Individualized medicine enabled by genomics in Saudi Arabia

Prognostic value of glucose transporter proteins-1 (GLUT1) in breast carcinoma

Several studies have reported increased glucose transporters (GLUT) expression in different cancer types, including breast cancer. The primary purpose of this study is to examine GLUT1 immunoexpression in breast cancer patients in Saudi Arabia and to determine its significance. The study examined the association between GLUT1 immunophenotype and the clinicopathological characteristics in breast cancer. GLUT1 expression was analyzed in retrospectively collected tissue samples (n = 578) from breast cancer patients using immunohistochemistry. A total of 311 (54%) of the cases expressed GLUT1 cytoplasmic immunohistochemical staining. In univariate analysis, we found a significant association between GLUT1 expression and high-grade tumors (p < 0.0001). Positive estrogen and progesterone receptor results predicted lower GLUT1 immunoexpression (p < 0.0001 for both). Vascular invasion showed a significant association with GLUT1 immunoexpression (p = 0.045). Our findings support that GLUT1 immunohistochemistry can be used as a marker to determine the grade and hormonal receptor status in breast cancer.

AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants

BACKGROUND & OBJECTIVE

Genomic medicine stands to be revolutionized by understanding single nucleotide variants (SNVs) and their expression in single-gene disorders (Mendelian diseases). Computational tools can play a vital role in the exploration of such variations and their pathogenicity. Consequently, we developed the ensemble prediction tool AllelePred to identify deleterious SNVs and disease causative genes.

RESULTS

The model utilizes different population genetics backgrounds and restricted criteria for features selection to help generate high accuracy results. In comparison to other tools, such as Eigen, PROVEAN, and fathmm-MKL our classifier achieves higher accuracy (98%), precision (96%), F1 score (93%), and coverage (100%) for different types of coding variants. The new method was also compared against a bioinformatics analytical workflow, which uses gnomAD overall AFs (less than 1%) and CADD (scaled C-score of at least 15). Furthermore, this research highlights the stature of genetic variant sharing and curation. We accumulated a list of highly probable deleterious variants and recommended further experimental validation before medical diagnostic usage.

CONCLUSIONS

The ensemble prediction tool AllelePred enables increased accuracy in recognizing deleterious SNVs and the genetic determinants in real clinical data.

Empowering quality data - the gordian knot of bringing real innovation into healthcare system

OBJECTIVES

The introduction of Personalised Medicine (PM) into healthcare systems could benefit from a clearer understanding of the distinct national and regional frameworks around the world. Recent engagement by international regulators on maximising the use of real-world evidence (RWE) has highlighted the scope for improving the exploitation of the treasure-trove of health data that is currently largely neglected in many countries. The European Alliance for Personalised Medicine (EAPM) led an international study aimed at identifying the current status of conditions.

METHODS

A literature review examined how far such frameworks exist, with a view to identifying conducive factors - and crucial gaps. This extensive review of key factors across 22 countries and 5 regions revealed a wide variety of attitudes, approaches, provisions and conditions, and permitted the construction of a comprehensive overview of the current status of PM. Based on seven key pillars identified from the literature review and expert panels, the data was quantified, and on the basis of further analysis, an index was developed to allow comparison country by country and region by region.

RESULTS

The results show that United States of America is leading according to overall outcome whereas Kenya scored the least in the overall outcome.

CONCLUSIONS

Still, common approaches exist that could help accelerate take-up of opportunities even in the less prosperous parts of the world.

Perceived risks of over-the-counter medication use among pregnant Saudi mothers: A cross-sectional study

Objectives

Many women use over-the-counter (OTC) medicines, particularly during pregnancy. Therefore, this study investigated the perceived risks of using OTC medicines among pregnant Saudi mothers.

Methods

With a cross-sectional design and purposive sampling, the 28-item Drug Use Health Belief Scale was used to collect data from pregnant Saudi mothers (n = 366) in a general tertiary hospital. The data were analyzed with descriptive and inferential statistics. After normality testing, the percentages, mean scores, and standard deviations were used to examine the demographic data. One-way ANOVA was used to identify the relationships between perceived risks on the Health Belief Scale and the participants' sociodemographic profile variables. Post-hoc tests were used to identify differences in the independent variables among groups. The statistical significance threshold was set at p ≤ 0.05.

Results

Across the five domains of the Health Belief Scale, the perceived susceptibility domain had the highest rank (0.36). Significant differences were observed between the mean scores of pregnant Saudi mothers' perceptions of susceptibility and the benefits of using OTC medications (p = 0.05), perceptions of susceptibility (p < 0.001), and benefits while using OTC medications (p = 0.018) than those who did not use OTC medications. However, no significant differences were observed in the degree of perceived severity, barriers, and self-efficacy in mothers using OTC medications (p > 0.05).

