A Population-Oriented Genetic Scoring System to Predict Phenotype: A Pathway to Personalized Medicine in Iraqis With β-Thalassemia

To assess the roles of genetic modifiers in Iraqi β-thalassemia patients, and determine whether a genotype-based scoring system could be used to predict phenotype, a total of 224 Iraqi patients with molecularly characterized homozygous or compound heterozygous β-thalassemia were further investigated for α-thalassemia deletions as well as five polymorphisms namely: rs7482144 C > T at HBG2, rs1427407 G > T and rs10189857 A > G at BCL11A, and rs28384513 A > C and rs9399137 T > C at HMIP. The enrolled patients had a median age of 14 years, with 96 males and 128 females. They included 144 thalassemia major, and 80 thalassemia intermedia patients. Multivariate logistic regression analysis revealed that a model including sex and four of these genetic modifiers, namely: β+ alleles, HBG2 rs7482144, α-thalassemia deletions, and BCL11A rs1427407 could significantly predict phenotype (major versus intermedia) with an overall accuracy of 83.9%. Furthermore, a log odds genetic score based on these significant predictors had a highly significant area under curve of 0.917 (95% CI 0.882-0.953). This study underscores the notion that genetic scoring systems should be tailored to populations in question, since genetic modifiers (and/or their relative weight) vary between populations. The population-oriented genetic scoring system created by the current study to predict β-thalassemia phenotype among Iraqis may pave the way to personalized medicine in this patient's group.

Silent Cerebral Infarcts in Iraqi Patients with Sickle Cell Disease

Silent ischemic infarcts have been reported to be the most frequent neurological abnormalities in sickle cell disease (SCD) in several studies worldwide. However, no previous studies investigated this neurological disorder in Iraqi SCD patients. To address this issue, a total of 52 patients with a median age of 20 years (range 10-46) and including 46.2% males were enrolled. Patients were clinically evaluated and their records were reviewed. They had full blood and reticulocyte counts, hemoglobin F estimation, serum lactic dehydrogenase and bilirubin assayed, as well as brain magnetic resonance imaging (MRI) to screen for silent cerebral infarcts. Six out of the 52 patients (11.5%) had silent cerebral infarcts, all of which were in the deep white matter, ranging from 6 to 10 mm in their largest diameters. There were no significant differences in age, sex, or sickle cell genotype between those with silent cerebral infarcts and those without it. Those with silent cerebral infarcts had lower median hemoglobin, higher reticulocytes and lower pain frequencies than those without it, yet again this was not significant. Follow up MRI in four out of the six silent infarct patients showed no additional lesions and no increase in size of the original ones after six to eight months. In conclusion, it appears that the frequency of silent cerebral infarcts in Iraqi SCD patients is lower than the bulk of the literature from other populations. Further studies to screen for genetic polymorphisms that may explain this lower rate may be informative.

A Novel β0-Thalassemia Mutation, HBB: c.356_357delTT [Codon 118 (-TT)] in an Iraqi Kurd

We report a novel frameshift β-thalassemia (β-thal) mutation due to a two-nucleotide deletion at codon 118 of the β-globin gene (HBB: c.356_357delTT) in a 4-year-old Iraqi Kurd female presenting as transfusion-dependent β-thal. This frameshift mutation, unlike many others involving the third exon, behaved as a recessive β⁰ defect and not as dominant β-thal mutation.

Deferasirox Effect on Serum Ferritin in Iraq Patients with Hemoglobinopathies: A Single Center Experience

BACKGROUND: The introduction of deferasirox as an oral iron chelator for hemoglobinopathies has been hailed by many as an important milestone in the management of iron overload in the latter disorders. AIM: The objectives of the study were to evaluate the effectiveness of deferasirox in patients with hemoglobinopathies and to assess predictors of response. METHODS: In this cross-sectional study, 160 patients diagnosed with hemoglobinopathies were included retrospectively from Jin hematology and oncology center in Duhok city, Iraqi Kurdistan. The Jin center offers patients with hemoglobinopathies clinical advice, examination, follow-up, treatment, and blood transfusions. RESULTS: The median age of enrolled patients was 12 years (range 3–34 years), and included 86 females and 74 males. All patients were on deferasirox with a compliance rate of 77.5%. Furthermore, 32.3% were on concomitant deferoxamine at their last follow-up. After a median follow-up of 2.1 years (range 1–4 years), there was a mean reduction of serum ferritin level of −478.7 overall and −821.1 ng/ml in complaint patients (both being significant at p of 0.042 and 0.001, respectively). Univariate analysis revealed that older age at enrollment, and older age at starting therapy, and initial serum ferritin (>3000 ng/ml) were all significantly associated with more mean reduction in serum ferritin; while only the latter remained so by multivariate analysis (p = 0.04). CONCLUSIONS: Deferasirox was found to be effective in reducing the level of serum ferritin among this cohort of hemoglobinopathy patients, to a degree comparable to that reported in other studies worldwide. Furthermore, there were significant associations between the reduction of serum ferritin level and age, age at starting treatment, drug compliance, and the initial serum ferritin levels.

