 analysis, skin/ muscle biopsy, biochemical studies, and DNA testing) before WES testing. For most of patients, both parents DNA were tested. The cost of WES was billed to insurance companies in the UAE.
Fourteen (16 %) patients had IEM (Table 2), 17 (20 %) had genetic syndromes (Table 3), 12 (14 %) had variants of unknown significance confirmed to be pathogenic (Table 1A), and 12 (14 %) had variants of unknown significance likely to be pathogenic (Table 1B). Therefore, WES information was clinically useful in 55 (65 %) patients and diagnostic in 43 (50 %) patients.
Forty-one (75 %) of the 55 patients had consanguineous families. All patients with autosomal recessive diseases had consanguineous families (Tables 1–3); except the patient with MTHFR mutation and the patient with TBX19 mutation (Table 2) who had families of the same tribe/ region; the patient with compound heterozygous mutations in MPDZ (Table 1) and the patients with PCSK1, AHI1, and DOCK7 mutations (Table 3). The patients with autosomal dominant mutation in CHRNB1 and FOXG1 (Table 1), the patient with mitochondrial mutation in tRNA Ala (Table 2), and the patient with X-linked mutation in PDHA1 (Table 2) had non-consanguineous families. In Table 3, the patients with X-linked or autosomal dominant conditions had non-consanguineous families, except for the patient with MYBPC3 mutations.
One hundred twenty-eight variants were identified. Forty-four (34 %) variants were pathologic. Twenty (15 %) of these variants were previously reported and 24 (19 %) were novel.
Eleven (13 %) patients had autosomal dominant disorders. Five patients had truncating or missense mutations which were previously reported. Three of these mutations were de novo (Table 3). Six patients had autosomal dominant (Table 1); three were de novo variant, one was inherited from symptomatic parent, and two were inherited from parents of unknown phenotype.
Forty (47 %) patients had autosomal recessive diseases. Thirty-five patients had homozygous variants and five patients had compound heterozygous variants. Eleven pathogenic mutations involved inborn errors of metabolism (Table 2). Five of these mutations were novel, including a compound heterozygous mutation (Table 2). Eleven pathogenic homozygous mutations involved genetic syndromes (Table 3). Five of these mutations were previously reported and six were novel (Table 3).
Of the reported variants of unknown significance, nine were confirmed pathogenic homozygous mutations on further testing, six of which were novel (Table 1A). Seven of these disorders were IEM (Table 1A). In addition, six homozygous and three compound heterozygous variants were likely pathogenic; only one of these variants was previously reported (Table 1B).
The three patients with X-linked disorders had de novo mutations; one had pyruvate dehydrogenase e1-alpha deficiency (Table 2) and one had mental retardation, X-linked 30 (Table 3). The patient with epileptic encephalopathy, early infantile had mosaic de novo variant (Table 1A).
Two female patients had known pathogenic mutations. The patient with Leigh disease had 56 % heteroplasmic m.13513G > A (p. D393N, ND5) mutation in the mitochondrial ND5 gene. The second patient had mitochondrial myopathy with 59 % heteroplasmic m.5591G > A (tRNAAla), Table 2.
Carrier status for Mendelian recessive disorders was detected in nine patients. Two patients had sickle cell trait, two had β-thalassemia trait, one had CFTR gene mutation (cystic fibrosis heterozygosity), and four females had G6PD gene mutations (glucose-6-phosphatase dehydrogenase heterozygosity).
Medically actionable genetic variants unrelated to the clinical phenotype were identified in eight patients. Seven patients had mutations in the G6PD gene (c.563C > T in five patients, c.1003G > A in one patient, andc.634A > G in one patient) and one had mutation in the MYBPC3 gene (c.2148 + 1G > A) that causes dilated cardiomyopathy.
In this study, WES provided useful clinical information in most patients in whom several other tests were not revealing. It attained a diagnostic rate of 50 % compared with25–42%in other studies [6–11]. This higher yield is a result of the frequent autosomal recessive diseases (mostly homozygous mutations) in the region and the multiple affected children in the same family.
Thirty-one of the 43 (72 %) patients with confirmed molecular diagnoses had autosomal recessive disorders compared with 34 % in another study [8]. Twenty-nine of these patients were homozygous for the rare allele, indicating consanguinity played a major role in making autosomal recessive disorders frequent in this culture.