Conclusion

Notable differences were found in pregnant women's perceptions of the risks of using OTC medications. Greater awareness of the risks of OTC medication use during pregnancy is required. To ensure mothers' safety, a collaboration between prenatal multidisciplinary team of professionals (e.g., doctors, nurses, midwives) in community and hospital settings should be prioritized.

Genetic data sharing and artificial intelligence in the era of personalized medicine based on a cross-sectional analysis of the Saudi human genome program

The success of the Saudi Human Genome Program (SHGP), one of the top ten genomic programs worldwide, is highly dependent on the Saudi population embracing the concept of participating in genetic testing. However, genetic data sharing and artificial intelligence (AI) in genomics are critical public issues in medical care and scientific research. The present study was aimed to examine the awareness, knowledge, and attitude of the Saudi society towards the SHGP, the sharing and privacy of genetic data resulting from the SHGP, and the role of AI in genetic data analysis and regulations. Results of a questionnaire survey with 804 respondents revealed moderate awareness and attitude towards the SHGP and minimal knowledge regarding its benefits and applications. Respondents demonstrated a low level of knowledge regarding the privacy of genetic data. A generally positive attitude was found towards the outcomes of the SHGP and genetic data sharing for medical and scientific research. The highest level of knowledge was detected regarding AI use in genetic data analysis and privacy regulation. We recommend that the SHGP’s regulators launch awareness campaigns and educational programs to increase and improve public awareness and knowledge regarding the SHGP’s benefits and applications. Furthermore, we propose a strategy for genetic data sharing which will facilitate genetic data sharing between institutions and advance Personalized Medicine in genetic diseases’ diagnosis and treatment.

A Narrative Review of Implementing Precision Oncology in Metastatic Castration-Resistant Prostate Cancer in Emerging Countries

The therapeutic landscape of metastatic castration-resistant prostate cancer (mCRPC) has evolved considerably with the introduction of newer agents, such as poly-ADP ribose polymerase (PARP) inhibitors targeting DNA damage repair mutations. Combining and sequencing novel and existing therapies appropriately is necessary for optimizing the management of mCRPC and ensuring better treatment outcomes. The purpose of this review is to provide evidence-based answers to key clinical questions on treatment selection, treatment sequencing patterns, and factors influencing treatment decisions in the management of mCRPC in the era of PARP inhibitors. This article can also serve as a comprehensive guide to clinicians for optimizing genetic testing and counseling and management of patients with mCRPC. Although the PROfound study has validated the concept of PARP sensitivity across multiple genes associated with homologous recombination repair (HRR) in mCRPC and highlighted the importance of genomic testing in this at-risk patient population, it still remains unclear how patients with rarer HRR mutations will respond to PARP inhibitors. Therefore, real-world data obtained through registry-based randomized controlled trials in the future may help produce robust scientific evidence for supporting optimal clinician decision-making in the management of mCRPC.

Pharmacogenetics: Knowledge assessment amongst Syrian pharmacists and physicians

Background

Pharmacogenetics targets genetic variations that influence drug response. It is relatively a new science that has not been vastly employed in most developing countries including Syria. Therefore we aimed at evaluating the depth of knowledge in pharmacogenetics and the attitude towards it amongst Syrian pharmacists and physicians.

Methods

We carried out an internet-based questionnaire consisted of 26 questions, sent through specialized websites and private groups with a large number of pharmacists and physicians members. The survey was available online for a period of 1 month.

Results

The total number of respondents was 154, mostly female pharmacists. Our statistical analysis showed a strong positive association between profession (in favour of pharmacists) and pharmacogenetics knowledge p = 0.049; however, no correlation with experience p = 0.811 was found. A significant difference was reported between the knowledge of pharmacists and physicians p = 0.001 concerning drugs that need pharmacogenetics testing before being prescribed. The majority of respondents had no information about applying genetic tests in Syria before prescribing medications nor did they possess the knowledge regarding drugs that show differential responses in patients according to their unique genotypes. In our study, the percentage knowledge assessment score was low in general (mean ± Standard deviation, SD) (46% ± 13.9%). The majority of the respondents agreed that pharmacists should provide counselling to patients on the subject of pharmacogenetics. Respondents’ opinions varied concerning making pharmacogenetics learning a priority.

Conclusion

Lack of pharmacogenetics knowledge was found amongst respondents in general. Our findings raise concerns about the lack of awareness amongst physicians, which may hinder the implementation of this crucial field in Syria. We suggest an emphasis on the role of education, training, and conducting genotyping research on the Syrian population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12913-021-07040-9.

