Using whole-exome sequencing to identify inherited causes of autism.

Despite significant heritability of autism spectrum disorders (ASDs), their extreme genetic heterogeneity has proven challenging for gene discovery. Studies of primarily simplex families have implicated de novo copy number changes and point mutations, but are not optimally designed to identify inherited risk alleles. We apply whole-exome sequencing (WES) to ASD families enriched for inherited causes due to consanguinity and find familial ASD associated with biallelic mutations in disease genes (AMT, PEX7, SYNE1, VPS13B, PAH, and POMGNT1). At least some of these genes show biallelic mutations in nonconsanguineous families as well. These mutations are often only partially disabling or present atypically, with patients lacking diagnostic features of the Mendelian disorders with which these genes are classically associated. Our study shows the utility of WES for identifying specific genetic conditions not clinically suspected and the importance of partial loss of gene function in ASDs.

Hereditary cutaneomucosal venous malformations are caused by TIE2 mutations with widely variable hyper-phosphorylating effects.

Mutations in the angiopoietin receptor TIE2/TEK have been identified as the cause for autosomal dominantly inherited cutaneomucosal venous malformation (VMCM). Thus far, two specific germline substitutions (R849W and Y897S), located in the kinase domain of TIE2, have been reported in five families. The mutations result in a fourfold increase in ligand-independent phosphorylation of the receptor. Here, we report 12 new families with TEK mutations. Although the phenotype is primarily characterized by small multifocal cutaneous vascular malformations, many affected members also have mucosal lesions. In addition, cardiac malformations are observed in some families. Six of the identified mutations are new, with three located in the tyrosine kinase domain, two in the kinase insert domain, and another in the carboxy terminal tail. The remaining six are R849W substitutions. Overexpression of the new mutants resulted in ligand-independent hyperphosphorylation of the receptor, suggesting this is a general feature of VMCM-causative TIE2 mutations. Moreover, variation in the level of activation demonstrates, to the best of our knowledge for the first time, that widely differing levels of chronic TIE2 hyperphosphorylation are tolerated in the heterozygous state, and are compatible with normal endothelial cell function except in the context of highly localized areas of lesion pathogenesis.

Impact of consanguinity on cancer in a highly endogamous population.

BACKGROUND: Many epidemiological studies have indicated that inbreeding has little or no effect on the incidence of cancer. Due to the high prevalence of consanguinity in Qatar (54%), its influence may nevertheless be of special importance. AIM: The aim of this study was to examine whether parental consanguinity affects the risk of cancer in a local Arab highly inbred population. DESIGN: Matched case-control study. SETTING: The study was carried out in Al-Amal cancer hospital and primary health care centers in Qatar over a period from August 2008 to February 2009. SUBJECTS AND METHODS: The study included 370 Qataris and other Arab expatriates with various types of cancers and 635 controls matched by age and ethnicity. A questionnaire that included socio-demographic information, type of consanguinity, medical history, and tumor grade was designed to collect the information of cases and controls. RESULTS: The study revealed that the rate of parental consanguinity was similar in both cases (29.5%) and controls (29.9%) with a higher inbreeding coefficient in controls (0.017-/+0.03), compared to cancer patients (0.0155-/+0.03). Other Arab expatriates had a higher incidence of cancer (61.1%) than Qataris (38.9%). The inbreeding coefficient was higher in male cancer patients (0.0189-/+0.03), but lower in female cancer patients (0.014-/+0.03) as compared to controls. Controls were more inbred in the overall studied subjects (23.6%) and women (23.8%) than cases. The coefficient of inbreeding was lower in patients with breast (0.014), skin (0.012), thyroid (0.008) and female genital (0.014) cancers, whereas it was higher in cases for leukemia and lymphoma (0.018), colorectal (0.025) and prostate (0.017), with no significant difference between cases and controls. No significant differences were observed between cases and controls in the parental consanguinity, mean coefficient of inbreeding and proportion of more inbred subjects. CONCLUSIONS: The study findings revealed that although the consanguinity rate is high in our Arab population, it has no effect on the incidence of cancers overall. However, there was an increased risk found for leukemia and lymphoma, colorectal and prostate cancer groups, but a reduced risk in breast, skin, thyroid and female genital cancer groups.