Doppler-defined pulmonary hypertension in β-thalassemia major in Kurdistan, Iraq

Cardiopulmonary complications are among the most important complications of thalassemia major. Pulmonary hypertension is among these complications and studies addressing its frequency and associations in the latter disorder are sparse from Iraq. For this purpose a total 100 thalassemia major patients (≥ 8 years old) were enrolled from a main thalassemia center in Kurdistan, Northern Iraq. All patients had a full history and clinical examination. Full blood count, biochemical tests and viral screen including hepatitis B surface antigen and hepatitis C virus antibody, in addition to transthoracic Doppler echocardiography for tricuspid regurgitation jet velocity (TRV). The enrolled patients had a mean (SD) age of 17.6 (5.5) years, and included 52 males and 48 females. Pulmonary hypertension as defined by TRV> 2.8 m/s coupled with both exertional dyspnea and an absence of left sided heart failure, was identified in nine patients (9%). The latter subgroup of patients had significantly higher reticulocyte counts, S. LDH, S. ferritin, and hepatitis C sero-positivity compared to those without this complication by univariate analysis. While by multivariate logistic regression only reticulocytes and hepatitis C sero-positivity remained significant. Furthermore, TRV as a continuous variable was positively correlated with reticulocytes, S. bilirubin and LDH (p<0.001, p = 0.002 and p<0.001 respectively), but not with age or S. ferritin (p = 0.77, and p = 0.93 respectively). In conclusion, pulmonary hypertension is not uncommon in Iraqi patients with thalassemia major, and it appears to be linked to chronic hemolysis rather than iron overload.

Genetic polymorphisms in early-onset myocardial infarction in a sample of Iraqi patients: a pilot study

OBJECTIVES

Early-onset myocardial infarction constitutes nearly one third of cases of myocardial infarction among Iraqis, which is rather higher than the proportions reported in many Western countries. Thus this study was initiated to investigate the role of some genetic polymorphisms, as well as acquired risk factors in this condition.

RESULTS

A total of 102 Iraqi patients with first myocardial infarction aged 50 years, and 77 matched controls were enrolled. The DNAs of participants were screened for nine polymorphisms, namely: β-Fibrinogen (- 455G > A), Factor XIII (V34L), Plasminogen Activator inhibitor-1 (PAI-1, 4G/5G), Human Platelet Antigen-1 (HPA1a/b), 5,10-Methylenetetrahydrofolate Reductase MTHFR (C677T) and MTHFR (A1298C), Angiotensin-Converting Enzyme (ACE) 287 bp insertion/deletion (I/D), Apolipoprotein-B (ApoB: R3500Q), and Apolipoprotein-E (Apo E: E2/E3/E4), using PCR and reverse hybridization technique. Among traditional risk factors, univariate analysis revealed that smoking (OR 2.86 [95%CI 1.53-5.34]), hyperlipidemia (OR 5.23 [95%CI 2.66-10.29]), and diabetes mellitus (OR 4.05 [95% CI 1.57-10.41]) were significantly higher among patients compared to controls (P<0.001, <0.001 and 0.002 respectively), while none of the nine genetic polymorphisms reached significance. Multivariate Logistic regression, however, revealed that only smoking and hyperlipidemia retained significance (P of < 0.001 each). The need to initiate further studies on larger cohorts is paramount to understand the higher than expected frequency of early-onset myocardial infarction in our population.

HBG2 -158 (C>T) polymorphism and its contribution to fetal hemoglobin variability in Iraqi Kurds with beta-thalassemia minor

PURPOSE

Hemoglobin (Hb) F% is increased in up to half of beta-thalassemia (β-thal) carriers. Several polymorphisms have been linked to such variability in different populations, including HBG2 - 158(C>T) (Xmn I polymorphism) on chromosome 11. To determine the role of this polymorphism in such variability among Iraqi Kurds, the current study was initiated.

MATERIALS AND METHODS

A total of 102 consecutive patients diagnosed as β-thal minor were enrolled. The enrollees had their diagnosis based on peripheral blood counts and high-performance liquid chromatography to determine HbA2 and HbF. All enrollees had their DNA extracted by phenol-chloroform method and Xmn I polymorphism detected by restriction fragment length polymorphism-polymerase chain reaction.

RESULTS

The mean age (standard deviation [SD]) of the 102 enrollees was 25.4 (14.0) years, and the enrollees included 48 males and 54 females. Xmn I polymorphism was identified in heterozygous state in 46 (45.1%) patients and in homozygous state in one patient (0.98%). Thus, the minor allele frequency of this polymorphism was 0.235 in the studied group. There were no significant differences in red cell indices and HbA2% in carriers of the minor allele compared to noncarriers, while HbF% and absolute HbF concentrations were significantly higher in the former subgroup (P = 0.032 and 0.014, respectively). This polymorphism's contribution to HbF variability was found to be 5.8% in the studied sample. Furthermore, those with HbF ≥2% were 3.2 folds more likely to carry the minor allele.

CONCLUSIONS

Xmn I polymorphism is frequently encountered in Iraqi Kurds with β-thal minor, and it is significantly associated with higher fetal hemoglobin in these patients.

