Molecular characterization of glucose-6-phosphate dehydrogenase deficient variants in Baghdad city - Iraq

Molecular Characterization of Glucose-6-phosphate Dehydrogenase Deficiency in Oman

Objectives

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most encountered abnormality of red blood cell metabolism worldwide and has a high prevalence in Oman. The objective of the study was to characterize the mutation variants of G6PD deficiency in a cohort of the Omani population with partial and complete enzyme deficiency.

Methods

This prospective study included newborns and children less than one year of age with partial or complete G6PD enzyme deficiency identified on routine screening using a fluorescent spot test from 31 January 2017 to 12 September 2017 in Sultan Qaboos University Hospital. The identified samples were analyzed for the presence of C563T, G1003A, and other mutations using direct DNA sequencing of the polymerase chain reaction.

Results

Out of 3679 newborn samples screened, 21.0% were found to have complete or partial G6PD enzyme deficiency. A total of 145 participants were included in the genetic analysis, of which 133 (91.7%) were completely deficient in G6PD enzyme activity and 12 (8.3%) had partial deficiency. The Mediterranean variant (C563T) was identified in 129 (89.0%). Other variants were found as follows: eight (5.5%) had variant A-, three (2.1%) had the Chatham variant (G1003A), one (0.7%) had the Cosenza variant, and one (0.7%) had exon 11 variant. No mutation was found in two subjects.

Conclusions

The most common mutation in the Omani population is the Mediterranean mutation (C563T) followed by the variant A- mutation. However, not all participants were found to have a mutation.

Seven novel glucose-6-phosphate dehydrogenase (G6PD) deficiency variants identified in the Qatari population

Background

Glucose-6-phosphate dehydrogenase deficiency (G6PDD) is the most common red cell enzymopathy in the world. In Qatar, the incidence of G6PDD is estimated at around 5%; however, no study has investigated the genetic basis of G6PDD in the Qatari population yet.

Methods

In this study, we analyzed whole-genome sequencing data generated by the Qatar Genome Programme for 6045 Qatar Biobank participants, to identify G6PDD variants in the Qatari population. In addition, we assessed the impact of the novel variants identified on protein function both in silico and by measuring G6PD enzymatic activity in the subjects carrying them.

Results

We identified 375 variants in/near G6PD gene, of which 20 were high-impact and 16 were moderate-impact variants. Of these, 14 were known G6PDD-causing variants. The most frequent G6PD-causing variants found in the Qatari population were p.Ser188Phe (G6PD Mediterranean), p.Asn126Asp (G6PD A +), p.Val68Met (G6PD Asahi), p.Ala335Thr (G6PD Chatham), and p.Ile48Thr (G6PD Aures) with allele frequencies of 0.0563, 0.0194, 0.00785, 0.0050, and 0.00380, respectively. Furthermore, we have identified seven novel G6PD variants, all of which were confirmed as G6PD-causing variants and classified as class III variants based on the World Health Organization’s classification scheme.

Conclusions

This is the first study investigating the molecular basis of G6PDD in Qatar, and it provides novel insights about G6PDD pathogenesis and highlights the importance of studying such understudied population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40246-021-00358-9.

Development of allelic discrimination assay to detect Mediterranean G6PD mutation and its linked inheritance with normal vision and/colorblindness loci for 4 generations among Egyptian and Emirati families

