Map of autosomal recessive genetic disorders in Saudi Arabia: Concepts and future directions

CffDNA screening for Niemann-pick disease, type C1: a case series

Cell-free fetal DNA (cffDNA) screening is a valuable tool in clinical practice for detecting chromosomal abnormalities and autosomal dominant (AD) conditions. This study introduces a novel proof-of-concept assay designed for autosomal recessive (AR) cffDNA screening, focusing on cases involving the NPC1 gene. We aim to illustrate the significant benefits of AR cffDNA screening in managing high-risk pregnancies, specifically where biallelic pathogenic variants in NPC1 cause Niemann-Pick disease, type C1 (NPC), a disorder marked by progressive neurodegeneration. Three participants for this study were recruited and gave consent to a hospital in Saudi Arabia. These participants were either carriers of NPC or had a first- or second-degree relative affected by the disorder. No specific criteria were set for the age of the participants. All were between 15 and 18 weeks of gestation. Using amplicon-based next-generation sequencing (NGS), we analyzed the zygosity and variants in cffDNA extracted from maternal peripheral blood. After amplicon NGS, analysis was completed by a custom data analysis pipeline that included in-house-built data processing scripts and commonly used software packages. Importantly, the results were not disclosed to the patients. Our findings showed that in all three cases, AR cffDNA screening results were consistent with standard invasive diagnostic testing. This screening method offers several advantages: it provides critical information to families earlier in the pregnancy compared to invasive diagnostic tests, and it helps to alleviate parental anxiety. Moreover, this non-invasive method can determine pregnancy status in the first trimester for known familial variants. Future research may extend this approach to screen for known disease-causing variants in common AR conditions.

Prevalence, Risk Factors, and Complications of Sickle Cell Disease in Saudi Arabia: A Systematic Review

This study examined sickle cell disease (SCD) in Saudi Arabia. A systematic search of relevant databases was conducted to identify studies investigating SCD in the Saudi population. Studies were then screened based on predefined criteria and critically appraised for methodological quality. Data was extracted and synthesized to provide an overall picture of the SCD burden in Saudi Arabia. The most commonly reported complications were vaso-occlusive crises (VOC), acute chest syndrome (ACS), acute painful crisis, splenic sequestration, osteomyelitis, aplastic crisis, hemolytic crisis, serious bacterial infections, chronic vascular occlusion (CVO), depression, sickle cell nephropathy (SCN), obstructive sleep apnea (OSA), and renal complications. Reduced blood levels of antioxidant trace elements (Cu, Zn, and Se) may encourage oxidative stress, which in turn may contribute to the pathophysiology of SCD. Infections and ACS were common among young children (<7 years) while pain attacks were common in older children (>7 years). The high rate of hospitalizations among SCD patients highlights the need for better management strategies. Future research should focus on understanding the underlying causes of SCD complications and developing new ways to control them.

The perception of genetic diseases and premarital screening tests in the central region of Saudi Arabia

The prevalence of consanguineous marriages (CMs) varies worldwide from one country to another. However, the Middle East stands out as a region with a notably high rate of CMs. CM is particularly widespread in Saudi Arabia, where the prevalence of autosomal recessive genetic diseases has increased. This study aims to identify the Saudi population's awareness of genetic diseases and premarital screening tests (PMSTs). It also seeks to understand couples' perceptions of genetic diseases before and after marriage and their attitudes towards PMSTs and genetic counselling (GC) in reducing the risk of CM. Through the administration of online questionnaires, this cross-sectional study surveyed 2,057 participants to assess their awareness of genetic diseases and their understanding of testing and preventive measures for inherited diseases. Descriptive analysis, nonparametric chi-square tests and logistic regressions were performed to assess the association of categorical responses. This study included 2,035 Saudi Arabian respondents. A significant correlation was found between positive family history and partner selection (p = 0.001), as well as between partnering within the same tribe (p = 0.000139), with a different tribe (p = 0.000138) and from another family (p = 0.000489). About 91.3% of participants expressed agreement regarding the need to enhance public awareness and knowledge concerning genetic disorders, while 87% agreed that increased government regulations are required to prevent the spread of genetic diseases in affected families. Despite increased awareness of genetic diseases and PMSTs, there appears to be a lack of understanding regarding the limitations of PMSTs. The persistently high rate of CM underscores the challenge of altering marriage customs. Further governmental efforts are required to promote awareness of alternative reproductive options, establish new regulations and expand screening programmes.

Founder mutations and rare disease in the Arab world

Founder mutations are disease-causing variants that occur frequently in geographically or culturally isolated groups whose shared ancestor(s) carried the pathogenic variant. While some disease alleles may vanish from the genetic pool due to natural selection, variants with weaker effects may survive for a long time, thereby enhancing the prevalence of some rare diseases. These are predominantly autosomal recessive diseases but can also be autosomal dominant traits with late-onset or mild phenotypes. Cultural practices, such as endogamy and consanguinity, in these isolated groups lead to higher prevalence of such rare diseases compared to the rest of the population and worldwide. In this Perspective, we define population isolates and the underlying genetic mechanisms for accumulating founder mutations. We also discuss the current and potential scientific, clinical and public-health implications of studying founder mutations in population isolates around the world, with a particular focus on the Arab population.

Phenotypic and Molecular Spectrum of Guanidinoacetate N-Methyltransferase Deficiency: An Analytical Study of a Case Series and a Scoping Review of 53 Cases of Guanidinoacetate N-Methyltransferase

Background

Guanidinoacetate methyltransferase deficiency (GAMT) is an autosomal recessive inborn error of metabolism. A condition that results from a pathogenic variant in the GAMT gene that maps to 19p13.3. The prevalence can be estimated to be up to 1:2,640,000 cases; countries such as Saudi Arabia could have a higher prevalence due to high consanguinity rates. The clinical manifestations that a patient could obtain are broad and start to manifest in the patients' early childhood years.

Materials and Methods

A thorough review of case reports in January 2022 was conducted. The retrieved literature was screened for demographic data. Patients of all ages were included. Qualitative variables were described as number and percentage (%), and quantitative data were described by the mean and standard deviation. In bivariate data, Chi-square test (χ2) was used and t-test for nonparametric variables.

Results

Gender distribution was 53% of males and 47% females. Reported age ranged from 8 to 31 months. At the age of onset, 50% of the cases were infants, 28% were toddlers, and 15% were children, concluding that 79% of the reported cases developed symptoms before 5 years old. 68% of the cases developed generalized seizures throughout their life. 84% of the cases expressed a form of developmental delay. 43% of the cases had intellectual disabilities and mental retardation that affected their learning process; most cases required special care. 23% of the affected cases were of consanguineous marriages, and 7% had affected relatives.

Conclusion

We described four novel case reports, the first to be reported in Saudi Arabia. Seizure was a leading finding in the majority of the cases. Developmental delay was broadly observed. Intellectual delay and language impairments are primary hallmarks. Further understanding and early diagnosis are recommended. Premarital testing of neurogenetic diseases using whole-exome sequencing is probably a future direction, especially in populations with high consanguinity rates.