Molecular breakpoint mapping of 6q11-q14 interstitial deletions in seven patients.

Interstitial deletions involving 6q11-q14 have been reported in less than 20 patients, with the breakpoints studied by G-banding alone. We report on seven patients with 6q11-q14 interstitial deletions of variable size. The breakpoints were studied by G-banding, dual-color BAC-FISH and SNP array. The results showed the molecular breakpoints differed significantly from the ones obtained from G-banding. The breakpoints studied by BAC-FISH were consistent with the ones from SNP array. Some characteristics from this cohort are consistent with previous reports, but many typical features are lacking in our patients. The cardinal features of 6q11-q14 interstitial deletions in this cohort include: umbilical hernia, hypotonia, short stature, characteristic facial features of upslanting palpebral fissures, low set and/or dysplastic ears, high arched palate, urinary tract anomalies, and skeletal/limb anomalies.

A novel non-sense mutation in the SLC2A10 gene of an arterial tortuosity syndrome patient of Kurdish origin.

Arterial tortuosity syndrome (ATS) is a rare autosomal recessive disorder in which patients display tortuosity of arteries in addition to hyperextensible skin, joint laxity, and other connective tissue features. This syndrome is caused by mutations in the SLC2A10 gene. In this article we describe an ATS girl of Kurdish origin who, in addition to arterial tortuosity and connective tissue features, displays stomach displacement within the thorax and bilateral hip dislocation. Clinical details of this patient have been reported previously. Sequencing of the SLC2A10 gene identified a novel homozygous non-sense c.756C>A mutation in this patient's DNA. This mutation in the SLC2A10 gene replaces a cysteine encoding codon with a stop signal. This is believed to cause a premature truncation of GLUT10 protein in this patient. We conclude that patients of Kurdish origin who display arterial tortuosity associated with skin hyperextensibility, joint hypermobility, and characteristic facial features may carry mutations in the SLC2A10 gene.

A novel missense and a recurrent mutation in SLC2A10 gene of patients affected with arterial tortuosity syndrome.

Arterial tortuosity syndrome is an autosomal recessive disorder characterized by severe tortuosity of greater and systemic arteries in affected individuals. In addition, patients display connective tissue features which include hyperextensible skin, hypermobility of joints and characteristic facial features. This syndrome is caused by mutation in SLC2A10 gene which encodes for the facilitative glucose transporter, GLUT10. We describe seven patients of two unrelated Saudi Arabian families who display tortuosity, dilatation and stenosis of arteries, pulmonary hypertension and other cardiovascular manifestations. These patients exhibit characteristic connective tissue phenotypes and distinctive facial features. In the single patient of Family 1, sequencing of the candidate gene, SLC2A10, identified a novel missense c.313C>T mutation encoding a p.Arg105Cys substitution in the second extracellular domain of GLUT10. The Arg105 in GLUT10 is highly conserved across species and its replacement with cysteine is predicted to be pathogenic. In the second family, all of the six affected individuals carry recurrent c.243C>G missense mutation encoding a p.Ser81Arg change in the third transmembrane domain of GLUT10. The present study suggests that there exists an intra- and inter-familial phenotypic variability in arterial tortuosity patients carrying identical or different mutations in SLC2A10 gene. While skin hyperextensibility, small joint hypermobility, and facial features are similarly expressed in these patients, there is a range of other phenotypes which include arterial tortuosity and associated complications, and abnormalities of other organs.

The prevalence of attention deficit hyperactivity symptoms in schoolchildren in a highly consanguineous community.

