Mutations in the paralogous human alpha-globin genes yielding identical hemoglobin variants

A New α1-Globin Variant, Hb Ormylia [HBA1:c.63C > G; p.His21Gln]. Report of Eleven Cases in Northern Greece

The first identification of a novel α1-Globin variant, Hb Ormylia in 11 Greeks originating from a small village, Ormylia, Chalkidiki, Greece is reported. The new genetic variant leads to the production of a hemoglobin variant that can be identified and quantified by High-Performance Liquid Chromatography. Capillary and classic electrophoresis were not informative. Direct DNA sequencing revealed a new mutation C > G mutation at codon 21 of α1 gene (His > Gln). The new variant has been named Hb Ormylia and this is the first description of this genetic variant of α1 gene in the literature.

Gene duplication as a major force driving the genome expansion in some giant viruses

IMPORTANCE

Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.

Hemoglobin profile and molecular characteristics of the complex interaction of hemoglobin Doi-Saket [α9(A7) asn > lys, HBA2:c.30C > a], a novel α2α1 hybrid globin variant, with hemoglobin E [β26(B8) Glu > lys, HBB:c.79G > A] and deletional α+-thalassemia in a Thai family

BACKGROUND

An increasing number of α-hemoglobin (Hb) variants is causing various clinical symptoms; therefore, accurate identification of these Hb variants is important.

OBJECTIVE

This study aimed to describe the molecular and hematological characteristics of novel Hb Doi-Saket that gives rise to a typical α+-thalassemia phenotype in carriers with and without other hemoglobinopathies.

MATERIALS AND METHODS

Biological samples from a proband and his family members were analyzed. Hematological profiles were analyzed using a standard automated cell counter. Hb was analyzed by capillary electrophoresis and high-performance liquid chromatography. Mutations and globin haplotype were identified by DNA analysis. Novel diagnostic tools based on allele-specific polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism were developed.

RESULTS

Hb analysis showed a major abnormal Hb fraction, moving slower than HbA, and a minor Hb fraction alongside HbA2 in the proband, his father, and son. DNA analysis of the α-globin gene identified the -α3.7 deletion and in cis the C > A mutation on codon 9 of the α2α1 gene, corresponding to Hb Doi-Saket [α9(A7) Asn > Lys]. This mutation could be identified using newly developed allele-specific PCR-based assays. The Hb Doi-Saket al.lele was significantly associated with haplotype [- + M + + 0 -]. Interaction of αDoi-Saket with βE globin chains led to a new Hb variant (HbE Doi-Saket). Phenotypic expression was clinically silent in heterozygotes and might present slight microcytosis.

CONCLUSIONS

Hb Doi-Saket emphasizes a great diversity present in α-globin gene. The mutation in this family from Thailand was linked to -α3.7 and caused mild microcytosis in the carriers. The combination of this variant with deletions in α genes might cause a severe clinical phenotype. Different methods of separation can provide useful information in diagnosis, and a complete molecular approach is needed for confirmation before considering patient management.

Adapting the ACMG/AMP variant classification framework: A perspective from the ClinGen Hemoglobinopathy Variant Curation Expert Panel

Accurate and consistent interpretation of sequence variants is integral to the delivery of safe and reliable diagnostic genetic services. To standardize the interpretation process, in 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published a joint guideline based on a set of shared standards for the classification of variants in Mendelian diseases. The generality of these standards and their subjective interpretation between laboratories has prompted efforts to reduce discordance of variant classifications, with a focus on the expert specification of the ACMG/AMP guidelines for individual genes or diseases. Herein, we describe our experience as a ClinGen Variant Curation Expert Panel to adapt the ACMG/AMP criteria for the classification of variants in three globin genes (HBB, HBA2, and HBA1) related to recessively inherited hemoglobinopathies, including five evidence categories, as use cases demonstrating the process of specification and the underlying rationale.

Identification of Hemoglobin Variants Prevalent in China and Their Effects on Hemoglobin A1c Measurements

OBJECTIVES

We aimed to evaluate the effects of hemoglobin (Hb) variants prevalent in China on HbA1c measurements and to identify them during HbA1c measurements.

METHODS

We evaluated a cation-exchange high-performance liquid chromatography (HPLC) method (Bio-Rad D-100), a capillary electrophoresis (CE) method (Capillarys 3 TERA), an immunoassay (Cobas c501), and a boronate affinity method (Premier Hb9210, as a comparative method) for HbA1c measurements in the presence of Hb variants prevalent in China.

RESULTS

The Bio-Rad D-100 and Capillarys 3 TERA gave specific retention times and numeric migration positions for each Hb variant, respectively, showing excellent interindividual reproducibility. All methods showed statistically significant differences (P < .01) for several variants. Clinically significant effects were observed for the Bio-Rad D-100 (Hb New York and Hb J-Bangkok), Capillarys 3 TERA (Hb New York and Hb J-Bangkok), and Cobas c501 (Hb New York). Among 297 samples with Hb variants, there were 75 (25.3%) unacceptable results for Bio-Rad D-100, 28 (9.4%) for Capillarys 3 TERA, and 19 (6.4%) for Cobas c501 compared with the results from Premier Hb9210.