Incidence of Inborn Errors of Metabolism in Newborn Infants: Five Years' Single-Center Experience, Jeddah, Saudi Arabia

Inborn errors of metabolism (IEMs) are inherited biochemical/metabolic disorders that are commonly present in the immediate neonatal period. The aim of this retrospective study was to determine the incidence and distribution of IEMs in newborn infants delivered in our hospital and to evaluate its outcome. A total of 16 494 (99.9%) newborn infants were screened for IEMs. We found 29 newborn infants diagnosed with IEMs, representing an incidence of 1 per ~569 live births and a cumulative incidence of 176 per 100 000 live births of the IEM-positive newborn infants. We detected 11 different types of IEMs, and the top 6 categories were endocrinopathies followed by carbohydrates disorders, vitamin-responsive disorders, organic acid defects, and ketogenesis and ketolysis defects. This study does reflect upon the importance of educating the general population about the perils of Consanguineous Marriages (CMs) in order to reduce related disorders significantly, especially in families who have a history of IEMs.

Clinical and Genetic Characterization of Patients with Primary Ciliary Dyskinesia in Southwest Saudi Arabia: A Cross Sectional Study

BACKGROUND

Primary ciliary dyskinesia (PCD, MIM 244400) is an inherited ciliopathy disorder characterized by recurrent sinopulmonary infections, subfertility, and laterality defects. The true incidence of PCD in Saudi Arabia is not known, but it is likely underdiagnosed due to the high prevalence of consanguineous marriages. In this study, we aim to study the clinical and genetic characteristics of PCD patients in the southwestern region of Saudi Arabia to provide guidance to clinicians and researchers studying PCD.

METHODS

This was a cross-sectional study conducted between 2019 and 2023 in Abha Maternity and Children's Hospital. Twenty-eight patients with clinically diagnosed PCD were recruited. The diagnosis of PCD was confirmed via whole-exome sequencing.

RESULTS

A total of 28 patients from 20 families were identified and recruited for this study. The median age of patients was 7.5 years (IQR = 3, 13 years). The people of different sexes were evenly distributed, and 18 patients (64%) had neonatal respiratory distress (NRD). The median age of diagnosis was 5.5 years (IQR = 2, 11 years), while the age when the first symptoms appeared was 3 months old (IQR = 1, 6 months). The prevalence of a chronic wet cough, chronic rhinosinusitis, ear infections were 100% (n = 28), 78.6% (n = 22), and 67.9% (19), respectively. The most common gene in our study was DNAH5, which represented 17.9% (five out of twenty-eight) of the cases. Furthermore, the remaining pathogenic variants included: 14.3% with RSPH9 in four individuals (three families), 14.3% with DNAI2 in four individuals (two families), and 10.7% with LRRC56 in three individuals (one family). The most common findings on the chest CT scans were consolidation (seen in all patients), mucus plugging (seen in 95%), and bronchiectasis (seen in 77%). In the patients with bronchiectasis, the most commonly affected lobes were the right lower lobe (88%) and left lower lobe (76%). The patients with PCD and situs inversus were more likely to experience NRD than the patients with PCD and situs solitus. The median PICADAR score in the patients with PCD and situs inversus (median: 11.5; Q1: 10-Q3: 12.5) was significantly higher compared to those with PCD and situs solitus (median: 7.5; Q1: 5.8-Q3: 8) (U = 10.5; p < 0.001).

CONCLUSION

This study provides preliminary data on the clinical and genetic characteristics of PCD patients in the southwestern region of Saudi Arabia. We found that DNAH5 and RSPH9 genes were the most common genes among the studied population. Furthermore, PCD should be considered for each child with early NRD and laterality defects, and further confirmatory tests are recommended. These findings also highlight the need for greater awareness of the disease in daily clinical practice to facilitate early diagnosis and avoid irreversible lung damage.

Whole Exome Sequencing Achieved a Definite Diagnosis of Kaufman Oculocerebrofacial Syndrome in a Bahraini Family: A Case Report

A 1 year and 7 months old girl presented to the medical genetic clinic as a referral from the pediatrics clinic. Upon examining the patient and assessing past medical history, an autosomal recessive disorder was suspected. The family underwent whole exome sequencing, which resulted in the diagnosis of Kaufman oculocerebrofacial syndrome (OMIM #244450) in the patient due to the fact that both parents were heterozygous carriers of a novel pathogenic variant in the gene UBE3B that lies on 12q24. It has been recommended for the family that preimplantation genetic testing should be considered for future pregnancies. In this case report, we present a novel variant of the gene and highlight the support of whole exome sequencing in the unveiling of genetic disorders.

Identification of Variants Underlying Phenylalanine Hydroxylase Deficiency in Saudi Arabia

Background: Deleterious mutations in the human gene phenylalanine hydroxylase (PAH) encoding the phenylalanine hydroxylase enzyme give rise to classic phenylketonuria and hyperphenylalaninemia. Our study was designed to characterize the spectrum of variants in the PAH gene in Saudi patients. Materials and Methods: We screened a cohort of 72 Saudi patients with clinical and biochemical diagnoses of hyperphenylalaninemia at the largest tertiary care center in Saudi Arabia; the King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh. All patient's charts were reviewed under an approved study by Institutional Review Board. Results: Twenty-one different PAH variants were identified among the 144 PAH alleles assessed by targeted gene sequencing. Within the studied cohort, 60 of 72 patients had homozygous mutations with the the remaining 12 being compound heterozygotes. The most prevalent of the disease alleles identified in this study was the p.(Arg252Trp) mutation, which accounted for 38 of 144 alleles (26.4%). With the high incidence of genetic disorders in the population, religiously permissible preventive reproductive measures are a priority in our practice. Prenatal diagnoses carried out on four fetuses revealed two that were homozygous for PAH pathogenic variants. In addition, pre-implantation genetic diagnoses were initiated for 19 families. Eight of these families completed more than one full cycle of treatment, from which one healthy newborn was delivered. Conclusions: This study describes the spectrum of PAH variants in the Saudi population and highlights the molecular heterogeneity underlying phenylketonuria and hyperphenylalaninemia. These results add to the existing knowledge about PAH variants in Middle Eastern Countries. These results can be further translated to provide: informed counseling; cascade carrier testing in extended family members; and pre-marital screening.

Health inequity in genomic personalized medicine in underrepresented populations: a look at the current evidence

Improvements in sequencing technology coupled with dramatic declines in the cost of genome sequencing have led to a proportional growth in the size and number of genetic datasets since the release of the human genetic sequence by The Human Genome Project (HGP) international consortium. The HGP was undeniably a significant scientific success, a turning point in human genetics and the beginning of human genomics. This burst of genetic information has led to a greater understanding of disease pathology and the potential of employing this data to deliver more precise patient care. Hence, the recognition of high-penetrance disease-causing mutations which encode drivers of disease has made the management of most diseases more specific. Nonetheless, while genetic scores are becoming more extensively used, their application in the real world is expected to be limited due to the lack of diversity in the data used to construct them. Underrepresented populations, such as racial and ethnic minorities, low-income individuals, and those living in rural areas, often experience greater health disparities and worse health outcomes compared to the general population. These disparities are often the result of systemic barriers, such as poverty, discrimination, and limited access to healthcare. Addressing health inequity in underrepresented populations requires addressing the underlying social determinants of health and implementing policies and programs which promoted health equity and reduce disparities. This can include expanding access to affordable healthcare, addressing poverty and unemployment, and promoting policies that combat discrimination and racism.