The association of HBG2, BCL11A, and HMIP polymorphisms with fetal hemoglobin and clinical phenotype in Iraqi Kurds with sickle cell disease

INTRODUCTION

Fetal hemoglobin (HbF) is the major modifier for sickle cell disease (SCD) severity. HbF is modulated mainly by three major quantitative trait loci (QTL) on chromosomes 2, 6, and 11.

METHODS

Five SNPs in the three QTLs (HBG2, rs7482144; BCL11A, rs1427407 and rs10189857; and HBS1L-MYB intergenic region, rs28384513 and rs9399137) were investigated by multiplex PCR and reverse hybridization, and their roles in HbF and clinical phenotype variability in Iraqi Kurds with SCD were assessed.

RESULTS

HBG2 rs7482144 with minor allele frequency (MAF) of 0.133 was the most significant contributor to HbF variability, contributing 18.1%, followed by rs1427407 (MAF of 0.266) and rs9399137 (MAF of 0.137) at 14.3% and 8.8%, respectively. The other two SNPs were not significant contributors. Furthermore, when the cumulative numbers of minor alleles in the three contributing SNPs were assessed, HbF% and hemoglobin concentration increased with increasing number of minor alleles (P < 0.0005 and 0.001, respectively), while serum lactic dehydrogenase, reticulocytes, leukocytes, transfusion, and pain frequencies decreased (P = 0.003, 0.004, <0.0005, <0.0005, and 0.017, respectively).

CONCLUSIONS

It was demonstrated that SNPs in all three major HbF QTLs contribute significantly to HbF and clinical variability in Iraqi Kurds with SCD and that the cumulative number of minor alleles at contributing SNPs may serve as a better predictor of such variability in this population.

Recessive thrombocytopenia likely due to a homozygous pathogenic variant in the FYB gene: case report

Background

Inherited thrombocytopenias (IT) are a heterogeneous group of rare diseases characterized by a reduced number of blood platelets. The frequency of IT is probably underestimated because of diagnostic difficulties and because not all the existing forms have as yet been identified, with some patients remaining without a definitive diagnosis. Exome Sequencing has made possible the identification of almost all variants in the coding regions of protein-coding genes, thereby providing the opportunity to identify the disease causing gene in a number of patients with indefinite diagnoses, specifically in consanguineous families.

Case presentation

Familial thrombocytopenia with small size platelets was present in several members of a highly consanguineous family from Northern Iraq. Genotyping of all affected, their unaffected siblings and parents, followed by exome sequencing revealed a strong candidate loss of function variant in a homozygous state: a frameshift mutation in the FYB gene. The protein encoded by this gene is known to be a cytosolic adaptor molecule expressed by T, natural killer (NK), myeloid cells and platelets, and is involved in platelet activation and controls the expression of interleukin-2. Knock-out mice were reported to show isolated thrombocytopenia.

Conclusion

Inherited thrombocytopenias differ in their presentation, associated features, and molecular etiologies. An accurate diagnosis is needed to provide appropriate management as well as counseling for the individuals and their family members. Exome sequencing may become a first diagnostic tool to identify the molecular basis of undiagnosed familial IT. In this report, the clinical evaluation combined with the power and efficiency of genomic analysis defined the FYB gene as the possible underlying cause of autosomal recessive thrombocytopenia with small platelet size. This is the first report linking pathogenic variants in FYB and thrombocytopenia in humans.

Diagnostic exome sequencing to elucidate the genetic basis of likely recessive disorders in consanguineous families

Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders

Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease.

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

BACKGROUND

Although G6PD deficiency is the most common genetically determined blood disorder among Iraqis, its molecular basis has only recently been studied among the Kurds in North Iraq, while studies focusing on Arabs in other parts of Iraq are still absent.

METHODS

A total of 1810 apparently healthy adult male blood donors were randomly recruited from the national blood transfusion center in Baghdad. They were classified into G6PD deficient and non-deficient individuals based on the results of methemoglobin reduction test (MHRT), with confirmation of deficiency by subsequent enzyme assays. DNA from deficient individuals was studied using a polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) for four deficient molecular variants, namely G6PD Mediterranean (563 C→T), Chatham (1003 G→A), A- (202 G→A) and Aures (143 T→C). A subset of those with the Mediterranean variant, were further investigated for the 1311 (C→T) silent mutation.

RESULTS

G6PD deficiency was detected in 109 of the 1810 screened male individuals (6.0%). Among 101 G6PD deficient males molecularly studied, the Mediterranean mutation was detected in 75 cases (74.3%), G6PD Chatham in 5 cases (5.0%), G6PD A- in two cases (2.0%), and G6PD Aures in none. The 1311 silent mutation was detected in 48 out of the 51 G6PD deficient males with the Mediterranean variant studied (94.1%).

CONCLUSIONS

Three polymorphic variants namely: the Mediterranean, Chatham and A-, constituted more than 80% of G6PD deficient variants among males in Baghdad. Iraq. This observation is to some extent comparable to other Asian Arab countries, neighboring Turkey and Iran.