Medical genetics in the genomic medicine of the 21st century

Service provision of genetics health care in Portugal

In recent decades, genetics has undergone important technological advances. The rapid shift to genomics has made a strong impact on health systems around the world. In Portugal, this huge increase in consultations and typologies of genetic tests has joined the serious limitations of the few existing genetics services. The following study aims to characterize the current state of the network of genetics services in Portugal regarding its functioning, main challenges, and opportunities. Five semi-structured interviews were conducted, corresponding to 83.33% of the directors of the public genetics services of the National Health Service. Four thematic categories emerged from the analysis: (1) specialty and technical developments, (2) structural difficulties, (3) potentialities, and (4) future directions. The developments are due to the emergence of more comprehensive genetic applications, specific protocols and patient referral standards, and accreditation of services. The main difficulties encountered in the functioning of the services were difficulty in obtaining funding, lack of human resources, service overload, and lack of exclusive time for training and research. The potentialities mentioned were the establishment of multidisciplinary teams and the best articulation with specialists from other areas. Among the various future directions pointed out, better management of patients' waiting lists, the importance of research, the simplification of test request procedures, and the creation of specialized units inside the genetic services, were reported. The results showed several gaps in the practice of medical genetics that should be addressed with the development of public policies for the recognition and restructuring of medical genetics in health care.

Global Regulatory and Public Health Initiatives to Advance Pediatric Drug Development for Rare Diseases

The literature thoroughly describes the challenges of pediatric drug development for rare diseases. This includes (1) generating interest from sponsors, (2) small numbers of children affected by a particular disease, (3) difficulties with study design, (4) lack of definitive outcome measures and assessment tools, (5) the need for additional safeguards for children as a vulnerable population, and (6) logistical hurdles to completing trials, especially with the need for longer term follow-up to establish safety and efficacy. There has also been an increasing awareness of the need to engage patients and their families in drug development processes and to address inequities in access to pediatric clinical trials. The year 2020 ushered in yet another challenge—the COVID-19 pandemic. The pediatric drug development ecosystem continues to evolve to meet these challenges. This article will focus on several key factors including recent regulatory approaches and public health policies to facilitate pediatric rare disease drug development, emerging trends in product development (biologics, molecularly targeted therapies), innovations in trial design/endpoints and data collection, and current efforts to increase patient engagement and promote equity. Finally, lessons learned from COVID-19 about building adaptable pediatric rare disease drug development processes will be discussed.

Identification of a novel homozygous variant in the alkaline phosphate (ALPL) gene associated with hypophosphatasia

The lack of awareness of patient risk factors, failure to obtain adequate family history, was discussed by clinical experience in prenatal testing of hypophosphatasia with a novel variant in the ALPL gene identified in the index case of the family.

[Medical genetics services in VenezuelaServiços de genética médica na Venezuela]

Objetivo.

Caracterizar los servicios de genética médica de Venezuela con el fin de conocer la distribución de sus recursos, servicios, tecnologías y formación profesional.

Métodos.

Se realizó una investigación descriptiva, de tipo documental, entre febrero y noviembre de 2016 de los servicios de genética, mediante la revisión de fuentes documentales primarias y el uso de una ficha de recolección de datos en las instituciones de investigación para información referente a disponibilidad de recursos humanos, servicios de atención y diagnóstico, así como formación profesional, y la base de datos de la Sociedad Venezolana de Genética Humana, que permitió identificar los recursos humanos en centros de genética. El criterio de inclusión fue instituciones con recursos humanos formados en genética.

Resultados.

Los criterios fueron cumplidos por cuatro instituciones de investigación, siete universidades y cuatro hospitales, todos del sector público. En estas instituciones trabajan 124 profesionales, 56 son médicos y 68 se desempeñan en el área de laboratorio. Sesenta y dos por ciento de los profesionales pertenecen a las instituciones de investigación; estas cuentan con servicios de atención clínico, diagnóstico molecular, bioquímico y, con menos frecuencia, los análisis citogenéticos, prenatales y forenses. Cinco regiones del país tienen entre dos y cuatro médicos genetistas por millón de habitantes. El 96% de los profesionales de laboratorio se localizan en dos regiones (Capital y Zuliana), cinco regiones carecen de ellos. Las instituciones de investigación han formado en genética el 40% de los recursos humanos actuales del país.

Conclusiones.

Los servicios de genética presentan gran variabilidad de opciones diagnósticas, un acceso limitado y grandes aportes en formación profesional; se requieren políticas coordinadas que los integre y disminuya las brechas.

