Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population.

We report the results of clinical exome sequencing (CES) on >2,200 previously unpublished Saudi families as a first-tier test. The predominance of autosomal-recessive causes allowed us to make several key observations. We highlight 155 genes that we propose to be recessive, disease-related candidates. We report additional mutational events in 64 previously reported candidates (40 recessive), and these events support their candidacy. We report recessive forms of genes that were previously associated only with dominant disorders and that have phenotypes ranging from consistent with to conspicuously distinct from the known dominant phenotypes. We also report homozygous loss-of-function events that can inform the genetics of complex diseases. We were also able to deduce the likely causal variant in most couples who presented after the loss of one or more children, but we lack samples from those children. Although a similar pattern of mostly recessive causes was observed in the prenatal setting, the higher proportion of loss-of-function events in these cases was notable. The allelic series presented by the wealth of recessive variants greatly expanded the phenotypic expression of the respective genes. We also make important observations about dominant disorders; these observations include the pattern of de novo variants, the identification of 74 candidate dominant, disease-related genes, and the potential confirmation of 21 previously reported candidates. Finally, we describe the influence of a predominantly autosomal-recessive landscape on the clinical utility of rapid sequencing (Flash Exome). Our cohort's genotypic and phenotypic data represent a unique resource that can contribute to improved variant interpretation through data sharing.

Autozygome and high throughput confirmation of disease genes candidacy.

PURPOSE: Establishing links between Mendelian phenotypes and genes enables the proper interpretation of variants therein. Autozygome, a rich source of homozygous variants, has been successfully utilized for the high throughput identification of novel autosomal recessive disease genes. Here, we highlight the utility of the autozygome for the high throughput confirmation of previously published tentative links to diseases. METHODS: Autozygome and exome analysis of patients with suspected Mendelian phenotypes. All variants were classified according to the American College of Medical Genetics and Genomics guidelines. RESULTS: We highlight 30 published candidate genes (ACTL6B, ADAM22, AGTPBP1, APC, C12orf4, C3orf17 (NEPRO), CENPF, CNPY3, COL27A1, DMBX1, FUT8, GOLGA2, KIAA0556, LENG8, MCIDAS, MTMR9, MYH11, QRSL1, RUBCN, SLC25A42, SLC9A1, TBXT, TFG, THUMPD1, TRAF3IP2, UFC1, UFM1, WDR81, XRCC2, ZAK) in which we identified homozygous likely deleterious variants in patients with compatible phenotypes. We also identified homozygous likely deleterious variants in 18 published candidate genes (ABCA2, ARL6IP1, ATP8A2, CDK9, CNKSR1, DGAT1, DMXL2, GEMIN4, HCN2, HCRT, MYO9A, PARS2, PLOD3, PREPL, SCLT1, STX3, TXNRD2, WIPI2) although the associated phenotypes are sufficiently different from the original reports that they represent phenotypic expansion or potentially distinct allelic disorders. CONCLUSIONS: Our results should facilitate the timely relabeling of these candidate disease genes in relevant databases to improve the yield of clinical genomic sequencing.

Developmental and/or epileptic encephalopathy with spike-and-wave activation in sleep in Saudi Arabia: Electroclinical, etiologic, genetic, and outcome multicenter study.

OBJECTIVES: To investigate the clinical features of developmental and/or epileptic encephalopathy with spike-and-wave activation in sleep (D/EE-SWAS), its electrographic characteristics, and etiology and to compare the effects of different treatment strategies on the outcomes using a Saudi Arabian database. METHODS: This multicenter study included children with D/EE-SWAS who were evaluated between 2010 and 2020 at 11 tertiary centers. Data were collected on their baseline clinical features, etiologies, and treatment modalities. Seizure reduction, spike-wave index, and cognitive state were examined as potential therapeutic outcomes. RESULTS: Ninety-one children were diagnosed with D/EE-SWAS, with a median age of 7 years (IQR: 3-5) and an almost equal sex distribution. The average age at which epilepsy was diagnosed was 3 years (IQR: 5-2). A genetic/metabolic etiology was found in 35.1% of the patients, and a structural etiology was found in 27.4%. Children with underlying genetic/metabolic diseases exhibited an earlier seizure onset (P = 0.001) than children with other etiologies. Benzodiazepines (76.6%) were the most common treatment, followed by steroids (51.9%). Sodium valproate (75%) was the most frequently used antiseizure medication, followed by levetiracetam (64.9%). Children with a later seizure onset were more likely to have better clinical responses (P = 0.046), EEG responses (P = 0.012), and cognitive outcomes (P = 0.006) than children with an earlier onset. Moreover, better seizure response and electrographic response were seen in patients with bilateral interictal discharges on the EEG than otherwise. Children had a higher likelihood of both clinical and electrographic improvement with combination therapy of benzodiazepines (P = 0.001) and steroids (P = 0.001) than with other therapies. SIGNIFICANCE: This study shows a higher prevalence of genetic/metabolic causes and suggests the superior efficacy of combination therapy with steroids and benzodiazepines in D/EE-SWAS. Prospective studies that strictly assess the treatment protocols and outcomes are needed.

