulations. They also rated the importance of racial/ethnic background almost as high as the importance of genetic information in the delivery of personalized medicine. Actual elements of personalized medicine rated highest include family history, drug-drug interaction alerts in medical records, and biomarker measurements to guide therapy. Costs of gene-based therapies and genetic testing were rated the most significant barriers. The ratings of several elements and barriers were associated with perceived availability of personalized medicine across subpopulations.

CONCLUSION

While physicians hold differing views about the availability and implementation of personalized medicine, they likewise establish complex relationships between race/ethnicity and personalized medicine that may carry serious implications for its clinical success.

"Would you test your children without their consent?" and other sticky dilemmas in the field of cancer genetic testing

Cancer genetic testing is surrounded by myriad ethical, legal, and psychosocial implications which are being revisited as testing expands into an everyday practice and into more complicated areas like whole exome and direct-to-consumer testing. We chose to survey cancer genetic counselors and physicians from a wide range of non-genetics specialties to determine what they would do if faced with the complex decisions associated with cancer genetic testing, how their views compare, and how they align with current guidelines and data. Genetic counselors were significantly more likely than non-genetics physicians to bill their insurance for testing (94.9 vs. 86.8 %; p = 0.001) and purchase life insurance before testing (86.6 vs. 68.6 %; p = 0.000) and were less likely to use an alias (3.2 vs. 13.2 %; p = 0.000) or order testing on their own DNA (15.3 vs. 24.2 %; p = 0.004). They were also less likely to test their minor children (0.9 vs. 33.1 %; p = 0.000) or test their children without their knowledge and consent/assent (1.4 vs.11.5 %; p = 0.000). The results of our study indicate that there is wide variation regarding what clinicians predict they would do in the areas of ethical, legal and psychosocial issues in cancer genetic testing. Cancer genetic counselors' choices are more aligned with professional guidelines, likely due to their experience in the field and awareness of current guidelines. These data are a starting point for a broader discussion of who should offer cancer genetic counseling and testing to patients, particularly as the complexity of the available testing options and associated issues increase with whole exome sequencing.

Are health professionals ready for direct-to-consumer genetic and genomic testing?

Direct-to-consumer genetic and genomic tests have been offered for over a decade. With the reduction in the cost of sequencing, the options for consumers will increase, with subsequent pressure on health services to interpret data and integrate the results into healthcare management. However, indications are that health professionals are grossly unprepared to deal with requests for support from those who have undertaken direct-to-consumer genetic or genomic tests. While benefits may be derived from patient-driven investigations, distinction needs to be made between the mostly uncertain clinical utility of susceptibility testing and the potential benefits of a reliably interpreted sequencing result. It is essential that we develop strategies, including enhanced professional education, to cope with the potential impact on the health services, rather than ignoring these developments. There may also be implications for the future of genetic counseling, with potential changes in the current paradigm.

Whole brain approaches for identification of microstructural abnormalities in individual patients: comparison of techniques applied to mild traumatic brain injury

PURPOSE

Group-wise analyses of DTI in mTBI have demonstrated evidence of traumatic axonal injury (TAI), associated with adverse clinical outcomes. Although mTBI is likely to have a unique spatial pattern in each patient, group analyses implicitly assume that location of injury will be the same across patients. The purpose of this study was to optimize and validate a procedure for analysis of DTI images acquired in individual patients, which could detect inter-individual differences and be applied in the clinical setting, where patients must be assessed as individuals.

MATERIALS AND METHODS

After informed consent and in compliance with HIPAA, 34 mTBI patients and 42 normal subjects underwent 3.0 Tesla DTI. Four voxelwise assessment methods (standard Z-score, "one vs. many" t-test, Family-Wise Error Rate control using pseudo t-distribution, EZ-MAP) for use in individual patients, were applied to each patient's fractional anisotropy (FA) maps and tested for its ability to discriminate patients from controls. Receiver Operating Characteristic (ROC) analyses were used to define optimal thresholds (voxel-level significance and spatial extent) for reliable and robust detection of mTBI pathology.

RESULTS

ROC analyses showed EZ-MAP (specificity 71%, sensitivity 71%), "one vs. many" t-test and standard Z-score (sensitivity 65%, specificity 76% for both methods) resulted in a significant area under the curve (AUC) score for discriminating mTBI patients from controls in terms of the total number of abnormal white matter voxels detected while the FWER test was not significant. EZ-MAP is demonstrated to be robust to assumptions of Gaussian behavior and may serve as an alternative to methods that require strict Gaussian assumptions.

CONCLUSION

EZ-MAP provides a robust approach for delineation of regional abnormal anisotropy in individual mTBI patients.