The forty years of medical genetics in China

Medical genetics is the newest cutting-edge discipline that focuses on solving medical problems using genetics knowledge and methods. In China, medical genetics research activities initiated from a poor inner basis but a prosperous outer environment. During the 40 years of reform and opening-up policy, Chinese scientists contributed significantly in the field of medical genetics, garnering considerable attention worldwide. In this review, we highlight the significant findings and/or results discovered by Chinese scientists in monogenic diseases, complex diseases, cancer, genetic diagnosis, as well as gene manipulation and gene therapy. Due to these achievements, China is widely recognized to be at the forefront of medical genetics research and development. However, the significant progress and development that has been achieved could not have been accomplished without sufficient funding and a well-constructed logistics network. The successful implementation of translational and precise medicine sourced from medical genetics will depend on an open ethics policy and intellectual property protection, along with strong support at the national industry level.

Changes in Attitudes towards Marriage and Reproduction among People with a Genetic Illness

In this article, the change in attitude towards marriage and reproduction among Iranian people with a genetic illness called thalassemia has been investigated, along with an analysis of the impact brought by the national thalassemia prevention programmes, which were introduced to discourage marriage between carriers (thalassemia minor) and the birth of severe homozygous cases (thalassemia major). Marriage and reproductive choices of people with both thalassemia minor and thalassemia major were focused upon in order to prevent the birth of affected babies. Thalassemia carrier couples prefer to choose abortion of affected foetuses, rather than giving up their marriage, and some people with thalassemia major choose a person with thalassemia major as a marriage partner, though they must give up having their own child.

Sibling method increases risk assessment estimates for type 1 diabetes

We presented a risk assessment model to distinguish between type 1 diabetes (T1D) affected and unaffected siblings using only three single nucleotide polymorphism (SNP) genotypes. In addition we calculated the heritability from genome-wide identity-by-descent (IBD) sharing between full siblings. We analyzed 1,253 pairs of affected individuals and their unaffected siblings (750 pairs from a discovery set and 503 pairs from a validation set) from the T1D Genetics Consortium (T1DGC), applying a logistic regression to analyze the area under the receiver operator characteristic (ROC) curve (AUC). To calculate the heritability of T1D we used the Haseman-Elston regression analysis of the squared difference between the phenotypes of the pairs of siblings on the estimate of their genome-wide IBD proportion. The model with only 3 SNPs achieving an AUC of 0.75 in both datasets outperformed the model using the presence of the high-risk DR3/4 HLA genotype, namely AUC of 0.60. The heritability on the liability scale of T1D was approximately from 0.53 to 0.92, close to the results obtained from twin studies, ranging from 0.4 to 0.88.

Genomic medicine in gastroenterology: A new approach or a new specialty?

Throughout history, many medical milestones have been achieved to prevent and treat human diseases. Man's early conception of illness was naturally holistic or integrative. However, scientific knowledge was atomized into quantitative and qualitative research. In the field of medicine, the main trade-off was the creation of many medical specialties that commonly treat patients in advanced stages of disease. However, now that we are immersed in the post-genomic era, how should we reevaluate medicine? Genomic medicine has evoked a medical paradigm shift based on the plausibility to predict the genetic susceptibility to disease. Additionally, the development of chronic diseases should be viewed as a continuum of interactions between the individual's genetic make-up and environmental factors such as diet, physical activity, and emotions. Thus, personalized medicine is aimed at preventing or reversing clinical symptoms, and providing a better quality of life by integrating the genetic, environmental and cultural factors of diseases. Whether using genomic medicine in the field of gastroenterology is a new approach or a new medical specialty remains an open question. To address this issue, it will require the mutual work of educational and governmental authorities with public health professionals, with the goal of translating genomic medicine into better health policies.

An update to returning genetic research results to individuals: perspectives of the industry pharmacogenomics working group

The ease with which genotyping technologies generate tremendous amounts of data on research participants has been well chronicled, a feat that continues to become both faster and cheaper to perform. In parallel to these advances come additional ethical considerations and debates, one of which centers on providing individual research results and incidental findings back to research participants taking part in genetic research efforts. In 2006 the Industry Pharmacogenomics Working Group (I-PWG) offered some 'Points-to-Consider' on this topic within the context of the drug development process from those who are affiliated to pharmaceutical companies. Today many of these points remain applicable to the discussion but will be expanded upon in this updated viewpoint from the I-PWG. The exploratory nature of pharmacogenomic work in the pharmaceutical industry is discussed to provide context for why these results typically are not best suited for return. Operational challenges unique to this industry which cause barriers to returning this information are also explained.

Toward Best Practice in Using Molecular Diagnosis to Guide Medical Management, Are We There Yet?

Molecular genetics testing has made several huge breakthroughs in the past two decades and many molecular technologies have been applied to our daily medical progress. However, the clinical utility has not reach a consensus by the medical and genetic peers as well as third party payers. The predictive value and clinical applications are variable from one condition to the other. Numerous questions remain including technology deficits, data interpretation and unpredicted phenotypes in complex disorders. In this commentary, the authors reviewed the historical perspective of genetic testing and summarized the current technical deficit, clinical dilemma and suggested a few critical threshold to overcome before the implementation of useful genetic information in standard health care can become a reality.