G6PD deficiency c563T is the most common inherent blood disease among the Mediterranean populations and its molecular diagnosis is critical as the enzyme assay fails for heterozygous individuals. The purpose of the study is to estimate the ubiquity of the heterozygous G6PD Med (c563T) variants among Egyptians and UAE nationals living in Dubai. We validated two molecular methods, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and qPCR allelic discrimination assay for detection of G6PD Med variants. Among 100 screened individuals, G6PD c563T variants are 30% of whom 15% are carriers. Sanger sequencing validated the qPCR discrimination assays. In search of a phenotypic marker to detect G6PD heterozygous variants, inheritance of G6PD locus and red-green color vision genes is studied in 1 Egyptian and 2 Emirati families. Among the 3 families, G6PD is polymorphic, displaying 4 phenotypes: in phenotype-1, person is normal, in phenotype-2 the person has no G6PD deficiency but with deuteranopia/deuteranomaly, in phenotype-3 the person is G6PD Med variant with deuteranopia/deuteranomaly and in phenotype 4 the person is G6PD Med variant has normal vision. Based on the molecular analysis of G6PD and Ishihara vision test it can be concluded that the two mutations at the two loci arose independent of each other without any interaction (epistatic effect) between them. Following the pedigree analysis of the two genes for 4 generations it is presumed that it is infeasible to use "deuteranopia /deuteranomaly" as a phenotypic marker to detect G6PD c563T heterozygous individuals among the Egyptian populations.

Molecular analysis of CFTR gene mutations among Iraqi cystic fibrosis patients

Background

Cystic fibrosis (CF) is an autosomal recessive multisystem disease that results from mutation(s) of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. More than 2100 mutations and polymorphisms have been reported in this gene so far. Incidence and genotyping of CF are under-identified in Iraq. This study aims to determine the types and frequencies of certain CFTR mutations among a sample of Iraqi CF patients. Two groups of patients were included: 31 clinically confirmed CF patients in addition to 47 clinically suspected patients of CF. All confirmed patients had typical, moderate-severe clinical presentation and course of the disease. Molecular analysis was performed on the majority of enrolled patients using the CF-stripAssay® kit supplied by ViennaLab diagnostics, GmbH, Austria.

Results

The mutation-detection rate from the tested 34 mutations in this study was 19.5% and the 8 detected mutations were as follows: 3120+1G>A and W1282X were found in 3 (4.17%) patients each; F508del and R1162X were found in 2 (2.78%) patients each; 3272-26A>G, R347P, I507del, and 2183AA>G were found in 1 (1.38%) patient each. Polymorphic variants of IVS8, namely 5T, 7T, and 9T, were detected in ~ 70%. These results were nearly similar to what was reported in regional countries.

Conclusion

Cystic fibrosis seems to be not rare as previously thought. 3120+1G>A and W1282X are the two most commonly detected mutations. F508del needs to be included in all future tests, while the I507del mutation was uniquely reported in this study but not in regional studies.

G6PD Deficiency Prevalence as a Cause of Neonatal Jaundice in a Neonatal Ward in Dohuk, Iraq

OBJECTIVE

The current study initiated to address the effect of glucose-6-phosphate dehydrogenase (G6PD) deficiency on the pathogenesis and the severity of neonatal hyperbilirubinemia (NHB).

STUDY DESIGN

A total of 100 newborns with moderate to severe indirect hyperbilirubinemia and 50 normal neonates without hyperbilirubinemia had been enrolled in the current case-control study. All enrolled neonates had been tested for ABO and Rh(D) blood grouping, Total serum bilirubin measurement, complete blood count, morphology, reticulocyte counts, direct Coombs' test, and G6PD enzyme assay.

RESULTS

From all enrolled hyperbilirubinemic neonates, 16% were G6PD deficient and this displays a statistically significant difference in comparison to controls (only 6% were G6PD deficient). Also, significant difference was found in the level of serum indirect bilirubin among G6PD-deficient neonate in comparison to G6PD nondeficient neonates which had contributed significantly to the difference in the duration of phototherapy and hospitalization among deficient neonate. Despite this, no significant difference found in the onset of presentation, reticulocytes count, and age of neonates between the two groups (G6PD-deficient and G6PD nondeficient neonates).

CONCLUSION

The current study augments the etiological role of G6PD in the causation and severity of NHB in the region; however, in the absence of significant difference in the reticulocytes and the hemoglobin level, the underlying mechanism cannot be backed to the excess hemolysis alone.