A single-centre study of genetic mutations, audiology, echocardiogram and pulmonary function in Saudi children with osteogenesis imperfecta

OBJECTIVES

Osteogenesis imperfecta (OI) is a heterogeneous group of inherited connective tissue disorders, characterised by skeletal fragility. Patients with OI may also exhibit extra-skeletal features like blue or grey scleral colour, fragile skin, easy bruising, joint laxity, short stature, deafness, cardiac valve abnormalities and abnormal pulmonary function. The objective of this study is to describe genetic mutations, prevalence of hearing issues, cardiac complications and impaired pulmonary function in children with OI.

METHODS

This is a cross-sectional study of 23 Saudi children aged 6 months to 18 years who were diagnosed with OI. The revised Sillence classification (2,105) was used to classify the OI type. Whole exome sequencing was performed for genetic mutations. The hearing was assessed by either pure-tone audiometry and/or otoacoustic emission testing. Cardiac defects were screened by echocardiograms. Spirometry was performed to assess pulmonary function. Data were analysed with descriptive statistics.

RESULTS

Based on the Sillence classification, 16 patients had OI type III, 6 had type IV and 1 had type I. Of the18 patients who had genetic sequencing, 66.6% had autosomal dominant and 33.3% had autosomal recessive mutations. Among children who had screening, hearing loss was diagnosed in 53% (9/17), congenital cardiac malformations in 26% (5/19) and restrictive lung disease in 70% (7/10).

CONCLUSIONS

We found significant extra-skeletal features and a high yield of genetic mutations associated with OI. We suggest further studies to develop a screening protocol for extra-skeletal features in children with OI.

Assessing Medical Students' Knowledge of Genetics: Basis for Improving Genetics Curriculum for Future Clinical Practice

PURPOSE

The knowledge of genetics among medical students was assessed to identify and analyze gaps that serve as bases for the revision of the current genetics curriculum of the (Bachelor of Medicine, Bachelor of Surgery) MBBS Program of the College of Medicine at Princess Nourah bint Abdulrahman University (PNU).

METHODS

A 65-item multiple-choice (MCQs) test in Genetics was administered to 71 second and fourth-year medical students to assess their knowledge in Genetics. MCQs were validated and tested for their reliability. Self-assessment of students' genetics knowledge was also determined by asking them whether their knowledge in genetics is sufficient or not sufficient for their future clinical practice. Data were analyzed using the Statistical Package for the Social Sciences (SPSS) version 20.

RESULTS

Forty-one second-year and thirty fourth-year medical students took the Genetic test. Exam results showed insufficient knowledge of Genetics, with 43.85% among the students answering the exam correctly. In self-assessment, the majority (83.3% to 87.8%) of the respondents considered their knowledge of genetics insufficient for future clinical practice. A higher knowledge level of basic genetics compared with clinically related genetics concepts was observed. Generally, second-year students significantly scored higher in molecular and cytogenetics (P=0.012), principles of genetic transmission (P=0.022), and inheritance of genetic diseases (P=0.024), compared with the fourth-year medical students who only scored higher in items related to cancer genetics (P=0.022).

CONCLUSION

Medical students' genetics knowledge is insufficient, especially on clinically oriented concepts like genetic testing and genetic counseling and should be strengthened for future clinical practice. The fourth-year medical students do not retain the knowledge of genetics; thus, integrating medical genetics in clinical years is imperative.

Mapping the Diverse Genetic Disorders and Rare Diseases Among the Syrian Population: Implications on Refugee Health and Health Services in Host Countries

The aim of this systematic review is to provide physicians and researchers with a comprehensive list of reported genetic disorders in patients of Syrian origin-those who have become part of the largest displaced population globally-and to highlight the need to consider migrant population-based risk for the development of genetic disease control and prevention programs. This review was performed based on the 2015 PRISMA and the international prospective register of systematic reviews. The present review reports on a total of 166 genetic disorders (only 128 reported on OMIM) identified in the Syrian population. Of these disorders, 27% are endocrine-, nutritional- and metabolic-related diseases. Second to metabolic disorders are congenital malformations, deformations and chromosomal abnormalities. Diseases of the blood and the blood-forming organs accounted for 13% of the total genetic disorders. The majority of the genetic disorders reported in Syrian patients followed an autosomal recessive mode of inheritance. These findings are a reflection of the high rates of consanguineous marriages that favor the increase in incidence of these diseases. From the diseases that followed an autosomal recessive mode of inheritance, 22% are reported to be only present in Syria and other regional countries. Twelve of these genetic diseases were identified to be strictly diagnosed in individuals of Syrian origin. The present systematic review highlights the need to develop programs that target genetic disorders affecting Syrian migrants in host countries. These programs would have potential financial and economic benefits, as well as a positive impact on the physical and mental health of members of the Syrian refugee community and those of their host societies. In turn, this would decrease the burden on the health systems in host countries.

25-Hydroxylase vitamin D deficiency in 27 Saudi Arabian subjects: a clinical and molecular report on CYP2R1 mutations

Vitamin D deficiency remains a major cause of rickets worldwide. Nutritional factors are the major cause and less commonly, inheritance causes. Recently, CYP2R1 has been reported as a major factor for 25-hydroxylation contributing to the inherited forms of vitamin D deficiency. We conducted a prospective cohort study at King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia, to review cases with 25-hydroxylase deficiency and describe their clinical, biochemical, and molecular genetic features. We analyzed 27 patients from nine different families who presented with low 25-OH vitamin D and not responding to usual treatment. Genetic testing identified two mutations: c.367+1G>A (12/27 patients) and c.768dupT (15/27 patients), where 18 patients were homozygous for their identified mutation and 9 patients were heterozygous. Both groups had similar clinical manifestations ranging in severity, but none of the patients with the heterozygous mutation had hypocalcemic manifestations. Thirteen out of 18 homozygous patients and all the heterozygous patients responded to high doses of vitamin D treatment, but they regressed after decreasing the dose, requiring lifelong therapy. Five out of 18 homozygous patients required calcitriol to improve their biochemical data, whereas none of the heterozygous patients and patients who carried the c.367+1G>A mutation required calcitriol treatment. To date, this is the largest cohort series analyzing CYP2R1-related 25-hydroxylase deficiency worldwide, supporting its major role in 25-hydroxylation of vitamin D. It is suggested that a higher percentage of CYP2R1 mutations might be found in the Saudi population. We believe that our study will help in the diagnosis, treatment, and prevention of similar cases in the future.