Knowledge, perception, and confidence of hospital pharmacists toward pharmacogenetics in Jeddah, Kingdom of Saudi Arabia

Background

Integrating pharmacogenetics (PGx) testing into clinical practice leads to personalized medicine, which improves treatments’ efficacy and safety. Successful implementation of such a service requires sufficient knowledge, perception, and self-confidence among healthcare providers, especially pharmacists.

Objectives

To evaluate governmental hospital pharmacists’ knowledge, perception, and self-confidence toward PGx testing in Jeddah, Kingdom of Saudi Arabia.

Method

This cross-sectional study was conducted using previously validated questionnaire. Pharmacists working in five randomly selected general governmental hospitals in Jeddah between August and October 2019 were interviewed. Comparative and descriptive analyses were used to analyze the data, and the significance level was at P-value < 0.05.

Results

A total of 119 pharmacists with a mean (±SD) age of 31.2 (±5.05) years were included with a response rate of 79.3%. The average total mean (±SD) score for PGx knowledge-based questions was low (2.4 ± 1.09 out of 5). Most of the participants, with a total mean score of (10.1 ± 1.6 out of 12), revealed a positive perception toward PGx testing and its implications. A moderate self-confidence score for utilizing PGx testing (4.3 ± 2.3 out of 8) was observed among the participants. Pharmacists who had completed postgraduate studies had a statistically higher mean knowledge score (P = 0.006) compared with pharmacists with undergraduate degrees.

Conclusion

Governmental hospital pharmacists have limited knowledge and understanding about PGx testing; however, the majority expressed a high level of awareness and agreed that PGx testing is a valuable tool for enhancing drug efficacy and safety. The study also highlighted the importance of improving pharmacists’ knowledge about PGx testing, which will help them in implementing such a valuable service into their clinical practice in Saudi hospitals.

Knowledge, Attitudes, and Perceived Barriers toward Genetic Testing and Pharmacogenomics among Healthcare Workers in the United Arab Emirates: A Cross-Sectional Study

In order to successfully translate the scientific models of genetic testing and pharmacogenomics into clinical practice, empowering healthcare workers with the right knowledge and functional understanding on the subject is essential. Limited research in the United Arab Emirates (UAE) have assessed healthcare worker stances towards genomics. This study aimed to assess healthcare workers’ knowledge and attitudes on genetic testing. A cross-sectional study was conducted among healthcare workers practicing in either public or private hospitals or clinics as pharmacists, nurses, physicians, managers, and allied health. Participants were recruited randomly and via snowball techniques. Surveys were collected between April and September 2019; out of 552 respondents, 63.4% were female, the mean age was 38 (±9.6) years old. The mean knowledge score was 5.2 (±2.3) out of nine, which shows a fair level of knowledge. The scores of respondents of pharmacy were 5.1 (±2.5), medicine 6.0 (±2.0), and nursing 4.8 (±2.1). All participants exhibited a fair knowledge level about genetic testing and pharmacogenomics. Of the respondents, 91.9% showed a positive attitude regarding availability of genetic testing. The top identified barrier to implementation was the cost of testing (62%), followed by lack of training or education and insurance coverage (57.8% and 57.2%, respectively). Building upon the positive attitudes and tackling the barriers and challenges will pave the road for full implementation of genetic testing and pharmacogenomics in the UAE. We recommend empowering healthcare workers by improving needed and tailored competencies related to their area of practice. We strongly urge the stakeholders to streamline and benchmark the workflow, algorithm, and guidelines to standardize the health and electronic system. Lastly, we advocate utilizing technology and electronic decision support as well as the translational report to back up healthcare workers in the UAE.

Clinical pharmacology applications in clinical drug development and clinical care: A focus on Saudi Arabia

Drug development, from preclinical to clinical studies, is a lengthy and complex process. There is an increased interest in the Kingdom of Saudi Arabia (KSA) to promote innovation, research and local content including clinical trials (Phase I-IV). Currently, there are over 650 registered clinical trials in Saudi Arabia, and this number is expected to increase. An important part of drug development and clinical trials is to assure the safe and effective use of drugs. Clinical pharmacology plays a vital role in informed decision making during the drug development stage as it focuses on the effects of drugs in humans. Disciplines such as pharmacokinetics, pharmacodynamics and pharmacogenomics are components of clinical pharmacology. It is a growing discipline with a range of applications in all phases of drug development, including selecting optimal doses for Phase I, II and III studies, evaluating bioequivalence and biosimilar studies and designing clinical studies. Incorporating clinical pharmacology in research as well as in the requirements of regulatory agencies will improve the drug development process and accelerate the pipeline. Clinical pharmacology is also applied in direct patient care with the goal of personalizing treatment. Tools such as therapeutic drug monitoring, pharmacogenomics and model informed precision dosing are used to optimize dosing for patients at an individual level. In KSA, the science of clinical pharmacology is underutilized and we believe it is important to raise awareness and educate the scientific community and healthcare professionals in terms of its applications and potential. In this review paper, we provide an overview on the use and applications of clinical pharmacology in both drug development and clinical care.

