In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016–December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most “negative” clinical exome tests are unsolved due to interpretation rather than technical limitations.Electronic supplementary materialThe online version of this article (doi:10.1007/s00439-017-1821-8) contains supplementary material, which is available to authorized users.

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.

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Celiac disease (CD) is an immune-mediated disease affecting the small intestine secondary to gluten exposure. The currently available treatment is lifelong adherence to a gluten-free diet (GFD). Several disorders are known to be associated with celiac disease, including Down syndrome (DS). In several studies, the prevalence of CD in DS ranged between 4 and 17%.CD is prevalent in Arabs; however, few studies have been performed to determine the prevalence of CD in DS patients. Our study aimed to determine the prevalence of CD in Saudi Down syndrome patients using serological markers and small bowel biopsy.This is a retrospective study in which files relating to Down syndrome patients who were followed up in a general pediatric clinic at King Faisal Specialist Hospital and Research Center were reviewed regarding demographic data, serological markers and biopsy results.Of the total number of patients reviewed (91), 7 were excluded because data were missing; the remaining 84 patients included 35 females and 49 males. The age range of the patients at the time of screening was from 1 to 18 years. Patient demographic data are shown in Table 1. Among the studied patients, antigliadin antibody (AGA) IgA was high in 27 patients (32.14%), and AGA IgG was high in 44 patients (52.38%). Twelve patients (14.28%) tested positive and 58 (69.04%) tested negative for anti-endomysial antibodies. Anti-tissue glutaminase antibody IgA was found to be high in 13 patients (15.5%) and normal in 54 patients (64.28%). Serum IgA levels were normal in 36 patients (43%) and low in 1 patient (1.2%). Biopsy was performed in 22 patients who tested positive for anti-endomysial or anti-tissue transglutaminase antibodies. The biopsies provided positive results in 9 patients (10.7%).Our study showed a confirmed prevalence of 10.7% for celiac disease in Saudi patients with Down syndrome based on serology and biopsy; together with previous cases reported in the literature, this result indicates a need to screen these patients for celiac disease.

Congenital glucose-galactose malabsorption (cGGM) is a rare autosomal recessive disorder, caused by mutations in the SLC5A1 gene, encoding the sodium/glucose cotransporter 1, which may result in severe life-threatening osmotic diarrhea due to the accumulation of unabsorbed sugars in the intestinal lumen. If treated early with elimination of glucose and galactose from the diet, patients usually recover and develop normally. We present clinical and molecular data from 16 unrelated cGGM diagnosed Saudi patients from consanguineous families with majority of them having previous positive family history of cGGM. Sanger sequencing for the full coding regions of SLC5A1 for all patients resulted in the identification of 4 allelic variants in a homozygous state. Two mutations are novel; c.265G>A (p.G89R) and c.1304 G>A (p.G435D), and 2 have been previously reported to cause cGGM, c.765 C>G (p.C255W) and c.1136 G>A (p.R379Q). This is the first report delineating the clinical and molecular basis of cGGM in patients from this region.