Attitude and awareness of public towards genetic testing in Riyadh, Saudi Arabia

The current study was designed to evaluate the attitude of the Saudi general population towards knowledge, perception and awareness about genetic testing. Using a convenience sampling technique, an online survey was used to collect the data. The survey consisted of 16 questions that covered basic demographics and several scenarios that assess subjects’ perceptions regarding genetic testing. Answering all questions was required for completing the survey. Among 333 subjects, 53.5% were male, 18.9% were married, and 99.4% were muslims. Around 75% has/will have a bachelor degree. About 59% were students. About 87% would consider genetic testing before marriage and similar percentage would not consider conceiving a child if the genetic screening indicated that there is 100% chance the child will be born with genetic disorder. Neither marital status (Single = 87.04%, married = 87.30% (P = 0.955)) nor gender (male = 85.96, female = 88.39 (P = 0.509)) affected the aforementioned decision. When subjects were asked if they would choose abortion knowing that the embryo has a severe genetic disorder, 62.7% answered yes. In general, 80.4% were willing to be recruited into a genetics study, married subjects were more reluctant to be recruited compared to singles (30% and 17% (P = 0.018) respectively). There was no difference between males and females in the decision of joining a genetic study. Also 78.4% supported creation of genetic disease database and family maps. 69.7% of the participants supported government enforcement of the genetic testing, 56.2% supported government-run facilities for Saudi citizens to have genetic tests. We conclude that married people were in favor of genetic testing than the single counterparts, secondly, single status people supported the idea of having genetic tests before their marriage they were supportive of the idea of the government taking a leading role in enforcing the genetic testing and creation of the genetic banks.

Population structure of indigenous inhabitants of Arabia

Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world's major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world's major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.

Categorized Genetic Analysis in Childhood-Onset Cardiomyopathy

BACKGROUND

Childhood-onset cardiomyopathy is a heterogeneous group of conditions the cause of which is largely unknown. The influence of consanguinity on the genetics of cardiomyopathy has not been addressed at a large scale.

METHODS

To unravel the genetic cause of childhood-onset cardiomyopathy in a consanguineous population, a categorized approach was adopted. Cases with childhood-onset cardiomyopathy were consecutively recruited. Based on the likelihood of founder mutation and on the clinical diagnosis, genetic test was categorized to either (1) targeted genetic test with targeted mutation test, single-gene test, or multigene panel for Noonan syndrome, or (2) untargeted genetic test with whole-exome sequencing or whole-genome sequencing. Several bioinformatics tools were used to filter the variants.

RESULTS

Two-hundred five unrelated probands with various forms of cardiomyopathy were evaluated. The median age of presentation was 10 months. In 30.2% (n=62), targeted genetic test had a yield of 82.7% compared with 33.6% for whole-exome sequencing/whole-genome sequencing (n=143) giving an overall yield of 53.7%. Strikingly, 96.4% of the variants were homozygous, 9% of which were found in 4 dominant genes. Homozygous variants were also detected in 7 novel candidates (ACACB, AASDH, CASZ1, FLII, RHBDF1, RPL3L, ULK1).

CONCLUSIONS

Our work demonstrates the impact of consanguinity on the genetics of childhood-onset cardiomyopathy, the value of adopting a categorized population-sensitive genetic approach, and the opportunity of uncovering novel genes. Our data suggest that if a founder mutation is not suspected, adopting whole-exome sequencing/whole-genome sequencing as a first-line test should be considered.

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.

Inherited Metabolic Disorders in Adults: A view from Saudi Arabia

The incidence of inherited metabolic disorders (IMD) in Saudi Arabia is one of the highest in the world. Early diagnosis and advances in the treatment of these diseases have led to improved survival of these patients resulting in a rapidly growing number of adults with IMD. This is the first report from a single tertiary care center, on the experience of managing a large cohort of adult patients with a wide range of IMD. We describe the common IMD seen in adult patients in Saudi Arabia, highlighting the variations from the Caucasian populations, and unique challenges in providing care to these adults. We mention the pitfalls causing the delay in the diagnosis particularly in cases of late-onset IMD in adults. We also discuss some unusual complications seen in adult patients during the course of their disease. We describe the role of genetic prevention services in Saudi Arabia and the importance of research in this field.

Optic neuropathy in classical methylmalonic acidemia

Background: Classical MMA, caused by methylmalonyl-CoA mutase deficiency, may result in late-onset dysfunction in several organ systems. To date, 10 cases of optic neuropathy have been reported. The prevalence of optic neuropathy in visually asymptomatic patients has not been determined. This study sought to identify overt and subclinical optic neuropathy in a cohort with classical MMA. Methods and Materials: Neuroophthalmic examinations were performed on 21 patients identified with classical MMA, older than 10years. Diagnosis of optic neuropathy was determined by a combination of visual acuity, optic nerve appearance and electrodiagnostic tests. Tabulated data were analyzed for association of variables using SAS software. Significance was set at p < .05. Results: Two-thirds were Saudi nationals and one third, Syrian. Age range was 11-29years. Eleven (52.4%) patients had optic neuropathy. Nine (81.8%) of these were bilateral, seven (57.9% to 63.6%) reported decreased vision and four (33.1% to 36.4%) were asymptomatic. Two patients had catastrophic vision loss, following acute metabolic crises. Sixteen patients had chronic renal impairment while three had renal hypertension. Seventeen patients had short stature and eight, chronic pancreatitis. Methylmalonic acid levels ranged from 82 to 3,324µmol/L (Normal<1µmol/L). There was a significant association between optic neuropathy and female gender (p = .011) and none with age, nationality, renal impairment, pancreatitis or specific genotype. Conclusion: Optic neuropathy was a frequent finding in classical MMA. It was often bilateral and some cases were sub-clinical, lacking visual symptoms. These findings have important management implications. Full ophthalmic evaluations should be performed early and regularly in patients with MMA, even when patients are asymptomatic.

Prevalence and Determinants of Color Vision Defects among Preparatory University Students at Makkah, Saudi Arabia

PURPOSE

To estimate the magnitude and determinants of color vision defects (CVD) among preparatory health science students.

METHODS

A cross-sectional survey was conducted in 2017. Participants were assessed using 24-plate Ishihara's Test of Color Vision chart. If ≤9 plates were read correctly, the color vision was regarded as deficient. The CVD prevalence and its 95% confidence interval (CI) were calculated. CVD was associated with gender, family history of CVD, and other vision problems.

RESULTS

We evaluated 1126 students (552, 49% males; mean age: 18.7 ± 0.7 years). The prevalence of CVD was 1.77% (95% CI: 1.0, 2.6). Among male students, it was 3.5% (95% CI: 1.9, 5.0). Only one female student had CVD. The Duran CVD was found in 18 (1.6%) students. However, only two students had Tritan CVD. Three among twenty CVD students knew that they suffer from CVD. CVD was positively associated to a family history of CVD (odds ratio [OR] = 3.8; 95% CI: 1.4, 10.1;P = 0.02) and male gender (OR = 20.4 [95% CI: 2.7, 153]). CVD was not significantly associated to other vision problems (OR = 0.8 [95% CI: 0.3, 2.0]).

CONCLUSION

Eighteen in thousand health sciences students suffered from CVD. Ten percent of them had Tritan CVD. Duran CVD seems to be a male sex-related and/or a familial condition. Most of the CVD students seem to have adopted to this defect and were not aware of suffering from it. Screening for CVD is therefore debatable.

6-Pyruvoyltetrahydropterin Synthase Deficiency: Review and Report of 28 Arab Subjects

BACKGROUND

Tetrahydrobiopterin is an essential cofactor for the hydroxylation of aromatic amino acids phenylalanine, tyrosine, and tryptophan. Therefore, tetrahydrobiopterin deficiency results in hyperphenylalaninemia as well as dopamine and serotonin depletion in the central nervous system. The enzyme 6-pyruvoyltetrahydropterin synthase catalyzes the second step of de novo synthesis of tetrahydrobiopterin, and its deficiency is the most frequent cause of tetrahydrobiopterin metabolism disorders.