Applying a multiplexed primer extension method on dried blood spots increased the detection of carriers at risk of glucose-6-phosphate dehydrogenase deficiency in newborn screening program

BACKGROUND

Patients with glucose-6-phosphate dehydrogenase deficiency might develop acute hemolytic anemia, chronic hemolytic anemia, and neonatal hyperbilirubinemia when exposed to high levels of oxidative stress. Severe hemolysis may occur in not only patients but also female carriers under certain conditions. However, 80%-85% of female carriers were undetected in an existing newborn screening program because of their wide-ranging levels of enzyme activity.

METHODS

We developed a cost- and time-efficient multiplex SNaPshot assay using dried blood spots.

RESULTS

By detecting 21 common mutations in Taiwan and Southeast Asia, the assay could determine 98.2% of the mutant alleles in our cohort of Taiwanese newborns. The 9 undetermined mutant alleles were consequently detected by Sanger sequencing, of which 5 unpublished variations-c.187G > A (Pingtung), c.585G > C (Tainan), c.586A > T (Changhua), c.743G > A (Chiayi), and c.1330G > A (Tainan-2)-were detected. Furthermore, 13% of mild mutations were missed in male infants whose enzyme levels at 6.1-7.0 U/gHb in the newborn screening program when set the cutoff value at 6.0 U/gHb. We therefore suggest increasing the cutoff value and applying the multiplex SNaPshot assay as the second tier for neonatal screening.

CONCLUSIONS

Our approach could significantly increase the detection rate of male patients and female carriers with a reasonable cost and a reasonable number of clinic referrals.

Glucose-6-phosphate dehydrogenase deficiency allelic variants and their prevalence in malaria patients in Eritrea

Introduction

Glucose 6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy with a relatively high frequency in malaria-endemic regions. In Eritrea, there is scanty knowledge of G6PD deficiency. The aim of the study was to characterize and determine the prevalence of four common G6PD allelic variants.

Methods

Three hundred and fourteen dried blood spot samples from unrelated microscopically diagnosed malaria patient Eritrean ethnic groups living in five zobas (regions) of Eritrea were analysed by PCR-RFLP method to identify the G6PD B, G6PD A (A376G), G6PD A-(G202A), and G6PD Mediterranean (C563T) variants. To confirm the RFLP results, samples positive for A376G but negative for G202A variants were subjected to Sanger sequencing and a subset of PCR products (exon 5) directly sequenced to identify A376G and other mutations.

Results

For G6PD genotyping, G6PD B was detected in 87.5% and A376G detected in 12.5% of malaria patients, whereas G202A and C563T were absent. Bivariate Statistical analysis showed a statistically significant association between G6PD genotypes and zoba (P < 0.004 < 0.05). Sequencing revealed the expected A376G variant. In exon 5, four common (A376G) mutations, three uncommon mutations rs782669677 (535G→A) and one potentially new mutation (451G→C), relative to the reference, mRNA NM_001042351 were detected. Bioinformatic analysis of these mutations' potential functional impact suggests minimal effect on protein function.

Conclusion

This is the first report indicating that G6PD B and G6PD A genotypes are prevalent in Eritrea. Similar findings were reported in neighboring countries. Further studies including phenotype analysis are needed to corroborate the observed results.

Validation of the rapid test Carestart(tm) G6PD among malaria vivax-infected subjects in the Brazilian Amazon

INTRODUCTION

In the Brazilian Amazon, malaria infections are primarily caused by Plasmodium vivax. The only drug that kills the hypnozoite form of P. vivax is primaquine, thereby preventing relapse. However, treating glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals with primaquine can lead to severe hemolysis. G6PD deficiency (G6PDd) affects approximately 400 million people worldwide, most of whom live in malaria-endemic areas. Therefore, clinicians need tools that can easily and reliably identify individuals with G6PDd. This study estimated the accuracy of the Carestart(tm) G6PD rapid test (Access Bio) in the diagnosis of G6PDd in male participants with and without P. vivax acute malaria.

