What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations.

Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants. The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50-75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members. There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50-75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes

Prospect of genetic disorders in Saudi Arabia

Introduction: Rare diseases (RDs) create a massive burden for governments and families because sufferers of these diseases are required to undergo long-term treatment or rehabilitation to maintain a normal life. In Saudi Arabia (SA), the prevalence of RDs is high as a result of cultural and socio-economic factors. This study, however, aims to shed light on the genetic component of the prevalence of RDs in SA.Methodology: A retrospective study was conducted between September 2020 and December 2021 at King Saud Medical City, a tertiary hospital of the Ministry of Health (MOH), SA. A total of 1080 individuals with 544 potentially relevant variants were included. The index was 738, and the samples were tested in a commercialized laboratory using different molecular techniques, including next-generation sequencing.Result: A total of 867 molecular genetics tests were conducted on 738 probands. These tests included 610 exome sequencing (ES) tests, four genome sequencing (GS) tests, 82 molecular panels, 106 single nucleotide polymorphism (SNP) array, four methylation studies, 58 single-gene studies and three mitochondrial genome sequencing tests. The diagnostic yield among molecular genetics studies was 41.8% in ES, 24% in panels, 12% in SNP array and 24% in single gene studies. The majority of the identified potential variants (68%) were single nucleotide variants (SNV). Other ascertained variants included frameshift (11%), deletion (10%), duplication (5%), splicing (9%), in-frame deletion (3%) and indels (1%). The rate of positive consanguinity was 56%, and the autosomal recessive accounted for 54%. We found a significant correlation between the ES detection rate and positive consanguinity. We illustrated the presence of rare treatable conditions in DNAJC12, SLC19A3, and ALDH7A1, and the presence of the founder effect variant in SKIC2. Neurodevelopmental disorders were the main phenotype for which genetics studies were required (35.7%).Conclusion: This is the sixth-largest local study reporting next-generation sequencing. The results indicate the influence of consanguineous marriages on genetic disease and the burden it causes for the Kingdom of SA. This study highlights the need to enrich our society’s knowledge of genetic disorders. We recommend utilising ES as a first-tier test to establish genetic diagnosis in a highly consanguineous population

Clinical reassessment of post-laboratory variant call format (VCF) files

Background: Next-generation sequencing has been leading the genetic study of human disease for the past 10 years, generating a huge amount of sequence variant data, which are stored in variant call format (VCF) files. The aim of the study was to reassess the utility of VCF files for reanalysis. Methodology: This is a descriptive observational study of Saudi patients with undiagnosed genetic conditions. VCF files from 20 samples were referred to the molecular laboratory by physicians for reanalysis using variant interpretation software. Results: Seven cases (n = 20) have been reported differently from the outside laboratory. This accounts for almost 35% of all cases and is mainly due to the ability to gather more information about the patient's phenotype. One whole-genome sequence (WGS) case changed from inconclusive to negative. In addition, we identified variants related to the patient's phenotype in six cases; two of them were WGS and four were whole-exome sequence, all reported as negative before the reanalysis. Conclusion: Comprehensive phenotyping of individuals is a crucial step in identifying candidate phenotype-related variants. We outline the benefit obtained from access to the patient's medical records and communication with referring physicians. [JBCGenetics 2018; 1(1.000): 31-36

Knowledge and attitude of physicians, cancer patients, and the public concerning cancer-related genetic tests in Saudi Arabia

Background: To evaluate knowledge and attitude toward cancer genetic tests (CGT) and cancer genetic counseling for improving underdeveloped CGT services and to achieve a better understanding of how cancer genetic services are being perceived in the Saudi society. Methodology: An electronic survey was conducted targeting three different types of subjects; physicians, cancer patients, and public participants. Characteristics of the study population were summarized as frequencies, means, and standard deviations. The association between two categorical variables was evaluated by the Chisquare test and cross-tabulation. Multiple logistic regression analyses, using a backward stepwise elimination procedure, were performed to examine the potential impact of the variables. All the explanatory variables were calculated using the Statistical Package for Social Sciences (16.0) software program. Continuous variables were grouped into ordinal categories to facilitate inclusion in the multiple logistic regression analysis. Analysis of variance was used to measure knowledge scores with different independent variables. Results: The public cohort showed a higher knowledge score than the patient cohort. A willingness to undergo CGT correlated with high knowledge in the public cohort [r (n = 1,083) = 0.12, p < 0.001), but with positive family history in the patient cohort [r (n= 100) = 0.29, p < 0.01]. Attitudes toward CGT were not correlated with a fear of stigma or privacy in the public cohort. The majority of physicians reported an increase in the number of patients seeking CGT and agreed that testing should not be performed without counseling as they would refer to appropriate patients accordingly. Physicians self-reported significant levels of uncertainty regarding CGT, such as qualifications, attitudes toward CGT, and confounding factors. Conclusion: There is an overall positive attitude toward CGT in Saudi society. Public health actions are needed to enhance cancer genetic services for high-risk families. [JBCGenetics 2019; 2(2.000): 107-115