METHOD

We conducted a retrospective chart review of 28 subjects from 24 families with molecularly confirmed 6-pyruvoyltetrahydropterin synthase deficiency from six centers in three Arab countries. We reviewed clinical, biochemical, and molecular data. We also reviewed previously published cohorts of subjects with 6-pyruvoyltetrahydropterin synthase deficiency.

RESULTS

Similar to previous observations, we show that early treatment (less than two months) is associated with better outcome. We identify eight PTS variants in 24 independent families. The most common variant is (c.238A>G; p.M80V) with an allele count of 33%. We also identify one novel variant (c.2T>G; p.?).

CONCLUSION

The deficiency of 6-pyruvoyltetrahydropterin synthase is relatively common in the Arab population and should be considered in individuals with hyperphenylalaninemia. More natural history studies with comprehensive biochemical and molecular genetics data are needed for a robust base for the development of future therapy.

Phenotypic variability in a series of four pediatric patients with Andersen-Tawil syndrome: A Saudi experience

Andersen-Tawil syndrome (ATS) is a rare genetic disorder characterized by periodic paralysis, ventricular arrhythmia, and dysmorphic features. However, the classical features are not always seen in the syndrome; therefore, the diagnosis can be challenging. We describe our experience with ATS in Riyadh, Saudi Arabia, by presenting a case series involving four patients in the pediatric cardiology clinic confirmed to have ATS. Despite the diversity in phenotypes and clinical course among the four cases, all patients had bidirectional ventricular tachycardia and were confirmed to have ATS by performing genetic testing. In this case series, we identified one novel and three previously described KCNJ2 mutations. We also confirmed the beneficial effect of AAI pacing in one of our patients, together with medical therapy with β-blockers and flecainide. In Saudi Arabia, there is a distinct genetic pool and a high incidence of inherited diseases. Raising awareness about these diseases is crucial, especially in a country such as Saudi Arabia, wherein consanguinity remains a significant factor leading to an increased incidence of inherited diseases. Furthermore, because of the limited information available regarding this rare syndrome, we believe that this case series would offer an opportunity to provide a better understanding of ATS in our local region and worldwide.

The landscape of early infantile epileptic encephalopathy in a consanguineous population

PURPOSE

Epileptic encephalopathies (EE), are a group of age-related disorders characterized by intractable seizures and electroencephalogram (EEG) abnormalities that may result in cognitive and motor delay. Early infantile epileptic encephalopathies (EIEE) manifest in the first year of life. EIEE are highly heterogeneous genetically but a genetic etiology is only identified in half of the cases, typically in the form of de novo dominant mutations.

METHOD

This is a descriptive retrospective study of a consecutive series of patients diagnosed with EIEE from the participating hospitals. A chart review was performed for all patients. The diagnosis of epileptic encephalopathy was confirmed by molecular investigations in commercial labs. In silico study was done for all novel mutations. A systematic search was done for all the types of EIEE and their correlated genes in the literature using the Online Mendelian Inheritance In Man and PubMed databases.

RESULTS

In this case series, we report 72 molecularly characterized EIEE from a highly consanguineous population, and review their clinical course. We identified 50 variants, 26 of which are novel, causing 26 different types of EIEE. Unlike outbred populations, autosomal recessive EIEE accounted for half the cases. The phenotypes ranged from self-limiting and drug-responsive to severe refractory seizures or even death.

CONCLUSIONS

We reported the largest EIEE case series in the region with confirmed molecular testing and detailed clinical phenotyping. The number autosomal recessive predominance could be explained by the society's high consanguinity. We reviewed all the EIEE registered causative genes in the literature and proposed a functional classification.

Awareness and Attitude of University Students About Screening and Testing for Hemoglobinopathies: Case Study of the Aseer Region, Saudi Arabia

Hemoglobinopathies can disturb a patient's life style leading to community problems. Premarital screening is an important tool to control and minimize hemoglobinopathies. This study aimed to assess and improve the awareness and attitude of King Khalid University (KKU) [Abha, Kingdom of Saudi Arabia (KSA)] students in the Aseer Region, regarding hemoglobinopathies and the National Premarital Screening Programme (NPMS) in addition to screening for hemoglobin (Hb) variants of students who agreed to participate. This study was an interventional educational prospective study of electronic-lectures (e-lectures) that addressed some important issues of hemoglobinopathies and premarital screening. Six hundred and eleven students were interviewed during the academic year 2017/2018, using closed-ended questionnaires that distributed before and after intervention. Blood samples were taken from 114 students who agreed to check their Hb type by the D-10 Hemoglobin Testing System. The results revealed significant changes in knowledge and attitude of students toward hemoglobinopathies and premarital counseling after intervention. These results reflected the need for easily accessible and continuous health education programs for students to increase their awareness and attitude toward hemoglobinopathies. Laboratory results for 114 students revealed seven cases with microcytic hypochromic anemia (6.1%); they were all females. Blood screening for Hb variants revealed another two females (1.75%) with sickle cell trait (Hb AS). Electronic-health (E-health) is an efficient tool for improving the awareness and attitude of the community toward hemoglobinopathies. Screening blood tests for detection of hemoglobinopathies should be provided to young adults at an earlier stage (before marriage) to decrease the incidence of hereditary diseases in the community.

Clinical, Endocrine, and Molecular Genetic Analysis of a Large Cohort of Saudi Arabian Patients with Laron Syndrome

BACKGROUND/AIMS

Laron syndrome (LS) is an autosomal recessive disease characterized by marked short stature and very low serum IGF-1 and IGFBP-3 levels. This study assessed the clinical and endocrine features alongside determining the growth hormone receptor gene (GHR) mutation in Saudi Arabian patients with LS in order to establish whether or not a genotype/phenotype correlation is evident in this large cohort.

SUBJECTS AND METHODS

A total of 40 Saudi Arabian patients with a suspected diagnosis of LS were recruited and subjected to a full clinical and endocrine investigation together with direct sequencing of the coding regions of the GHR gene.

RESULTS

GHR mutations were identified in 34 patients from 22 separate nuclear families. All 34 molecularly confirmed patients had the typical clinical and endocrinological manifestations of LS. Eleven different mutations (9 previously unreported) were detected in this cohort of patients, all inherited in an autosomal recessive homozygous form. No genotype/phenotype correlation was apparent.

CONCLUSION

The identification of pathogenic mutations causing LS will be of tremendous use for the molecular diagnosis of patients in Saudi Arabia and the region in general, with respect to prevention of this disease in the forms of future carrier testing, prenatal testing, premarital screening and preimplantation genetic diagnosis.