METHODS

Male participants were recruited in Manaus. Malaria diagnosis was determined by thick blood smear. G6PD quantitative analysis was performed spectro photometrically at a wave length of 340nm. The Carestart(tm) G6PD test was performed using venous blood. Genotyping was performed for individuals whose samples had an enzyme activity less than 70% of the normal value.

RESULTS

Six hundred and seventy-four male participants were included in this study, of whom 320 had a diagnosis of P. vivax malaria. In individuals with enzyme activity lower than 30% (n=13), the sensitivity, specificity, positive predictive value, and negative predictive value of the Carestart(tm) G6PD test were as follows: 61.5% (95%CI: 35.5%-82.3%), 98.3% (95%CI: 97.0%-99.1%), 42.1% (95%CI: 23.1%-63.7%), and 99.2% (95%CI: 98.2%-82.3%), 98.3% (95%CI: 97.0%-99.1%), 42.1% (95%CI: 23.1%-63.7%), and 99.2% (95%CI: 98.2%-99.7%), respectively. Increases in sensitivity were observed when increasing the cut-off value.

CONCLUSIONS

Despite low sensitivity, Carestart(tm) G6PD remains a good alternative for rapid diagnosis of G6PDd in malaria-endemic regions.

Glucose-6-phosphate dehydrogenase deficiency: not exclusively in males

Glucose‐6‐phosphate (G6PD) deficiency is the most common human enzyme defect, often presenting with neonatal jaundice and/or acute hemolytic anemia, triggered by oxidizing agents. G6PD deficiency is an X‐linked, hereditary disease, mainly affecting men, but should also be considered in females with an oxidative hemolysis.

Molecular Analysis of CYP21A2 Gene Mutations among Iraqi Patients with Congenital Adrenal Hyperplasia

Congenital adrenal hyperplasia is a group of autosomal recessive disorders. The most frequent one is 21-hydroxylase deficiency. Analyzing CYP21A2 gene mutations was so far not reported in Iraq. This work aims to analyze the spectrum and frequency of CYP21A2 mutations among Iraqi CAH patients. Sixty-two children were recruited from the Pediatric Endocrine Consultation Clinic, Children Welfare Teaching Hospital, Baghdad, Iraq, from September 2014 till June 2015. Their ages ranged between one day and 15 years. They presented with salt wasting, simple virilization, or pseudoprecocious puberty. Cytogenetic study was performed for cases with ambiguous genitalia. Molecular analysis of CYP21A2 gene was done using the CAH StripAssay (ViennaLab Diagnostics) for detection of 11 point mutations and >50% of large gene deletions/conversions. Mutations were found in 42 (67.7%) patients; 31 (50%) patients were homozygotes, 9 (14.5%) were heterozygotes, and 2 (3.2%) were compound heterozygotes with 3 mutations, while 20 (32.3%) patients had none of the tested mutations. The most frequently detected mutations were large gene deletions/conversions found in 12 (19.4%) patients, followed by I2Splice and Q318X in 8 (12.9%) patients each, I172N in 5 (8.1%) patients, and V281L in 4 (6.5%) patients. Del 8 bp, P453S, and R483P were each found in one (1.6%) and complex alleles were found in 2 (3.2%). Four point mutations (P30L, Cluster E6, L307 frameshift, and R356W) were not identified in any patient. In conclusion, gene deletions/conversions and 7 point mutations were recorded in varying proportions, the former being the commonest, generally similar to what was reported in regional countries.

Next generation sequencing (NGS) in glucose-6-phosphate dehydrogenase (G6PD) deficiency studies

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is commonly observed in human males. It is a genetic disorder affecting the red blood cells. The diagnosis of G6PD is usually based on blood analysis and there is no specific molecular or genetic test. The complete gene sequence of G6PD is known for different ethnicities. Known single nucleotide polymorphism (SNP) associated with G6PD is available in the public databases. Hence, robust, fast and efficient sequencing of G6PD is critical in disease diagnosis. The application of next generation sequencing (NGS) with its high reliability is useful in G6PD diagnosis.