Knowledge, Perception, and Application of Pharmacogenomics Among Hospital Pharmacists in Saudi Arabia

Introduction

The accelerated transformation in the healthcare system supported by the Saudi Vision 2030 makes the present the best time to start the real application of pharmacogenomics in Saudi Arabia. The current study aimed to assess the knowledge, perception and the application status of pharmacogenomics among pharmacists in the hospital settings in Saudi Arabia.

Methods

This cross-sectional observational survey was conducted among 206 qualified pharmacists working in Saudi hospitals. A self-administered questionnaire was sent to all participants.

Results

Only 30% of the pharmacists had received any type of formal training on PGx. Of these, only nine participants had actually put the knowledge into practice. Participants showed a moderate to low level of knowledge when responded to the pharmacogenomic knowledge indicators used in the study. The low knowledge and the availability of the pharmacogenetic test are the main barriers for the low adoption of the pharmacogenomics in the clinical practice. Approximately 83% felt the need to know more about pharmacogenomics. Participants show positive perception with high motivation levels to incorporate this technology in practice. For example, 76% stated that pharmacogenetic testing should be applied to pharmacy practice. Around 38% of participants reported that the Saudi government and the Saudi FDA had been promoting the pharmacogenomics. However, 50% of the total participants reported that their hospital management is unaware of the pharmacogenomics importance in clinical practice.

Discussion

This study emphasizes on two needs which can help promote the use and implementation of pharmacogenomics. One is the need to update the pharmacy education and training programs with pharmacogenomic-related areas to raise the pharmacist’s knowledge and practical skill to apply pharmacogenomics in the clinical practice effectively. Another need is to increase the awareness of the decision and policy-makers with the importance of pharmacogenomics for the patient benefit and safety. This preliminary evaluation will provide future insight into the best approach to applying pharmacogenomics in the Saudi healthcare system.

GENE2D: A NoSQL Integrated Data Repository of Genetic Disorders Data

There are few sources from which to obtain clinical and genetic data for use in research in Saudi Arabia. Numerous obstacles led to the difficulty of integrating these data from silos and scattered sources to provide standardized access to large data sets for patients with common health conditions. To this end, we sought to contribute to this area and offer a practical and easy-to-implement solution. In this paper, we aim to design and implement a "not only SQL" (NoSQL) based integration framework to generate an Integrated Data Repository of Genetic Disorders Data (GENE2D) to integrate data from various genetic clinics and research centers in Saudi Arabia and provide an easy-to-use query interface for researchers to conduct their studies on large datasets. The major components involved in the GENE2D architecture consists of the data sources, the integrated data repository (IDR) as a central database, and the application interface. The IDR uses a NoSQL document store via MongoDB (an open source document-oriented database program) as a backend database. The application interface called Query Builder provides multiple services for data retrieval from the database using a custom query to answer simple or complex research questions. The GENE2D system demonstrates its potential to help grow and develop a national genetic disorders database in Saudi Arabia.

G3DMS: Design and Implementation of a Data Management System for the Diagnosis of Genetic Disorders

Current health information systems used in genetic research centers and clinics in the Kingdom of Saudi Arabia have failed to enable researchers and health care physicians to utilize genetic and clinical data in their research. In this paper, we aim to design and implement a Genetic Disorders Diagnosis Data Management System (G3DMS) to support clinicians in the process of diagnosing genetic diseases and conducting genetic studies. A case study was undertaken to analyze a health information system in Saudi to understand its design problems via a brainstorming method. We then used the Barker’s system design method and a prototype to validate our proposed system via usability testing. This research has resulted in the development of the G3DMS that comprises: electronic data-capture forms for data entry; a customized query builder to display and modify patient data as well as form research queries; a module that allows historical data to be uploaded in the form of bulk data using a template; export data options to Excel and JavaScript Object Notation (JSON) format; and authorization access for healthcare researchers and clinicians. The G3DMS was implemented in the Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Jeddah, KSA.