A retrospective biochemical, molecular, and neurocognitive review of Saudi patients with argininosuccinic aciduria

A retrospective review was compiled of 54 patients with argininosuccinic aciduria who were either identified through the Saudi National Newborn Screening Program or diagnosed clinically from January 2000 to December 2015. The duration of follow-up is from 2 to 19 years. The majority of patients (65%) originated from the central province of Saudi Arabia. The mean patient age at review was 10 years (2-19 years), 92% received an early diagnosis (<28 days of age) and most were symptomatic at the time of the diagnosis (n = 34). Normal ammonia at diagnosis was reported in 30% of patients, who were detected under the newborn metabolic screen (n = 5/16). A very high rate of consanguinity was observed in our cohort (98%). Developmental delay was the most detectable long term neurocognitive consequence followed by seizure disorder; 90.7% (n = 49) and 62.9% (n = 34) respectively. As expected, the severe neonatal form was the major presentation. The most common variant identified in this cohort was the previously reported founder c.1060C > T; p.(Gln354*) nonsense mutation in the ASL gene. In addition, the frequency of hyperammonemia was higher in patients homozygous for c.1060C > T; p.(Gln354*) compared to the other mutations. Interestingly, frequent thrombocytosis with the mean level of 717 × 10⁹/L (range = 457-1169 × 10⁹/L) was observed in 96% of the patients with no clear explanation.

Clinical, Biochemical, and Molecular Features in 37 Saudi Patients with Very Long Chain Acyl CoA Dehydrogenase Deficiency

BACKGROUND

Very long chain acyl CoA dehydrogenase (VLCAD) deficiency (OMIM#201475) is an autosomal recessive disorder of fatty acid beta oxidation caused by defect in the ACADVL. The aim of this study was to analyze the clinical, biochemical, and molecular features of VLCAD deficiency in Saudi Arabia, including the treatment and outcome.

METHODS

We carried out a retrospective chart review analysis of 37 VLCAD deficiency patients from two tertiary centers in Saudi Arabia, over a 14-year period (2002-2016). Twenty-three patients were managed at King Abdul-Aziz Medical City and fourteen patients at King Fahad Medical City.

RESULTS

Severe early onset VLCAD deficiency is the most frequent phenotype in our patients, caused by four different mutations in ACADVL; 31 patients (83.7%) had a homozygous nonsense mutation in exon 2 of ACADVL c.65C>A;p. Ser22X. Twenty-three patients died before the age of 2 years, despite early detection by newborn screening and implementation of treatment, including supplementation with medium chain triglycerides.

CONCLUSION

This study reports the clinical, biochemical, molecular findings, treatment, and outcome of patients with VLCAD deficiency over the last 14 years. We identified the most common variant and one new variant in ACADVL. Despite early diagnosis and treatment, the outcome of VLCAD deficiency in this Saudi Arabian population remains poor. Preventive measures, such as prenatal diagnosis, could be implemented.

Expanded Newborn Screening Program in Saudi Arabia: Incidence of screened disorders

AIM

To address the implementation of the National Newborn Screening Program (NBS) in Saudi Arabia and stratify the incidence of the screened disorders.

METHODS

A retrospective study conducted between 1 August 2005 and 31 December 2012, total of 775 000 newborns were screened from 139 hospitals distributed among all regions of Saudi Arabia. The NBS Program screens for 16 disorders from a selective list of inborn errors of metabolism (IEM) and endocrine disorders. Heel prick dry blood spot samples were obtained from all newborns for biochemical and immunoassay testing. Recall screening testing was performed for Initial positive results and confirmed by specific biochemical assays.

RESULTS

A total of 743 cases were identified giving an overall incidence of 1:1043. Frequently detected disorders nationwide were congenital hypothyroidism and congenital adrenal hyperplasia with an incidence of 1:7175 and 1:7908 correspondingly. The highest incidence among the IEM was propionic acidaemia with an incidence rate of 1:14 000.

CONCLUSION

The article highlights the experience of the NBS Program in Saudi Arabia and providing data on specific regional incidences of all the screened disorders included in the programme; and showed that the incidence of these disorders is one of the highest reported so far world-wide.

Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients

Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD’s heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400^th and 556^th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4⁺ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.

Etiology of optic atrophy: a prospective observational study from Saudi Arabia

BACKGROUND

Optic atrophy (OA) represents permanent retinal ganglion cell loss warranting study to establish etiology.

OBJECTIVES

To describe neurogenic causes of OA.

DESIGN

Prospective, observational.

SETTING

Tertiary care center, Riyadh, Saudi Arabia.

PATIENTS AND METHODS

We included consecutive patients of all ages with OA caused by lesions affecting the visual pathways who were referred over a 9-month period (November 2013 to July 2014). Diagnosis was based on visual acuity, ophthalmoscopic features and ancillary tests. Patient demographics, results of a clinical examination, test data and etiology were recorded. For each cause of OA, both gender and age group were analyzed as potential risk factors using simple univariate logistic regression. OA associated with glaucoma and retinal diseases was excluded.

MAIN OUTCOME MEASURE

Description of causes of OA.

RESULTS

Two hundred and four patients and 353 eyes met inclusion criteria. The median age was 27 years (range 3 months-77 years; interquartile range, 27 years) among 111(54.4%) females and 93(45.6%) males, with no statistically significant difference in age of presentation between the genders. The majority of lesions were bilateral (n=151, 74%). Tumors were the most common cause, accounting for 127 (62.2%) cases. These occurred mostly in adults (72.4%) compared to the pediatric group (OR=3.3, 95% CI: 1.79-6.03; P < .001). Hereditary neoplasia (OR=5.55; 95% CI: 1.67-18.42; P=.005) and metabolic diseases (OR=17.57; 95% CI: 2.15-143.62; P=.007) were more common causes in the pediatric group. There were no significant associations between gender or visual acuity and etiology of OA. In developed nations, OA is frequently the result of ischemia and neuritis. We found many other causes, especially orbital and intracranial tumors.

CONCLUSIONS

The frequency of tumors as the cause of OA may represent a higher incidence of aggressive tumors coupled with poor recognition/acknowledgement of symptoms and limited access, resulting in late presentations.

LIMITATIONS

These findings may reflect bias from selective referrals to a tertiary center and may not represent all of Saudi Arabia.

Clinical profile and mutation spectrum of long QT syndrome in Saudi Arabia: The impact of consanguinity

BACKGROUND

Congenital long QT syndrome (LQTS) is an inherited, potentially fatal arrhythmogenic disorder. At least 16 genes have been implicated in LQTS; the yield of genetic analysis of 3 genes (KCNQ1, KCNH2, and SCN5A) is about 70%, with KCNQ1 mutations accounting for ∼50% of positive cases. LQTS is mostly inherited in an autosomal dominant pattern. Systemic analysis of LQTS has not been previously conducted in a population with a high degree of consanguinity.

OBJECTIVES

To describe the clinical and molecular profiles of LQTS in the highly consanguineous Saudi population.

METHODS

Fifty-six Saudi families with LQTS were consecutively recruited and evaluated. Sequencing of KCNQ1, KCNH2, and SCN5A genes was conducted on all probands, followed by screening of family relatives.

RESULTS

Genetic analysis was positive in 32 (57.2%) families, with mutations in KCNQ1 identified in 28 families (50%). Surprisingly, 17 (53.1%) probands were segregating homozygous mutations. Family screening identified 123 individuals with mutations; 89 (72.4%) were heterozygous, 23 (18.7%) were homozygous, and 11 (8.9%) were compound heterozygous. Compared to heterozygous, the phenotype was more severe in homozygous individuals, with cardiac symptoms in 78.3% (vs 12.4%), family history of sudden death in 64.7% (vs 44.4%), and prolonged QT interval in 100% (vs 43.8%). Congenital deafness was found in 11 (47.8%) homozygous probands.