Novel mutation of the FHL1 gene associated with congenital myopathy and early respiratory muscles involvement: a case report

Background: Congenital myopathies are a diverse group of diseases that share features from the early onset of symptoms in the first year of life, such as hypotonia, muscle weakness, and developmental delays, and are often associated with respiratory insufficiency and feeding difficulties. Case presentation: Here, we report an 8-year-old boy having hypotonia and signs of respiratory insufficiency that ended with tracheostomy and ventilator-dependent status. Muscle biopsy showed histological findings of congenital fiber-type disproportion myopathy. The whole exome sequencing revealed a novel hemizygous missense variant (c.530A > C p.Gln177Pro) that confirms the diagnosis of FHL1-associated congenital myopathy. Conclusion: The findings in this study help to expand the genetic and mutational spectrum of the FHL1 gene associated with respiratory insufficiency and help in formulating a precise strategy for prognosis and future management of patients. [JBCGenetics 2020; 3(1.000): 45-51

Genetic carrier screening for disorders included in newborn screening in the Saudi population

Background: Inborn errors of metabolism (IEM) are prevalent autosomal recessive disorders in Saudi Arabia. Socio-economic factors, such as consanguineous marriages, play a role in the high rate of diseases. The government of Saudi Arabia created a newborn screening program (NBS) for the most prevalent disorders to facilitate early intervention and the prevention of severe complications. The study aimed to determine the carried pathogenic allele of the diseases included in the NBS and the most frequently carried phenotype in the Saudi population. Methodology: We performed targeted genetic screening for the genes associated with the IEM in the NBS. We used the results of the whole exome sequencing of 1,314 affected and unaffected individuals from 650 families. The results constitute the King Abdullah International Medical Research Center Genomic Database. Results: According to the data set, four diseases occurred most frequently in the Saudi population: adrenal hyperplasia, propionic acidemia, phenylketonuria, and maple syrup urine disease. In total, 12 pathogenic variants occurred frequently. Conclusion: This study generated an updated list of the most pathogenic variants in the Saudi population, based on the National Guard Hospital dataset. Additional research with larger data sets from the different regions will provide valuable information about the allele distribution in the Saudi population, creating a carrier screening program. [JBCGenetics 2021; 4(2.000): 70-75

Genetic impact of non-consanguineous marriages in Saudi Arabia.

Background: Physicians and geneticists face challenges in making accurate diagnoses during clinical evaluations; affecting patients and clinicians. The aim of this study was to estimate the hit rate of the non-consanguineous population. Moreover, prevalence of the genetic disorder in both the consanguineous and non- consanguineous population of Saudi Arabia at King Abdulaziz Medical City in Riyadh data. Methods: We reviewed 681 families and 1563 individuals with 2,565,335 variants in the King Abdullah International Medical Research Center (KAIMRC) Genomic Database (KGD), Riyadh, Saudi Arabia. All the ES requests were obtained from the physician and clinical geneticist of KAIMRC, and the test was performed either in-house or in a College of American Pathologists accredited laboratory center for clinical purposes. Results: A total of 151 non-consanguineous individuals with exome sequencing requests in the population genomic database of King Abdullah International Medical Research Center was considered for the study. In total, 27 had disease-causing variants, and the hit rate was 27/151 (18%). Among the 28 different variants in the 27 individuals, 50% were de novo variants and 50% inherited. The hit rate of the variants causing autosomal recessive disorders was 12/28 (42.8%), autosomal dominant disorders 13/28 (46.4%), and X-linked disorders 3/28 (10.7%). Conclusion: Non-consanguineous marriages have a lower risk of genetic disorders, and reducing consanguinity reduces the risk of genetic disorders by two to three times.   [JBCGenetics 2022; 5(2.000): 37-42