Assessment of healthcare professionals' knowledge, attitudes, and perceived challenges of clinical pharmacogenetic testing in Egypt

Aim: We evaluated healthcare practitioners' perspectives regarding clinical pharmacogenetics in Cairo, Egypt. Materials & methods: We administered a paper-based survey to pharmacists and physicians practicing at Children's Cancer Hospital Egypt. The survey assessed practitioners' knowledge, attitudes, and perspectives about pharmacogenetic testing. Results: The study included 184 respondents (67.9% pharmacists; 32.1% physicians. Overall, the pharmacogenetic knowledge was low (mean = 41.7%) but attitudes toward pharmacogenetic testing and its potential clinical application were generally positive. Pharmacists responded more favorably than physicians to statements attributing the responsibility of applying pharmacogenetics in the clinical setting to their profession. However, several challenges were identified; the most common being: lack of pharmacogenetic knowledge and skill, lack of pharmacogenetic testing devices, and limited funding. Conclusion: Future efforts to promote pharmacogenetic implementation should focus on foundational education, practical training, and exploration of potential funding sources.

The road towards data integration in human genomics: players, steps and interactions

Thousands of new experimental datasets are becoming available every day; in many cases, they are produced within the scope of large cooperative efforts, involving a variety of laboratories spread all over the world, and typically open for public use. Although the potential collective amount of available information is huge, the effective combination of such public sources is hindered by data heterogeneity, as the datasets exhibit a wide variety of notations and formats, concerning both experimental values and metadata. Thus, data integration is becoming a fundamental activity, to be performed prior to data analysis and biological knowledge discovery, consisting of subsequent steps of data extraction, normalization, matching and enrichment; once applied to heterogeneous data sources, it builds multiple perspectives over the genome, leading to the identification of meaningful relationships that could not be perceived by using incompatible data formats. In this paper, we first describe a technological pipeline from data production to data integration; we then propose a taxonomy of genomic data players (based on the distinction between contributors, repository hosts, consortia, integrators and consumers) and apply the taxonomy to describe about 30 important players in genomic data management. We specifically focus on the integrator players and analyse the issues in solving the genomic data integration challenges, as well as evaluate the computational environments that they provide to follow up data integration by means of visualization and analysis tools.

Prognostic value of Osteopontin (SPP1) in colorectal carcinoma requires a personalized molecular approach

Stratification of colorectal cancer for better management and tangible clinical outcomes is lacking in clinical practice. To reach this goal, the identification of reliable biomarker(s) is a prerequisite to deliver personalized colorectal cancer theranostics. Osteopontin (SPP1) is a key extracellular matrix protein involved in several pathophysiological processes including cancer progression and metastasis. However, the exact molecular mechanisms regulating its expression, localization, and molecular functions in cancer are still poorly understood. This study was designed to investigate the SPP1 expression profiles in Saudi colorectal cancer patients, and to assess its prognostic value. Hundred thirty-four (134) archival paraffin blocks of colorectal cancer were collected from King Abdulaziz University Hospital, Saudi Arabia. Tissue microarrays were constructed, and automated immunohistochemistry was performed to evaluate SPP1 protein expression patterns in colorectal cancer. About 20% and 23% of our colorectal cancer samples showed high SPP1 cytoplasmic and nuclear expression patterns, respectively. Cytoplasmic SPP1 did not correlate with age, gender, tumor size, and location. However, significant correlations were observed with tumor grade (p = 0.008), tumor invasion (p = 0.01), and distant metastasis (p = 0.04). Kaplan-Meier survival analysis showed a significantly lower recurrence rate in patients with higher SPP1 cytoplasmic expression (p = 0.05). At multivariate analysis, high SPP1 cytoplasmic expression was an independent favorable prognostic marker (p = 0.02). However, nuclear SPP1 expression did not show any prognostic value (p = 0.712). Our results showed a particular SPP1 prognostic relevance that is not in line with most colorectal cancer previous studies that may be attributed to the molecular pathophysiology of our colorectal cancer cohort. Saudi Arabia has both specific genomic makeup and particular environment that could lead to distinctive molecular roots of cancer. SPP1 has several isoforms, tissue localizations and molecular functions, signaling pathways, and downstream molecular functions. Therefore, a more individualized approach for CRC studies and particularly SPP1 prognosis outcomes' assessment is highly recommended toward precision oncology.

Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications

PURPOSE

Pre-implantation genetic diagnosis (PGD) for molecular disorders requires the construction of parental haplotypes. Classically, haplotype resolution ("phasing") is obtained by genotyping multiple polymorphic markers in both parents and at least one additional relative. However, this process is time-consuming, and immediate family members are not always available. The recent availability of massive genomic data for many populations promises to eliminate the needs for developing family-specific assays and for recruiting additional family members. In this study, we aimed to validate population-assisted haplotype phasing for PGD.