OBJECTIVE: The objective of the present study was to find the prevalence of attention deficit hyperactivity (ADH) symptoms in a sample of primary schoolchildren in Qatar and investigate the behaviour of the children with and without ADH symptoms in a highly consanguineous community. SUBJECTS AND METHODS: A total of 2,500 primary school students, aged 6-12 years, were randomly selected from the government primary schools, and 1,869 students (947 boys and 922 girls) gave consent to participate in this study. An Arabic questionnaire was used to collect the sociodemographic variables and a standardized Arabic version of the Conners' Teacher Rating Scale for ADH symptoms. RESULTS: Of the 947 boys, 158 (16.7%; 95% confidence interval, CI, 14.4-19.2) and of the 922 girls, 50 (5.4%; 95% CI 4.1-7.1) scored above the cut-off (>or=15) for ADH symptoms, thus giving an overall prevalence of 11.1% (95% CI 9.7-12.6). The children who had higher scores for ADH symptoms were in the age group of 6-9 years. Children who had higher scores for ADH symptoms had a poorer school performance than those with lower scores (p = 0.002). Two hundred (96.2%) children with ADH were disobedient, 126 (60.6%) noisy and hyperactive, 76 (36.5%) very cranky, 78 (37.5%) troublesome and 79 (37.9%) nervous. The logistic regression identified socio-economic condition, number of children, school performance and poor relationship between parents as the main contributors to ADH. Although the univariate analysis showed a significant relationship (p = 0.010) between ADH symptoms and consanguineous parents, logistic regression did not support this association (p = 0.075). This suggests that consanguinity has no impact on ADH children. CONCLUSION: The study revealed that ADH is a common problem among schoolchildren. The children with higher scores for ADH symptoms had a poorer school performance than those with lower scores. A significant difference exists between the behaviour of children with and without ADH.

Consanguineous marriages and their effects on common adult diseases: studies from an endogamous population.

OBJECTIVES: The aim of the study was to determine the extent and nature of consanguinity in the Qatari population and its effects on common adult diseases. SUBJECTS AND METHODS: The study was conducted in urban and semi-urban areas of Qatar between October 2004 and May 2005. The total sample of 1,050 married Qatari females 15 years of age and over were approached for study. The degree of consanguinity between each female and her spouse and the degree of consanguinity between their parents were recorded. RESULTS: Of 1,050 married Qatari females who were approached, 876 agreed to participate in the study, giving an 83.4% response. The rate of consanguinity in the present generation was 51% (95% confidence interval = 47.7-54.4) with a coefficient of inbreeding of 0.023724. The consanguinity rate and coefficient of inbreeding in the current generation were significantly higher than the maternal rate (51.0 vs. 40.3%; p < 0.001; 0.023724 vs. 0.016410 maternal). All types of consanguineous marriages were higher in this generation, particularly first cousins (26.7 vs. 21.4% paternal and 23.1% maternal) and double first cousins (4.3 vs. 2.9% paternal and 0.8% maternal). The current generation of consanguineous parents had a slightly higher risk for most diseases: cancer, mental disorders, heart diseases, gastro-intestinal disorders, hypertension, hearing deficit and diabetes mellitus. All reported diseases were more frequent in consanguineous marriages. CONCLUSION: The study showed that in a population with a high rate of consanguinity, there is a significant increase in the prevalence of common adult diseases like cancer, mental disorders, heart diseases, gastro-intestinal disorders, hypertension and hearing deficit.

Craniofacial anomalies, humero-radial synostosis, rhizomelic limb shortness: previously unrecognized autosomal recessive syndrome.

Humero-radial synostosis (HRS) is a rare skeletal anomaly that might be seen in some craniosynostosis syndromes, notably Antley-Bixler syndrome, and in other disorders in association with skeletal anomalies. Here we report on two daughters of first cousin Saudi parents with syndromic HRS. Both patients had distinctive craniofacial features including cranium bifidum occultum, hypertelorism, epicanthus inversus, capillary hemangiomata, and malformed ears. Musculoskeletal examination revealed rhizomelic shortness with normal hands and feet. Skeletal survey showed bilateral HRS with no evidence of craniosynostosis. The craniofacial manifestations in these two patients do not match any of the syndromes known to be associated with HRS. We consider that the constellation is unique and apparently represents a previously unrecognized syndrome.

Severe hypertelorism, midface prominence, prominent/simple ears, severe myopia, borderline intelligence, and bone fragility in two brothers: new syndrome?

