Exome sequencing of Saudi Arabian patients with ADPKD.

Purpose: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive development of kidney cysts and enlargement and dysfunction of the kidneys. The Consortium of Radiologic Imaging Studies of the Polycystic Kidney Disease (CRISP) cohort revealed that 89.1% had either a PKD1 or PKD2 mutation. Of the CRISP patients with a genetic cause detected, mutations in PKD1 accounted for 85%, while mutations in the PKD2 accounted for the remaining 15%. Here, we report exome sequencing of 16 Saudi patients diagnosed with ADPKD and 16 ethnically matched controls. Methods: Exome sequencing was performed using combinatorial probe-anchor synthesis and improved DNA Nanoballs technology on BGISEQ-500 sequencers (BGI, China) using the BGI Exome V4 (59 Mb) Kit. Identified variants were validated with Sanger sequencing. Results: With the exception of GC-rich exon 1, we obtained excellent coverage of PKD1 (mean read depth = 88) including both duplicated and non-duplicated regions. Of nine patients with typical ADPKD presentations (bilateral symmetrical kidney involvement, positive family history, concordant imaging, and kidney function), four had protein truncating PKD1 mutations, one had a PKD1 missense mutation, and one had a PKD2 mutation. These variants have not been previously observed in the Saudi population. In seven clinically diagnosed ADPKD cases but with atypical features, no PKD1 or PKD2 mutations were identified, but rare predicted pathogenic heterozygous variants were found in cystogenic candidate genes including PKHD1, PKD1L3, EGF, CFTR, and TSC2. Conclusions: Mutations in PKD1 and PKD2 are the most common cause of ADPKD in Saudi patients with typical ADPKD. Abbreviations: ADPKD: Autosomal dominant polycystic kidney disease; CFTR: Cystic fibrosis transmembrane conductance regulator; EGF: Epidermal growth factor; MCIC: Mayo Clinic Imaging Classification; PKD: Polycystic kidney disease; TSC2: Tuberous sclerosis complex 2.

Hemoglobin A2 (HbA2) has a measure of unreliability in diagnosing ß-thalassemia trait (ß-TT).

INTRODUCTION: Detection of ß-thalassemia trait or carriers (ß-TT) depends significantly on an increase in Hemoglobin A2 (HbA2) levels, which is found at low levels (<3%) in normal healthy individuals and elevated levels (≥3.5%) in ß-TT individuals. The study was designed to evaluate the reliability of the diagnostic parameter HbA2 in the differentiation of ß-TT and non-ß-TT in Saudis. METHODS: The widely used high performance liquid chromatography (Variant II Bio-Rad) was used to measure HbA2 levels in blood. Sanger sequencing was used to screen the variation in globin genes (HBB, HBD, HBA1, and HBA2). All the study subjects were divided into ßTT and non-ßTT (wild) categories based on the presence or absence of HBB variations and further sub-divided into false positive, true positive, false negative, and true negative, based on HbA2 values. RESULTS: Out of 288 samples, 96 had HBB gene mutations. Of the 96 ß-TT samples, sickle cell trait (SCT) samples (n = 58) were excluded, while the remaining (38 ß-TT) were included in the detailed analysis: seven subjects with the HBB mutation had normal HbA2 (<3%), and three were borderline (3.1-3.9%). The remainder (n = 28) had an elevated HbA2 level (>4%). Based on HbA2 analysis alone, both these groups would be incorrectly diagnosed as normal. Similarly, of the 189 non-ß-TT samples, 179 had normal HbA2, eight had borderline HbA2, and two had a HbA2 level above 4%. Based on HbA2 analysis alone, borderline and >4% HbA2 individuals, negative for ß-TT, can be incorrectly diagnosed as carriers. CONCLUSION: Given the percentage of samples falling in the HbA2 "borderline" and "normal" categories, it can be concluded that HbA2 has a measure of unreliability in the diagnosis of ß-thalassemia carriers.

The ­α3.7 deletion in α­globin genes increases the concentration of fetal hemoglobin and hemoglobin A2 in a Saudi Arabian population.

The regions of Al­Qatif and Al­Ahssa in the Eastern Province of Saudi Arabia are known for their high prevalence of hemoglobinopathies, including ß­thalassemia and sickle cell anemia. Previously, the α­gene deletion has been demonstrated as highly prevalent among populations residing in these two regions. The present study was conducted in order to investigate the implications of the α­globin gene deletion on fetal hemoglobin (HbF) and hemoglobin α2 (HbA2) concentrations in patients with transfusion­dependent ß­thalassemia. A total of 166 Saudi patients with transfusion­dependent ß­thalassemia and 337 healthy Saudi patients were included in the study. The ­α3.7, ­α4.2, -­FIL, -­SEA, -­MED and -­(20.5) gene deletions were identified using multiplex α­globin deletion polymerase chain reaction. The present study revealed that the ­α3.7 gene deletion is the most prevalent (43.5%) in the Saudi populations that were analyzed and is characterized by the deletion of 3,804 base pairs. Numerous genotypes, namely ­3.7α2/α1α2, ­3.7α2/α1α12, ­3.7α2/­3.7α2, ­3.7α2HphI/α1α2HphI, ­3.7α2/α1­4.2, ­3.7α2/α1polyA­1α2, ­3.7α12/α1α12, ­­FIL/­3.7α2 and ­3.7α2/­3.7α2Hb Villiers le Bel were also identified in the investigated population. Furthermore, a gradual increase in the concentration of HbF and HbA2 in patients with ß­thalassemia and the number of α­gene deletions was demonstrated; whereas in healthy patients the level of HbA2 was demonstrated to decrease as the number of α­gene deletions increased. Therefore, it can be concluded that the high HbF concentration in the present study is predominantly associated with other mutations associated with ß­thalassemia rather than α­globin deletions. Furthermore, the results of the present study also revealed novel α­gene deletion genotypes prevalent in the population studied, namely α1α2/α1α2HphI, α1α2HphI/α1α2HphI, α1α2/α1α2Hb Handsworth, ­3.7α2HphI/α1α2HphI, ­3.7α2/­3.7α2Hb Villiers le Bel and ­-MED/α1α2HphI.