METHODS

Targeted sequencing of CFTR gene variants and ~ 1700 flanking polymorphic SNPs (± 2 Mb) was performed on 54 individuals from 12 PGD families of (a) Full Ashkenazi (FA; n = 16), (b) mixed Ashkenazi (MA; n = 23 individuals with at least one Ashkenazi and one non-Ashkenazi grandparents), or (c) non-Ashkenazi (NA; n = 15) descent. Heterozygous genotype calls in each individual were phased using various whole genome reference panels and appropriate computational models. All computationally derived haplotype predictions were benchmarked against trio-based phasing.

RESULTS

Using the Ashkenazi reference panel, phasing of FA was highly accurate (99.4% ± 0.2% accuracy); phasing of MA was less accurate (95.4% ± 4.5% accuracy); and phasing of NA was predictably low (83.4% ± 6.6% accuracy). Strikingly, for founder mutation carriers, our haplotyping approach facilitated near perfect phasing accuracy (99.9% ± 0.1% and 98.2% ± 2.8% accuracy for W1282X and delF508 carriers, respectively).

CONCLUSIONS

Our results demonstrate the feasibility of replacing classical haplotype phasing with population-based phasing with uncompromised accuracy.

Genomics for All: International Open Science Genomics Projects and Capacity Building in the Developing World

Genomic medicine applications have the potential to considerably improve health care in developing countries in the coming years. However, if developing countries do not improve their capacity for research and development (R&D) in the field, they might be left out of the genomics revolution. Large-scale and widely accessible databases for storing and analyzing genomic data are crucial tools for the advancement of genomic medicine. Building developing countries' capacity in genomics is accordingly closely linked to their involvement in international human genomics research initiatives. The purpose of this paper is to conduct a pilot study on the impact of international open science genomics projects on capacity building in R&D in developing countries. Using indicators we developed in previous work to measure the performance of international open science genomics projects, we analyse the policies and practices of four key projects in the field: the International HapMap Project, the Human Heredity and Health in Africa Initiative, the Malaria Genomic Epidemiology Network and the Structural Genomics Consortium. The results show that these projects play an important role in genomics capacity building in developing countries, but play a more limited role with regard to the potential redistribution of the benefits of research to the populations of these countries. We further suggest concrete initiatives that could facilitate the involvement of researchers from developing countries in the international genomics research community and accelerate capacity building in the developing world.

Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy

Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple "transplantation of genomics" from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the "Fast-Second Winner" model of innovation that supports innovation commencing not only "upstream" of discovery science but also "mid-stream," building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective learning from other innovators' mistakes upstream in discovery science and boost the probability of success for translation and implementation when resources are limited. This à la carte model of global innovation and development strategy offers multiple entry points into the global genomics innovation ecosystem for developing countries, whether or not extensive and expensive discovery infrastructures are already in place. Ultimately, broadening our thinking beyond the linear model of innovation will help us to enable the vision and practice of genomics without borders in both developed and resource-limited settings.

The development of large-scale de-identified biomedical databases in the age of genomics-principles and challenges

Contemporary biomedical databases include a wide range of information types from various observational and instrumental sources. Among the most important features that unite biomedical databases across the field are high volume of information and high potential to cause damage through data corruption, loss of performance, and loss of patient privacy. Thus, issues of data governance and privacy protection are essential for the construction of data depositories for biomedical research and healthcare. In this paper, we discuss various challenges of data governance in the context of population genome projects. The various challenges along with best practices and current research efforts are discussed through the steps of data collection, storage, sharing, analysis, and knowledge dissemination.

Membranous or Cytoplasmic HER2 Expression in Colorectal Carcinoma: Evaluation of Prognostic Value Using Both IHC & BDISH

BACKGROUND

Human epidermal growth factor recptor-2 (HER2) was identified as a driver gene in several types of cancers with both prognostic and predictive value. However, the molecular association of HER2 gene mutation with HER2 gene amplification and/or protein expression in cancer tissues has not been clearly defined. Moreover, there is little information available on HER2 status role in tumor progression and metastasis in colorectal carcinoma (CRC) compared to other solid tumors. The aim of this study was to evaluate both HER2 amplification and protein expression profiles using immunohistochemistry (IHC) and bright-field dual in situ hybridization (BDISH) techniques, respectively.

PATIENTS AND METHODS

Tissue microarray (TMA) was constructed to accommodate a total of 243 CRC formalin-fixed paraffin embedded (FFPE) samples of consent patients and stained by IHC and BDISH methods. The expression patterns of HER2 protein status were evaluated and correlated to HER2 gene amplification status and then assessed for its prognostic value.