A multiplex method for detection of glucose-6-phosphate dehydrogenase (G6PD) gene mutations

INTRODUCTION

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect caused by G6PD gene mutations. This study aimed to develop a cost-effective, multiplex, genotyping method for detecting common mutations in the G6PD gene.

METHODS

We used a SNaPshot approach to genotype multiple G6PD mutations that are common to human populations in South-East Asia. This assay is based on multiplex PCR coupled with primer extension reactions. Different G6PD gene mutations were determined by peak retention time and colors of the primer extension products.

RESULTS

We designed PCR primers for multiplex amplification of the G6PD gene fragments and for primer extension reactions to genotype 11 G6PD mutations. DNA samples from a total of 120 unrelated G6PD-deficient individuals from the China-Myanmar border area were used to establish and validate this method. Direct sequencing of the PCR products demonstrated 100% concordance between the SNaPshot and the sequencing results.

CONCLUSION

The SNaPshot method offers a specific and sensitive alternative for simultaneously interrogating multiple G6PD mutations.

Molecular Characterization of G6PD Deficient Variants in Nineveh Province, Northwestern Iraq

Glucose-6-phosphate dehydrogenase (G6PD) deficiency considered to be the commonest inherited enzymopathies disorders worldwide including Iraq. Studies have addressed its prevalence and molecular characterization in several parts of the country, but no data were available from Nineveh province, northwestern-Iraq regarding molecular basis of this inherited enzymopathy. To determine the molecular basis of G6PD deficient variants in Nineveh province. A total of 61 G6PD deficient male individuals from Nineveh province were enrolled in this study. DNA from all enrolled individuals were extracted and analyzed for four deficient molecular variants using a polymerase chain reaction-restriction fragment polymorphism method. These deficient variants were G6PD-Mediterranean (563 C→T), G6PD-Chatham (1003 G→A), G6PD-A-(202 G→A) and G6PD-Cosenza (1376 G→C). Also enrolled individuals were screened for silent 1311 (C→T) mutation. It was found that 46 (75.41 %) were G6PD-Mediterranean, 1(1.64 %) were G6PD-Chatham, another 1(1.64 %) were G6PD-A-, and 13 (21.31 %) were remained uncharacterized. Also all G6PD-Mediterranean as well as one uncharacterized individuals were carriers of silent 1311 (C→T) mutation. This study documented that G6PD-Mediterranean constitute the bulk of G6PD deficient variants in this province and G6PD-Chatham and A- were encountered less frequently. Also that silent 1311 (C→T) mutation were common among G6PD-Mediterranean deficient variants individuals.

A population survey of the glucose-6-phosphate dehydrogenase (G6PD) 563C>T (Mediterranean) mutation in Afghanistan

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited enzyme defect and an important problem in areas with Plasmodium vivax infection because of the risk of haemolysis following administration of primaquine to treat the liver forms of the parasite. We undertook a genotypic survey of 713 male individuals across nine provinces of Afghanistan in which malaria is found, four in the north and five in the east. RFLP typing at nucleotide position 563 detected 40 individuals with the Mediterranean mutation 563C>T, an overall prevalence of 5.6%. This varied according to self-reported ethnicity, with prevalence in the Pashtun/Pashai group of 33/369 (8.9%) compared to 7/344 individuals in the rest of the population (2.0%; p<0.001, Chi-squared test). Multivariate analysis of ethnicity and geographical location indicated an adjusted odds ratio of 3.50 (95% CI 1.36-9.02) for the Pashtun/Pashai group, while location showed only a trend towards higher prevalence in eastern provinces (adjusted odds ratio = 1.73, 0.73-4.13). Testing of known polymorphic markers (1311C>T in exon 11, and C93T in intron XI) in a subset of 82 individuals wild-type at C563 revealed a mixture of 3 haplotypes in the background population and was consistent with data from the 1000 Genomes Project and published studies. By comparison individuals with G6PD deficiency showed a highly skewed haplotype distribution, with 95% showing the CT haplotype, a finding consistent with relatively recent appearance and positive selection of the Mediterranean variant in Afghanistan. Overall, the data confirm that the Mediterranean variant of G6PD is common in many ethnic groups in Afghanistan, indicating that screening for G6PD deficiency is required in all individuals before radical treatment of P. vivax with primaquine.