Of the patients with autosomal dominant disorders, 66 % had de novo mutations (Table 1 and Table 3). In addition, all patients with X-linked disorders had de novo mutations (Table 1A and Tables 2, 3). WES detected a low-level mosaicism in one patient with X-linked de novo variant in CDKL5, which was consistent with his phenotype (Table 1). WES identified a mutation in G6PC causing GSD1a (Table 1) in a patient who was clinically suspected to have GSD III or IX due to cardiomyopathy and hepatic manifestations but had normal leukocyte enzymes for GSD III and IX. Establishing GSD1a diagnosis in this patient enabled appropriate counseling and genetic screening of the family members.
WES was especially helpful in a few patients with suspected mitochondrial disorders in whom extensive mitochondrial work-up was not revealing. Mutations in FBXL4 and C10orf2 causing mitochondrial DNA depletion syndrome were identified (Table 2). WES facilitated a rapid diagnosis in these patients with mitochondrial disorders, avoiding a need for invasive muscle or skin biopsies.
WES also provided a relatively rapid diagnosis in patients with treatable conditions, such as glycogen storage diseases (Table 1B). In addition, it provided a diagnosis in patients with atypical features of rare diseases, such as the patient with global developmental delay, repetitive hand movements, and brain atrophy without the molar tooth sign. This patient was confirmed to have Joubert syndrome due to a homozygous mutation in AHI1, c.1051C > T (p.R351X) (Table 3). In addition, WES revealed pathological variants in ARID1B in two patients (Table 3); one of them was suspected to have mucopolysaccridosis. Founder mutations were identified in this tribal population, such as the pathologic variant causing transaldolase deficiency (Table 1). This finding facilitated further diagnoses in our community using single gene sequencing.
It is important to note that the results of WES should be appraised carefully. In one patient, WES reported a deleterious hemizygous mutation in SLC35A2, c.617_620del (p.Q206fs),congenital disorder of glycosylation, TYPE IIm (CDG2M). However, glycosylation screening was normal in this patient and three healthy brothers had the same mutation (not listed in the table). In another patient, WES reported a pathogenic mutation in MCCC2, c.1015G > A (p.V339M), but urine organic acids were normal and the patient had Sandhoff disease (confirmed by enzyme studies), Table 1.
In most cases, extensive and expensive investigations (including biochemical, genetic, and segregation studies) were necessary after the results of WES to determine the pathogenicity of the variants. In UAE, most families are consanguineous and have multiple affected individuals. Therefore, it was somewhat possible to stratify many of the variants of unknown significance as pathogenic vs non-pathogenic. Nevertheless, challenges remain in the interpretation of the 12 likely pathogenic variants (Table 1b). The availabilities of functional studies, improved knowledge of rare allele frequencies of healthy individuals, and more routine use of WES will improve the yield of this powerful analytical tool.
Competent staff is needed to explain WES results and to counsel patients and their families. The metabolic centers should develop and adhere to appropriate guidelines for utilizing WES as a diagnostic tool. Position statements and best practice guidelines are available from the American college of Medical Genetics, Canadian college of Medical Genetics and European society of Human Genetics [12–14].
Many variants are confined to ethnic populations and are, thus, difficult to diagnose by conventional genetic methods [2, 15]. The cost of diagnosing genetic disorders using conventional testing was estimated to be about $25,000 per patient [4]. However, it is unknown whether WES would increase or decrease this cost. In this study, the cost of WES was covered by local insurance companies for UAE citizens; the cost is a critical issue for the majority of patients who are not citizens of this country.
In this study, with the majority of patients had consanguineous families, WES identified pathogenic mutations in 50 % of cases. WES also provided population-specific information, which should facilitate molecular diagnosis of metabolic and genetic disorders in the region. However, further studies, including cost-effective assessments are needed before routine application of this test in IEM and genetic clinics.
Al Shamsi A, Hertecant JL, Al Hamad S, Souid A-K, Al-Jasmi FA. Mutation spectrum and prevalence of inborn errors of metabolism in United Arab Emirates. Sultan Qaboos Univ Med J. 2014;14:e42–9.
Woods CG, Cox J, Springell K, Hampshire DJ, et al. Quantification of homozygosity in consanguineous individuals with autosomal recessive disease. Am J Hum Genet.