RESULTS

The expression profile of 58% samples showed cytoplasmic expression patterns of different categories. Interestingly, only 1% showed strong (+3) membranous expression pattern of HER2 with perfect match with their corresponding gene amplification status (>2). However, the cytoplasmic HER2 protein status did not show significant correlation with most clinicopathological features and survival outcomes except with age (p = 0.04) and tumor size (p = 0.03).

CONCLUSION

We demonstrated that the membranous HER2 gene/protein status is infrequent, while the main fraction of HER2 overexpression was cytoplasmic and lacking prognostic value. This cytoplasmic HER2 overexpression was induced through a gene-amplification independent pathway, making the HER2 gene status evaluation approach in those cases not worthy. Further investigations about the molecular pathways of the cytoplasmic HER2 protein in CRC and its associations with survival outcomes are required to allow either a breakthrough in CRC management; or to confirm the hypothesis of a marginal role in CRC onset and progression.

Chromosomal abnormalities in infertile men with azoospermia and severe oligozoospermia in Qatar and their association with sperm retrieval intracytoplasmic sperm injection outcomes

Objective

To study the types and incidence of chromosomal abnormalities in infertile men with azoospermia and severe oligozoospermia in Qatar, and to compare the hormonal changes, testicular sperm retrieval rate, and intracytoplasmic sperm injection (ICSI) outcome between patients with chromosomal abnormalities and patients with idiopathic infertility.

Patients and methods

This study involved the retrospective chart review of 625 infertile male patients attending an academic tertiary medical centre in Qatar. Retrieved information included data on medical history, family history, clinical examination, semen analysis, initial hormonal profiles, and genetic studies, ICSI, and sperm retrieval results.

Results

The incidence of chromosomal abnormalities was 9.59% (10.6% amongst Qatari patients, 9.04% amongst non-Qataris). About 63.6% of the sample had azoospermia, of whom 10.8% had chromosomal abnormalities. Roughly 36.4% of the sample had oligozoospermia, of whom 7.5% had chromosomal abnormalities. There were no differences between patients with chromosomal abnormalities and those with idiopathic infertility for demographic and infertility features; but for the hormonal profiles, patients with idiopathic infertility had significantly lower luteinising hormone and follicle-stimulating hormone values. For ICSI outcomes, patients with chromosomal abnormalities had a significantly lower total sperm retrieval rate (47.4% vs 65.8%), surgical sperm retrieval rate (41.2% vs 58.1%), and lower clinical pregnancy rate (16.7% vs 26.6%) when compared to the idiopathic infertility group.

Conclusion

The incidence of chromosomal abnormalities in Qatar as a cause of severe male infertility is within a similar range as their prevalence internationally.

Assessment of knowledge about biobanking among healthcare students and their willingness to donate biospecimens

Background

Biobanks and biospecimen collections are becoming a primary means of delivering personalized diagnostics and tailoring individualized therapeutics. This shift towards precision medicine (PM) requires interactions among a variety of stakeholders, including the public, patients, healthcare providers, government, and donors. Very few studies have investigated the role of healthcare students in biobanking and biospecimen donations. The main aims of this study were (1) to evaluate the knowledge of senior healthcare students about biobanks and (2) to assess the students’ willingness to donate biospecimens and the factors influencing their attitudes.

Methods

A cross-sectional study was conducted among senior healthcare students at King Abdulaziz University (KAU), Saudi Arabia. The data were obtained using a self-administered questionnaire in English. In addition to the respondents’ biographical data section, the questionnaire assessed the respondents’ general knowledge about biobanking, the factors influencing their willingness to donate biospecimens to biobanks and their general attitudes towards biomedical research.

Results

A total of 597 senior healthcare students were included in the study. The general knowledge score was 3.2 (±1.6) out of 7. Only approximately 44% and 27% of students were aware of the terms “Human Genome Project” (HGP) and “biobank,” respectively. The majority of the students (89%) were willing to donate biospecimens to biobanks. Multiple factors were significantly associated with their willingness to donate, including their perceived general health (p < 0.001), past experience with both tissue testing (p < 0.04) and tissue donation (p < 0.001), biobanking knowledge score (p < 0.001) and biomedical research attitude score (p < 0.001). The main reasons for students’ willingness to donate were advancement of medical research and societal benefits, whereas misuse of biospecimens and confidentiality breaches were the main reasons for a reluctance to donate.

Conclusion

Despite their strong willingness to donate biospecimens, students exhibited a notable lack of knowledge about biobanking and the HGP. To expedite the transition towards PM, it is highly recommended to enhance healthcare curricula by including more educational and awareness programmes to familiarize students with OMICs technologies in addition to the scope of research and clinical applications.