CONCLUSION

Our study provides insight into the clinical and molecular profiles of LQTS in a consanguineous population. It underscores the importance of preemptive management in homozygous patients with LQTS and the value of clinical and molecular screening of at-risk relatives.

The role of biobanks in elucidating prevalent genetic diseases in Saudi Arabia

Biobanking entails large-scale collection of human biological specimens that are linked to the donors' health and personal information, and has several applications in clinical research. Human biological specimens, such as blood, urine and tissue, have become immensely important to medical research: they offer a valuable source of genetic material that researchers can use to identify disease-associated genetic variation and to determine interactions between genes and environmental factors. Identification of genetic contributions to disease can lead to the development of new diagnostic tests and targeted treatments. Over the last decade, both common diseases and rare genetic disorders have been reported in Saudi Arabia. The need to generate extensive genetic data on these diseases has led to the establishment of several Saudi Arabian biobanks. Fortunately, these vital efforts have the support of the Saudi Government and researchers. However, the success of any biobank also requires public support and the willingness of the population to donate their biological material along with information on their medical records. Thus, the Saudi public needs to be informed of the benefits of maintaining biobanks, their participation needs to be encouraged through donation of biological material, and any public concerns regarding the confidential treatment of medical data need to be addressed. This article reviews the most common genetic diseases identified in the Saudi population, it describes biobanks and it examines how biobanks can support biomedical research in the area. Moreover, this article proposes measures that might help to increase public awareness of biobanks and the preparedness of the Saudi Arabian population to donate biological material.

Molecular nature of alpha-globin genes in the Saudi population

Alpha-thalassemia (α-thal) is a disorder caused by the deletion of single or double α-globin genes, and/or point mutations in the α-globin genes. There are 2 common types of α-globin genes; HBA2 and HBA1. Recently, it has been discovered that the HBA2 gene is replaced by a unique HBA12 gene convert in 5.7% of the Saudi population. The α-globin genes have been emerging as a molecular target for the treatment of β-thalassemia (β-thal). Hence, it is essential to understand the molecular nature of α-globin genes to treat the most prevalent hemoglobin disorders, such as sickle cell disease, α-thal, and β-thal prevalent in the Kingdom of Saudi Arabia. Thirty-two different α-globin genotypes have been observed in the Saudi population. This review outlines the classification of the α-globin genes on the basis of their molecular nature and complex combinations of α-globin genes, and their variants predominant in Saudis.

Thirteen year retrospective review of the spectrum of inborn errors of metabolism presenting in a tertiary center in Saudi Arabia

Background

Inborn errors of metabolism (IEMs) are individually rare; however, they are collectively common. More than 600 human diseases caused by inborn errors of metabolism are now recognized, and this number is constantly increasing as new concepts and techniques become available for identifying biochemical phenotypes. The aim of this study was to determine the type and distribution of IEMs in patients presenting to a tertiary care center in Saudi Arabia. METHOD: We conducted a retrospective review of children diagnosed with IEMs presenting to the Pediatric Department of King Abdulaziz Medical City in Riyadh, Saudi Arabia over a 13-year period.

Results

Over the 13- year period of this retrospective cohort, the total number of live births reached 110,601. A total of 187 patients were diagnosed with IEMs, representing a incidence of 169 in 100,000 births (1:591). Of these, 121 patients (64.7 %) were identified to have small molecule diseases and 66 (35.3 %) to have large molecule diseases. Organic acidemias were the most common small molecule IEMs, while lysosomal storage disorders (LSD) were the most common large molecule diseases. Sphingolipidosis were the most common LSD.

Conclusion

Our study confirms the previous results of the high rate of IEMs in Saudi Arabia and urges the health care strategists in the country to devise a long-term strategic plan, including an IEM national registry and a high school carrier screening program, for the prevention of such disorders. In addition, we identified 43 novel mutations that were not described previously, which will help in the molecular diagnosis of these disorders.

Guidelines for acute management of hyperammonemia in the Middle East region

Background

Hyperammonemia is a life-threatening event that can occur at any age. If treated, the early symptoms in all age groups could be reversible. If untreated, hyperammonemia could be toxic and cause irreversible brain damage to the developing brain.

Objective

There are major challenges that worsen the outcome of hyperammonemic individuals in the Middle East. These include: lack of awareness among emergency department physicians about proper management of hyperammonemia, strained communication between physicians at primary, secondary, and tertiary hospitals, and shortage of the medications used in the acute management of hyperammonemia. Therefore, the urge to develop regional guidelines is extremely obvious.

Method

We searched PubMed and Embase databases to include published materials from 2011 to 2014 that were not covered by the European guidelines, which was published in 2012. We followed the process of a Delphi conference and involved one preliminary meeting and two follow-up meetings with email exchanges between the Middle East Hyperammonemia and Urea Cycle Disorders Scientific Group regarding each draft of the manuscript.

Results and discussion

We have developed consensus guidelines based on the highest available level of evidence. The aim of these guidelines is to homogenize and harmonize the treatment protocols used for patients with acute hyperammonemia, and to provide a resource to not only metabolic physicians, but also physicians who may come in contact with individuals with acute hyperammonemia.

Conclusion

These suggested guidelines aim to ease the challenges faced by physicians dealing with acute hyperammonemia in the region. In addition, guidelines have demonstrated useful collaboration between experts in the region, and provides information that will hopefully improve the outcomes of patients with acute hyperammonemia.

A novel homozygous PTH1R variant identified through whole-exome sequencing further expands the clinical spectrum of primary failure of tooth eruption in a consanguineous Saudi family

OBJECTIVES

The present study aimed to identify the genetic cause of non-syndromic primary failure of tooth eruption in a five-generation consanguineous Saudi family using whole-exome sequencing (WES) analysis.

DESIGN

The family pedigree and phenotype were obtained from patient medical records. WES of all four affected family members was performed using the 51 Mb SureSelect V4 library kit and then sequenced using the Illumina HiSeq2000 sequencing system. Sequence alignment, variant calling, and the annotation of single nucleotide polymorphisms and indels were performed using standard bioinformatics pipelines. The genotype of candidate variants was confirmed in all available family members by Sanger sequencing.

RESULTS

Pedigree analysis suggested that the inheritance was autosomal recessive. WES of all affected individuals identified a novel homozygous variant in exon 8 of the parathyroid hormone 1 receptor gene (PTH1R) (NM_000316: c.611T>A: p.Val204Glu).

CONCLUSION

To the best of our knowledge, this is the first report of primary failure of eruption caused by a homozygous mutation in PTH1R. Our findings prove the application of WES as an efficient molecular diagnostics tool for this rare phenotype and further broaden the clinical spectrum of PTH1R pathogenicity.