We report on two brothers, born to double first cousin Jordanian Arab parents, with a syndrome comprising severe hypertelorism with upslanted palpebral fissures, brachycephaly, abnormal ears, sloping shoulders, enamel hypoplasia, and osteopenia with repeated fractures. Both have severe myopia, mild to moderate sensori-neural hearing loss and borderline intelligence. Results of chromosome analysis were normal as was a FISH assay for subtelomeric rearrangements. The father has mild hypertelorism but the family history is otherwise unremarkable. We think that this represents a previously unrecognized autosomal or X-linked recessive syndrome.

Defective glycosylation of decorin and biglycan, altered collagen structure, and abnormal phenotype of the skin fibroblasts of an Ehlers-Danlos syndrome patient carrying the novel Arg270Cys substitution in galactosyltransferase I (beta4GalT-7).

The Ehlers-Danlos syndrome (EDS) is a heterogeneous group of connective tissue disorders affecting skin and joint function. Molecular defects in extracellular matrix proteins, including collagen (type I, III, and V) and tenascin X are associated with different forms of EDS. Compound heterozygous mutations in the B4GALT7 gene, resulting in aberrant glycosylation of the dermatan sulfate proteoglycan decorin, had been described in a single patient affected with the progeroid form of EDS. We have studied the molecular phenotype of decorin, biglycan, and collagen type I containing fibrils in skin fibroblasts of a patient carrying the novel homozygous C808T point mutation in the B4GALT7 gene, which causes an Arg270Cys substitution in beta4GalT-7. Compared to control fibroblasts, galactosyltransferase activity in beta4GalT-7(Arg270Cys) cells was approximately three times reduced over a temperature range of 25-41 degrees C. Pulse-chase experiments and confocal microscopy demonstrated that synthesis and secretion of decorin were normal in beta4GalT-7(Arg270Cys) cells. However, about 50% of decorin were synthesized as a protein core in addition to its proteoglycan form. Biglycan was found in a monoglycanated form in addition to its mature form. Glycosaminoglycan chains were of the dermatan/chondroitin sulfate type both in beta4GalT-7(Arg270Cys) and control cells, and epimerization was reduced for decorin and biglycan. Compared to control cells, beta4GalT-7(Arg270Cys) cells showed altered, highly spread or stretched phenotypes and decreased proliferation rates. At the ultrastructural level, an intracellular accumulation of multiple secondary lysosomes and degenerative vacuoles was seen in beta4GalT-7(Arg270Cys) cells. Furthermore, the collagen suprastructures were altered in the beta4GalT-7(Arg270Cys) cells. The reduced beta4GalT-7 activity resulting in defective glycosylation of decorin and biglycan may be responsible for the complex molecular pathology in beta4GalT-7 deficient EDS patients, given the role of these proteoglycans in bone formation, collagen fibrillogenesis, and skeletal muscle development.

Genetic diversity among the Arabs.

The Arabs in general are genetically diverse. Major factors that contributed to their diversity include the migrations of Semitic tribes from the Arabian Peninsula, the Islamic expansion in the 7th century AD, the Crusade wars and the recent migration dynamics. These events have resulted in the admixture of the original Arabs with other populations extending from east and south Asia to Europe and Africa. Their demographic features include high rates of consanguinity, a large family size and a rapid population growth. There is a high frequency of autosomal recessive disorders and increased frequencies of homozygosity for autosomal dominant traits, such as familial hypercholesterolemia and X-linked traits, such as glucose-6-phosphate dehydrogenase deficiency. The patterns of autosomal recessive disorders, including their mutations, may be different in various geographic locations within the Arab world. However, there are disorders that are specifically prevalent among the Arabs either uniformly or in certain locations. The Arab Genetic diseases include Bardet-Biedl syndrome, Meckel syndrome, autosomal recessive severe childhood muscular dystrophy, osteopetrosis and renal tubular acidosis, Sanjad-Sakati syndrome and others.

Newly recognized autosomal recessive acrofacial dysostosis syndrome resembling Nager syndrome.

We report on two patients with a unique constellation of anomalies resembling the Nager acrofacial dysostosis syndrome. Clinical manifestations which differentiate their condition from Nager syndrome include: microcephaly, cleft lip and palate, a peculiar beaked nose, blepharophimosis, microtia, symmetrical involvement of the thumbs, and great toes and developmental delay. We postulate that the inheritance is autosomal recessive on the basis of similarly affected male and female sibs.