Evaluation of liver and kidney function in favism patients

BACKGROUND

G6PD deficiency is the most common enzymopathy of red blood cells. The clinical symptoms of favism are jaundice, hematuria and haemolytic anaemia that seem to affect liver and kidney in long term. Thus we evaluate kidney and liver function of favism patients in an endemic area of the disease with a high rate of fava beans cultivation.

METHODS

This study was performed on favism patients and healthy controls referring to Iranshahr central hospital. Liver and kidney function tests were performed.

RESULTS

The results showed a statistically significant difference between these two groups (p <0.05) for liver function tests, (AST, ALT and ALP), but not for renal tests (BUN and creatinine) (p >0.05).

CONCLUSION

Due to abnormalities were seen in the liver function tests of these patients, we suggest that these tests be regularly performed for favism patients who are constantly exposed to oxidant agents.

Neonatal hyperbilirubinemia in infants with G6PD c.563C > T Variant

Background

There is a strong correlation between glucose-6-phosphate dehydrogenase (G6PD) deficiency and neonatal hyperbilirubinemia with a rare but potential threat of devastating acute bilirubin encephalopathy. G6PD deficiency was observed in 4–14% of hospitalized icteric neonates in Pakistan. G6PD c.563C > T is the most frequently reported variant in this population. The present study was aimed at evaluating the time to onset of hyperbilirubinemia and the postnatal bilirubin trajectory in infants having G6PD c.563C > T.

Methods

This was a case–control study conducted at The Aga Khan University, Pakistan during the year 2008. We studied 216 icteric male neonates who were re-admitted for phototherapy during the study period. No selection was exercised. Medical records showed that 32 were G6PD deficient while 184 were G6PD normal. Each infant was studied for birth weight, gestational age, age at the time of presentation, presence of cephalhematoma, sepsis and neurological signs, peak bilirubin level, age at peak bilirubin level, days of hospitalization, whether phototherapy or exchange blood transfusion was initiated, and the outcome. During hospital stay, each baby was tested for complete blood count, reticulocyte count, ABO and Rh blood type, direct antiglobulin test and quantitative G6PD estimation [by kinetic determination of G6PDH]. G6PDgenotype was analyzed in 32 deficient infants through PCR-RFLP analysis and gene sequencing.

Results

G6PD variants c.563C > T and c.131 C > G were observed in 21 (65%) and three (9%) of the 32 G6PD deficient infants, respectively. DNA of eight (25%) newborns remained uncharacterized. In contrast to G6PD normal neonates, infants with c.563C > T variant had significantly lower enzyme activity (mean ± 1SD; 0.3 ± 0.2 U/gHb vs. 14.0 ± 4.5 U/gHb, p < 0.001) experienced higher peak levels of total serum bilirubin (mean ± 1SD; 16.8 ± 5.4 mg/dl vs. 13.8 ± 4.6 mg/dl, p = 0.008) which peaked earlier after birth (mean ± 1SD 2.9 ± 1.6 vs. 4.3 ± 2.3 days, p = 0.007). No statistically significant difference was observed in mean weight, age at presentation, hemoglobin, reticulocyte count, TSH level, hospital stay or in the frequency of initiation of phototherapy or blood exchange between the two groups.

Conclusions

We concluded that infants with G6PD c.563C > T variant developed jaundice earlier than infants with normal G6PD enzyme levels. Compared to G6PD normal infants, G6PD c.563C > T carrying infants had significantly low G6PD activity.