A systematic review of factors that act as barriers to patient referral to genetic services

Patients who might benefit from genetic services may be denied access through failure to be referred. To investigate the evidence on barriers to referral to genetic services, we conducted a systematic review of empirical evidence on this topic. Nine studies were included in the review. Barriers related to non-genetic healthcare professionals were: lack of awareness of patient risk factors, failure to obtain adequate family history, lack of knowledge of genetics and genetic conditions, lack of awareness of genetic services, inadequate coordination of referral and lack of genetics workforce. Those related to individuals affected by or at risk of a genetic condition were: lack of awareness of personal risk, lack of knowledge and/or awareness of medical history of family members and lack of knowledge of genetic services. Research on access to genetic services is heterogeneous; stronger empirical evidence is needed on factors that are barriers, and further research is needed to develop 'targeted interventions' for equitable access to genetic services in a range of populations.

Bridge: a GUI package for genetic risk prediction

Background

Risk prediction models capitalizing on genetic and environmental information hold great promise for individualized disease prediction and prevention. Nevertheless, linking the genetic and environmental risk predictors into a useful risk prediction model remains a great challenge. To facilitate risk prediction analyses, we have developed a graphical user interface package, Bridge.

Results

The package is built for both designing and analyzing a risk prediction model. In the design stage, it provides an estimated classification accuracy of the model using essential genetic and environmental information gained from public resources and/or previous studies, and determines the sample size required to verify this accuracy. In the analysis stage, it adopts a robust and powerful algorithm to form the risk prediction model.

Conclusions

The package is developed based on the optimality theory of the likelihood ratio and therefore theoretically could form a model with high performance. It can be used to handle a relatively large number of genetic and environmental predictors, with consideration of their possible interactions, and so is particularly useful for studying risk prediction models for common complex diseases.

First decade of post-genomic era. Hopes, disappointments, new answers

Az első posztgenom évtized elteltével megállapítható, hogy a humán genom projekt hozadéka az alapkutatásra rendkívül jelentős volt, az orvosi ellátásban azonban a várt paradigmaváltás nem következett be, ami csalódottságot váltott ki a forradalmi változásban reménykedőkben. A kiváltó okok feltárása olyan gondolatrendszert igényel, amely alkalmas befogadni a biotechnológiai forradalom által szolgáltatott, korábban nem ismert mélységekből jövő ismereteket. A szerző egy új aspektust ajánl az eredmények értékelésére. Ha az új eredményeket a genetika eredendő transzgenerációs értelmezése mellett fejlődéstani nézőpontból is értékeljük, több kérdésben tisztább képet kapunk. A közlemény röviden bemutatja a genetika duális értelmezésének előnyeit 1. a molekuláris technológiákkal kapott eredmények klinikai értelmezésében, 2. a genetika–környezet kapcsolatának új, fejlődéstani aspektusból történő értelmezésében és 3. az új lehetőségekhez igazítandó ellátórendszer személyi feltételeinek megteremtésében. A genetika transzgenerációs aspektusa mellett a fejlődéstani szempont figyelembevétele hasznos támasz lehet kutatási stratégiák tervezésében, a kapott eredmények értékelésében, a genetika és környezet kapcsolatának értelmezésében és az egészségügyi ellátórendszer szervezésében egyaránt. Orv. Hetil., 2010, 151, 2099–2104.

Classification versus association models: should the same methods apply?

Association and classification models differ fundamentally in objectives, measurements, and clinical context specificity. Association studies aim to identify biomarker association with disease in a study population and provide etiologic insights. Common association measurements are odds ratio, hazard ratio, and correlation coefficient. Classification studies aim to evaluate biomarker use in aiding specific clinical decisions for individual patients. Common classification measurements are sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Good association is usually a necessary, but not a sufficient, condition for good classification. Methods for developing classification models have mainly used the criteria for association models, usually minimizing total classification error without consideration of clinical application settings, and therefore are not optimal for classification purposes. We suggest that developing classification models by focusing on the region of receiver operating characteristic (ROC) curve relevant to the intended clinical application optimizes the model for the intended application setting.

The medical geneticist as expert in the transgenerational and developmental aspects of diseases

The increased knowledge of genetics has raised new questions, and confusion has been growing about the evaluation of the results of recent research and the role of geneticists in the genomic medicine. If we focus on transgenerational and developmental aspects of diseases, the answers might be more evident.