Direct-to-consumer genomic testing from the perspective of the health professional: a systematic review of the literature

Since the 1990s, there has been a rapid expansion in the number and type of genetic tests available via health professionals; the last 10 years, however, have seen certain types of genetic and genomic tests available direct-to-consumer. The aim of this systematic review was to explore the topic of direct-to-consumer genetic testing from the health professional perspective. Search terms used to identify studies were 'direct-to-consumer', personal genom*, health* professional*, physician* 'genomic, genetic' in five bibliographic databases, together with citation searching. Eight quantitative papers were reviewed. Findings indicate a low level of awareness and experience of direct-to-consumer testing in health professionals. Inconsistent levels of knowledge and understanding were also found with two studies showing significant effects for gender and age. Concerns about clinical utility and lack of counselling were identified. Health professionals specialising in genetics were most likely to express concerns. There was also evidence of perceived increased workload for health professionals post-testing. However, some health professionals rated such tests clinically useful and cited benefits such as the increased opportunity for early screening. Despite limited awareness, knowledge and experience of actual cases, we concluded that the concerns and potential benefits expressed may be warranted. It may be useful to explore the attitudes and experiences of health professionals in more depth using a qualitative approach. Finally, it is essential that health professionals receive sufficient education and guidelines to equip them to help patients presenting with the results of these tests.

Use of next generation sequencing technologies in research and beyond: are participants with mental health disorders fully protected?

Background

Next Generation Sequencing (NGS) is expected to help find the elusive, causative genetic defects associated with Bipolar Disorder (BD). This article identifies the importance of NGS and further analyses the social and ethical implications of this approach when used in research projects studying BD, as well as other psychiatric ailments, with a view to ensuring the protection of research participants.

Methods

We performed a systematic review of studies through PubMed, followed by a manual search through the titles and abstracts of original articles, including the reviews, commentaries and letters published in the last five years and dealing with the ethical and social issues raised by NGS technologies and genomics studies of mental disorders, especially BD. A total of 217 studies contributed to identify the themes discussed herein.

Results

The amount of information generated by NGS renders individuals suffering from BD particularly vulnerable, and increases the need for educational support throughout the consent process, and, subsequently, of genetic counselling, when communicating individual research results and incidental findings to them. Our results highlight the importance and difficulty of respecting participants’ autonomy while avoiding any therapeutic misconception. We also analysed the need for specific regulations on the use and communication of incidental findings, as well as the increasing influence of NGS in health care.

Conclusions

Shared efforts on the part of researchers and their institutions, Research Ethics Boards as well as participants’ representatives are needed to delineate a tailored consent process so as to better protect research participants. However, health care professionals involved in BD care and treatment need to first determine the scientific validity and clinical utility of NGS-generated findings, and thereafter their prevention and treatment significance.

Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting

Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantitative evaluation of disease association for uncertain or novel gene variants in an objective manner. Here, complementary predictors for missense gene variants were incorporated into a weighted Consensus framework that includes calculated reference intervals from known disease outcomes. Data visualization for clinical reporting is also discussed.

How novel molecular diagnostic technologies and biomarkers are revolutionizing genetic testing and patient care

Technological applications and novel biomarkers in the field of molecular diagnostics have never been evolving at a more rapid pace. These novel applications have the promise to change the face of clinical care as we move into the era of personalized medicine. While some of these technologies and biomarkers have been adopted by some clinical laboratories, most laboratories face a steep learning curve in bringing these dramatically new and different molecular diagnostic applications on board. Furthermore, interpreting the vast amounts and new types of data produced by these novel applications brings forth challenges for laboratorians and clinicians alike. In this article, we discuss how some of these emerging novel molecular diagnostic technologies and analytes, such as next-generation sequencing, chromosomal microarray, microRNAs and circulating fetal nucleic acids are revolutionizing patient care and personalized medicine.

Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants

The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently many more gene variants that lack clear annotation or disease association. To date, there has been very limited coverage of gene-specific predictors in the literature. Here the evaluation is presented of "gene-specific" predictor models based on a naïve Bayesian classifier for 20 gene-disease datasets, containing 3986 variants with clinically characterized patient conditions. The utility of gene-specific prediction is then compared with "all-gene" generalized prediction and also with existing popular predictors. Gene-specific computational prediction models derived from clinically curated gene variant disease datasets often outperform established generalized algorithms for novel and uncertain gene variants.

Next generation sequencing--implications for clinical practice

BACKGROUND

Genetic testing in inherited disease has traditionally relied upon recognition of the presenting clinical syndrome and targeted analysis of genes known to be linked to that syndrome. Consequently, many patients with genetic syndromes remain without a specific diagnosis.

AREAS OF AGREEMENT

New 'next-generation' sequencing (NGS) techniques permit simultaneous sequencing of enormous amounts of DNA. A slew of research publications have recently demonstrated the tremendous power of these technologies in increasing understanding of human genetic disease.

AREAS OF CONTROVERSY

These approaches are likely to be increasingly employed in routine diagnostic practice, but the scale of the genetic information yielded about individuals means that caution must be exercised to avoid net harm in this setting.

AREAS TIMELY FOR DEVELOPING RESEARCH

Use of NGS in a research setting will increasingly have a major but indirect beneficial impact on clinical practice. However, important technical, ethical and social challenges need to be addressed through informed professional and public dialogue before it finds its mature niche as a direct tool in the clinical diagnostic armoury.