The Third International Genomic Medicine Conference (3rd IGMC, 2015): overall activities and outcome highlights

The Third International Genomic Medicine Conference (3^rd IGMC) was organised by the Centre of Excellence in Genomic Medicine Research (CEGMR) at the King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia (KSA). This conference is a continuation of a series of meetings, which began with the first International Genomic Medicine Conference (1^st IGMC, 2011) followed by the second International Genomic Medicine Conference (2^nd IGMC, 2013). The 3^rd IGMC meeting presented as a timely opportunity to bring scientists from across the world to gather, discuss, and exchange recent advances in the field of genomics and genetics in general as well as practical information on using these new technologies in different basic and clinical applications. The meeting undoubtedly inspired young male and female Saudi researchers, who attended the conference in large numbers, as evidenced by the oversubscribed oral and poster presentations. The conference also witnessed the launch of the first content for npj Genomic Medicine, a high quality new journal was established in partnership by CEGMR with Springer Nature and published as part of the Nature Partner Journal series. Here, we present a brief summary report of the 2-day meeting including highlights from the oral presentations, poster presentations, workshops, poster prize-winners and comments from the distinguished scientists.

Associations of recurrent miscarriages with chromosomal abnormalities, thrombophilia allelic polymorphisms and/or consanguinity in Saudi Arabia

BACKGROUND

Recurrent pregnancy loss (RPL) or recurrent spontaneous abortion is an obstetric complication that affects couples at reproductive age. Previous reports documented a clear relationship between parents with chromosomal abnormalities and both recurrent miscarriages and infertility. However, limited data is available from the Arabian Peninsula which is known by higher rates of consanguineous marriages. The main goal of this study was to determine the prevalence of chromosomal abnormalities and thrombophilic polymorphisms, and to correlate them with RPL and consanguinity in Saudi Arabia.

METHODS

Cytogenetic analysis of 171 consent patients with RPL was performed by the standard method of 72-h lymphocyte culture and GTG banding. Allelic polymorphisms of three thrombophilic genes (Factor V Leiden, Prothrombin A20210G, MTHFR C677T) were performed using PCR-RFLP (restriction fragment length polymorphism) and gel electrophoresis.

RESULTS

Data analysis revealed that 7.6 % of patients were carrier of numerical or structural chromosomal abnormalities. A high rate of translocations (46 %) was associated to increased incidence of RPL. A significant correlation between consanguineous RPL patients and chromosomal abnormalities (P < 0.05) was found. Both Factor V Leiden and Prothrombin A20210G allelic polymorphisms were significantly associated with a higher prevalence of RPL.

CONCLUSIONS

This study demonstrated a strong association between RPL and the prevalence of chromosomal abnormalities and inherited thrombophilia. Given the high rate of consanguineous marriages in the Saudi population, these results underline the importance of systematic cytogenetic investigation and genetic counseling preferably at the premarital stage or at least during early pregnancy phase through preimplantation genetic diagnosis (PGD).

Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer

BACKGROUND/AIM

To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses.

MATERIALS AND METHODS

FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed.

RESULTS

High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed.

CONCLUSION

This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine.

Polymorphisms of tumor necrosis factor alpha in Middle Eastern population with colorectal cancer

Tumor necrosis factor-alpha (TNF-α) contributes in inflammation and has been implicated in the development of colorectal cancer (CRC). Single nucleotide polymorphisms (SNPs) in TNF-α promoter could affect the risk of CRC by regulating TNF-α production. This is the first study to investigate TNF-α SNPs in a Middle Eastern population. In this study, we examined three SNPs in TNF-α for association with CRC. One hundred CRC patients and 100 controls were genotyped for TNF-α -308, -238, and -857 using TaqMan allelic discrimination assay. The TNF-α -238 (G/A) genotype was significantly associated with high risk of CRC (p = 0.003552). The distribution of three genotypes of -238 G/A was significantly different between the controls and CRC patients even after Bonferroni’s correction. The AA genotype of -238 G/A SNP was observed at considerably higher proportion (13 %) in CRCs compared to controls (1 %). Additionally, similar to genotypes, the allelic frequencies of -238 G/A were significantly different between the CRC cases and controls (odds ratios (OR) = 7.647, χ² = 18.50, p = 0.00002). The genotype frequencies of -308 and -857 were not notably different between the cases and controls. TNF-α -238A may be useful as a screening marker to identify individuals prior to their acquiring CRC in the Saudi population although, further validations in larger cohorts are needed.