The alkylglycerol monooxygenase (AGMO) gene previously involved in autism also causes a novel syndromic form of primary microcephaly in a consanguineous Saudi family

Autosomal recessive primary microcephaly (MCPH) refers to a genetically heterogeneous group of neurodevelopmental disorders in which patients exhibit a marked decrease in occipitofrontal head circumference at birth and a variable degree of intellectual disability. To date, 18 genes have been reported for MCPH worldwide. We enrolled a consanguineous family from Saudi Arabia presenting with primary microcephaly, developmental delay, short stature and intellectual disability. Whole exome sequencing (WES) with 100× coverage was performed on two affected siblings after defining common regions of homozygosity through genome-wide single nucleotide polymorphism (SNP) microarray genotyping. WES data analysis, confirmed by subsequent Sanger sequence validation, identified a novel homozygous deletion mutation (c.967delA; p.Glu324Lysfs12*) in exon 10 of the alkylglycerol monooxygenase (AGMO) gene on chromosome 7p21.2. Population screening of 178 ethnically matched control chromosomes and consultation of the Exome Aggregation Consortium database, containing 60,706 individuals' exomes worldwide, confirmed that this mutation was not present outside the family. To the best of our knowledge, this is the first evidence of an AGMO mutation underlying primary microcephaly and intellectual disability in humans. Our findings further expand the genetic heterogeneity of MCPH in familial cases.

Genetic counselors' scope of practice and challenges in genetic counseling services in Saudi Arabia

Genetic counseling is an evolving field in Saudi Arabia. In 2015, genetic counseling was recognized as a Master's program by the Saudi Commission for Health Specialties. Our genetic counselors combine their knowledge of genetics, counseling theory and interpersonal communication to serve Saudi and non-Saudi patients affected with a range of genetic conditions and/or birth defects. Most patients are referred to the clinic from different clinics at King Faisal Specialist Hospital and Research Centre (KFSHRC) and outside of KFSHRC for various indications. Carrier testing and preventative reproduction options rank highly on the reasons for referral to our clinics.

The Saudi population has unique customs and beliefs, such as consanguinity and the evil eye. Challenges that are routinely encountered in our genetic counseling clinics include, but are not limited to, preventative reproductive options and termination of pregnancy, manifesting carriers, stigmatization of women and approaches to complex molecular findings. Working with families from different backgrounds and beliefs undoubtedly requires professionals with a distinctive set of skills and a structured clinical setting. This review article presents the scope of genetic counseling practice and tackles some of the challenges faced in providing genetic counseling in Saudi Arabia.

Genetic testing and genomic analysis: a debate on ethical, social and legal issues in the Arab world with a focus on Qatar

In 2013 both Saudi Arabia and Qatar launched genome projects with the aim of providing information for better diagnosis, treatment and prevention of diseases and, ultimately to realize personalized medicine by sequencing hundred thousands samples. These population based genome activities raise a series of relevant ethical, legal and social issues general, related to the specific population structure as well as to the Islamic perspective on genomic analysis and genetic testing. To contribute to the debate, the Authors after reviewing the existing literature and taking advantage of their professional experience in the field and in the geographic area, discuss and provide their opinions. In particular, the Authors focus on the impact of consanguinity on population structure and disease frequency in the Arab world, on genetic testing and genomic analysis (i.e. technical aspects, impact, etc.) and on their regulations. A comparison between the Islamic perspective and the ethical, social and legal issues raised in other population contexts is also carried. In conclusion, this opinion article with an up-to-date contribution to the discussion on the relevance and impact of genomic analysis and genetic testing in the Arab world, might help in producing specific national guidelines on genetic testing and genomic analysis and help accelerate the implementation and roll out of genome projects in Muslim countries and more specifically in Qatar, and other countries of the Gulf.

Knowledge, Attitudes, and Practice Regarding Genetic Testing and Genetic Counselors in Jordan: A Population-Based Survey

Genetic testing has a potential in the prevention of genetic diseases, particularly in communities with high rates of consanguineous marriage. Therefore, knowledge, practice, and attitudes of the public in Jordan regarding genetic testing were investigated. Individuals (N = 3,196) were questioned about the concepts of genetic testing and genetic counselors, if they underwent any genetic tests, the type of test, the method of consenting to the test, as well as their level of satisfaction with the privacy of the genetic testing service. The likelihood of pursuing predictive genetic testing for cancer was also investigated. Although almost 70 % of respondents knew the term "genetic testing," only 18 % had undergone genetic testing, primarily the mandatory premarital test. In addition, there was a lack of general knowledge about genetic counselors. Many of those who had genetic testing (45 %) indicated they did not go through a consent process, and a lack of consent was significantly related to dissatisfaction with the privacy of the service. Approximately 55 % of respondents indicated they would potentially pursue predictive genetic testing for cancer. Going for routine health checkups was not significantly correlated with either actual or potential uptake of genetic testing, suggesting health care providers do not play an influential role in patients' testing decisions. Our results show a gap between the knowledge and uptake of genetic testing and may help to guide the design of effective strategies to initiate successful genetic counseling and testing services.

Marshall syndrome: further evidence of a distinct phenotypic entity and report of new findings

Marshall syndrome and type II Stickler syndrome are caused by mutations in COL11A1, which codes for the proα1chain of collagen XI. Collagen XI is a minor fibrillar collagen co-expressed with collagen II in cartilage and the vitreous of the eye. Characteristic features of Marshall syndrome include midfacial hypoplasia, high myopia, and sensorineural-hearing deficit. Deletions, insertions, splice site, and missense mutations in COL11A1 have been identified in Stickler syndrome and Marshall syndrome patients. In this study, we describe the clinical presentations of seven patients with Marshall syndrome from three unrelated Saudi families, inherited as autosomal dominant (two families) and autosomal recessive (one family). Cardinal clinical features of Marshall syndrome are manifested in all patients. One patient had ectodermal abnormalities. Mutations (c.2702G > A in exon 34,IVS50 + 1G > A, and IVS50 + lG > C) were identified in COL11A1 in affected members. Interestingly, the first report of autosomal recessive Marshall syndrome was from Saudi Arabia caused by the same mutation (c.2702G > A, p.Gly901Glu) as in one of our families. This study depicts detailed phenotypic and genetic description of dominant and recessive forms of Marshall syndrome due to COL11A1 mutations.

Is consanguinity prevalence decreasing in Saudis?: A study in two generations

BACKGROUND

Saudi population is unique in that there is a strong preference for cousin marriages in the general population. We studied the prevalence of consanguinity in educated Saudi females and compared the results with the results obtained in their parents, to access if a generation difference in which extensive educational activities have prevailed to inform the people of the influence of cousin marriages on health, has made any difference in prevalence of consanguineous marriages.

METHOD

A total of 600 Saudi women (421 university students and 179 women attending outpatients' clinics) were interviewed about their own and their parents' consanguinity.

RESULTS

The total consanguinity (first and second cousins) was 29.7% in the parents. Consanguinity was significantly higher among the daughters than the parents, where 37.9% of the 293 married women had consanguineous marriages. The prevalence of consanguinity was studied in different age groups, though no significant pattern was observed. A strong correlation was found between consanguinity of parents and their daughters; consanguinity was highest (52.3%) in the daughters of parents who were themselves consanguineous.

CONCLUSION

The results did not reveal any decrease in the prevalence of consanguinity over a generation. This shows that the tradition of marrying within the family is a preferred practice, despite the awareness that certain genetic disorders occur at a higher frequency in cousin marriages. There is a need at the primary health care level to inform the public of the consequences of this common practice.