Autosomal recessive hereditary spastic paraplegia with thin corpus callosum among Saudis.

OBJECTIVE: To assess the mutational and clinical spectrum of spatacsin associated with autosomal recessive hereditary spastic paraplegia (ARHSP) with thin corpus callosum (TCC). METHODS: A retrospective study was carried out at King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia from February 2008 until March 2011. Four unrelated Saudi Arabian families with ARHSP-TCC were studied, totaling 13 affected individuals. Clinical presentations included gait disturbance at variable ages (2-18 years), spastic paraplegia with mild to moderate cognitive impairment and evidence of peripheral neuropathy in 2 families. Brain MRI showed TCC accompanied by periventricular white matter changes and cortical atrophy. RESULTS: A genome wide scan demonstrated linkage to the SPG11 locus. Sequencing revealed 4 mutations. The first is an insertion/deletion (indel) consisting of a 3 base pair (bp) deletion and 23 bp insertion (L1268L fsX), the second is a one bp deletion (S1923R fsX), and the third and the fourth are nonsense mutations (Q341X and R651X). All mutations predict premature truncation of the spatacsin protein. CONCLUSION: We report 2 novel mutations in this gene, including an indel considerably larger than any other identified to date. The identification of these mutations further confirms the causative link between SPG11 and ARHSP-TCC in these families.

Case report: Aromatic L-amino acid decarboxylase deficiency in three patient cases from the Kingdom of Saudi Arabia.

Aromatic L-amino acid decarboxylase (AADC) deficiency is an ultra-rare and often severe neurometabolic disorder resulting from variants in the dopa decarboxylase (DDC) gene. A timely diagnosis is critical to prevent secondary complications, promote development, and optimize outcomes from future innovative treatment options, such as gene therapy. This article describes three patients with AADC deficiency managed in the Kingdom of Saudi Arabia (KSA). All three patients had homozygous variants within the DDC gene, including one novel gene variant (c.245G > A, p.Arg82Glu), and presented with symptoms from birth. In all cases, a diagnostic delay was observed owing to non-specific signs and symptoms, a lack of disease awareness among primary care physicians, and delays associated with outsourcing of genetic tests. All three patients were managed by a multidisciplinary team at a specialist tertiary center. Clinical outcomes for all three cases were poor, with one patient passing away at 3 years of age and the other two patients continuing to experience substantial disability and poor quality of life. There is an urgent need to raise awareness and improve diagnostic testing for rare diseases such as AADC deficiency in the KSA in order to improve outcomes, particularly as innovative disease-targeting therapies become available.

Phenotypical spectrum of cerebellar ataxia associated with a novel mutation in the CA8 gene, encoding carbonic anhydrase (CA) VIII.

We define the neurological characteristics of familial cases from multiple branches of a large consanguineous family with cerebellar ataxia, mental retardation (MR), and dysequilibrium syndrome type 3 caused by a mutation in the recently cloned CA8 gene. The linkage analysis revealed a high logarithm of the odds (LOD) score region on 8q that harbors the CA8 in which a novel homozygous c.484G>A (p.G162R) mutation was identified in all seven affected members. The patients had variable cerebellar ataxia and mild cognitive impairment without quadrupedal gait. The brain MRI showed variable cerebellar volume loss and ill-defined peritrigonal white matter abnormalities. The Fluorodeoxyglucose Positron Emission Tomography (FDG PET) revealed hypometabolic cerebellar hemispheres, temporal lobes, and mesial cortex. This report expands the neurological and radiological phenotype associated with CA8 mutations. CA8 involvement should be considered in the differential diagnosis of other genetically unresolved autosomal recessive cerebellar ataxias.