Using the optimal robust receiver operating characteristic (ROC) curve for predictive genetic tests

Current ongoing genome-wide association (GWA) studies represent a powerful approach to uncover common unknown genetic variants causing common complex diseases. The discovery of these genetic variants offers an important opportunity for early disease prediction, prevention, and individualized treatment. We describe here a method of combining multiple genetic variants for early disease prediction, based on the optimality theory of the likelihood ratio (LR). Such theory simply shows that the receiver operating characteristic (ROC) curve based on the LR has maximum performance at each cutoff point and that the area under the ROC curve so obtained is highest among that of all approaches. Through simulations and a real data application, we compared it with the commonly used logistic regression and classification tree approaches. The three approaches show similar performance if we know the underlying disease model. However, for most common diseases we have little prior knowledge of the disease model and in this situation the new method has an advantage over logistic regression and classification tree approaches. We applied the new method to the type 1 diabetes GWA data from the Wellcome Trust Case Control Consortium. Based on five single nucleotide polymorphisms, the test reaches medium level classification accuracy. With more genetic findings to be discovered in the future, we believe a predictive genetic test for type 1 diabetes can be successfully constructed and eventually implemented for clinical use.

Bagging optimal ROC curve method for predictive genetic tests, with an application for rheumatoid arthritis

Translation studies have been initiated to assess the combined effect of genetic loci from recently accomplished genome-wide association studies and the existing risk factors for early disease prediction. We propose a bagging optimal receiver operating characteristic (ROC) curve method to facilitate this research. Through simulation and real data application, we compared the new method with the commonly used allele counting method and logistic regression, and found that the new method yields a better performance. The new method was applied on the Wellcome Trust data set to form a predictive genetic test for rheumatoid arthritis. The formed test reached an area under the curve (AUC) value of 0.7.

Distress and burnout among genetic service providers

PURPOSE

To determine the nature, sources, prevalence, and consequences of distress and burnout among genetics professionals.

METHODS

Mailed survey of randomly selected clinical geneticists (MDs), genetic counselors, and genetic nurses.

RESULTS

Two hundred and fourteen providers completed the survey (55% response rate). Eight discrete sources of distress were identified forming a valid 28-item scale (alpha = 0.89). The greatest sources of distress were compassion stress, the burden of professional responsibility, negative patient regard, and concerns about informational bias. Genetic counselors were significantly more likely to experience personal values conflicts, burden of professional responsibility, and concerns about informational bias than MDs or nurses. Burnout scores were lower among those practicing more than 20 years and nurses. Distress scores were positively correlated with burnout and professional dissatisfaction (P < 0.0001). Eighteen percent of respondents think about leaving patient care, and burnout was the most significant predictor. Predictors of burnout included greater distress, fewer years in practice, working in university-based settings, being a genetic counselor or an MD, and deriving less meaning from patient care.

CONCLUSIONS

Genetic service providers experience various types of distress that may be risk factors for burnout and professional dissatisfaction. Interventions to reduce distress and burnout are needed for both trainees and practitioners.

Using the optimal receiver operating characteristic curve to design a predictive genetic test, exemplified with type 2 diabetes

Current extensive genetic research into common complex diseases, especially with the completion of genome-wide association studies, is bringing to light many novel genetic risk loci. These new discoveries, along with previously known genetic risk variants, offer an important opportunity for researchers to improve health care. We describe a method of quick evaluation of these new findings for potential clinical practice by designing a new predictive genetic test, estimating its classification accuracy, and determining the sample size required for the verification of this accuracy. The proposed predictive test is asymptotically more powerful than tests built on any other existing method and can be extended to scenarios where loci are linked or interact. We illustrate the approach for the case of type 2 diabetes. We incorporate recently discovered risk factors into the proposed test and find a potentially better predictive genetic test. The area under the receiver operating characteristic (ROC) curve (AUC) of the proposed test is estimated to be higher (AUC = 0.671) than for the existing test (AUC = 0.580).

Hereditary cancer syndrome diagnosis: molecular genetic clues and cancer control

Oncologists who are aware of the progress in hereditary cancer syndrome diagnosis, and, in particular, of how this effort may be effectively facilitated through a comprehensive family history in concert with molecular genetic studies, are in the envious position of designing highly targeted screening and management programs for the membership of these cancer-prone families. The Lynch syndrome is discussed as a clinical model wherein the presence of mismatch repair mutations provides a high level of diagnostic certainty for the initiation of targeted cancer screening and management. The familial atypical multiple mole melanoma-pancreatic cancer (FAMMM-PC) syndrome, on the other hand, provides another model with cancer-control potential. Given its phenotypic features of multiple atypical nevi, high total body mole count and cutaneous malignant melanoma, coupled with the integral association of PC in a subset of FAMMM kindreds with the CDKN2A germline mutation, this may result in a perhaps lower level of diagnostic certainty when compared with the Lynch syndrome. This knowledge may impact upon progress in the earlier diagnosis of melanoma and provide an impetus for creative diagnostic methods in PC, a disease that, at this time, demonstrates a mortality rate virtually identical to its incidence rate.