CONCLUSIONS

Some Hb variants prevalent in China affect HbA1c measurements. The HPLC retention time and CE migration position can aid in the presumptive identification of Hb variants.

Eleven Cases of Hb J-Paris-I [HBA2: c.38C>A (or HBA1)]: A Stable α Chain Variant Elutes in the P3 Window on High-Performance Liquid Chromatography

Hb J-Paris-I [HBA2: c.38C>A (or HBA1)] is a stable fast-moving hemoglobin (Hb) that elutes in the P3 window on high performance liquid chromatography (HPLC). The mutation can happen on either the α1- or α2-globin gene. Codon 12 changes from GCC to GAC to replace the alanine amino acid with aspartic acid. This change is external with no clinical significance. The elution in the P3 wave on HPLC can interfere with the glycated Hb assay by HPLC. In this study, data of 11 cases of Hb J-Paris-I were thoroughly presented. The majority of the cases were of Indian ethnicity. The mean value of Hb J-Paris-I on HPLC was 26.7 ± 2.0%. The retention time (RT) was 1.75 ± 0.03 min. The isoelectric focusing (IEF) mean value was -5.6 (range -6.1 to -4.9). Hb A₂ was consistently reduced to 1.8 ± 0.3%. A fraction of 0.8% corresponding to the Hb A₂-J-Paris-I (α₂^J-Paris-Iδ₂) is likely to be concealed within the A₀ peak of Hb A on HPLC. Interestingly, two cases were associated with two different polymorphisms [HBA2: c.-24C>G or Cap +14 (C>G) and HBA2: c.*136A>G polymorphism] without apparent effect on the variant expression.

Eight Cases of Hb Winnipeg [HBA2: c.226G>T (or HBA1)]: A Detailed Study

Hb Winnipeg [α75(EF4)Asp→Tyr (α2); HBA2: c.226G>T (or HBA1)] is a stable α-globin chain variant described in a few articles. The majority of reported cases in older articles were clustered in Canada. It can occur on both α1- and α2-globin genes and in different populations. In this study, eight cases of Hb Winnipeg were characterized by DNA sequencing during a wide-spectrum study of suspected α-globin gene variants collected in the United Kingdom. All cases detected peaked in the S window between 4.4 and 4.54 min. on high performance liquid chromatography (HPLC). The isoelectric focusing (IEF) averaged at 6.21 below Hb A. All the mutations were detected on the α1-globin gene except in one case. The ethnic origin of the majority of the patients was Canadian. Only one case was associated with the common polymorphism HBA2: c.-24C>G (or HBA1) [Cap +14 (C>G)] on both α-globin genes without any apparent effect on the variant expression. All cases were detected in a heterozygous state. Hb Winnipeg expression was consistently lower than the theoretical value for α chain variants, ranging between 11.8 and 15.8% of total hemoglobin (Hb). This study gave more details about Hb Winnipeg that may help in presumptive diagnosis, especially in routine laboratories.

Molecular Pathways Involved in the Development of Congenital Erythrocytosis

Patients with idiopathic erythrocytosis are directed to targeted genetic testing including nine genes involved in oxygen sensing pathway in kidneys, erythropoietin signal transduction in pre-erythrocytes and hemoglobin-oxygen affinity regulation in mature erythrocytes. However, in more than 60% of cases the genetic cause remains undiagnosed, suggesting that other genes and mechanisms must be involved in the disease development. This review aims to explore additional molecular mechanisms in recognized erythrocytosis pathways and propose new pathways associated with this rare hematological disorder. For this purpose, a comprehensive review of the literature was performed and different in silico tools were used. We identified genes involved in several mechanisms and molecular pathways, including mRNA transcriptional regulation, post-translational modifications, membrane transport, regulation of signal transduction, glucose metabolism and iron homeostasis, which have the potential to influence the main erythrocytosis-associated pathways. We provide valuable theoretical information for deeper insight into possible mechanisms of disease development. This information can be also helpful to improve the current diagnostic solutions for patients with idiopathic erythrocytosis.

[Radioiodine therapy outcome in toxic multinodular goiter patient with concomitant hereditary Hasharon hemoglobinopathy]

This research describes a clinical case of treatment of a patient with thyrotoxicosis with concomitant hematological pathology &ndash; carriage of unstable hemoglobin Hasharon. A patient diagnosed with &laquo;Diffuse toxic nodular goiter. Thyrotoxicosis of medium severity. Drug-induced hypothyroidism&raquo; was admitted to the Department of radionuclide therapy for the purpose of treatment with radioactive iodine. Onset of disease - summer 2018 (thyroid-stimulating hormone (TSH) &ndash; 0 mIU/ml). The instrumental studies (ultrasound, scintillation scanning of the thyroid gland) were performed at the pre-radioiodine therapy (RIT) diagnostic stage. The history of the disease indicates, that in 2000 the patient was suspected of having abnormal hemoglobin, since then no examinations have been conducted and anemia has never been detected. The diagnosis of ancestral hemoglobinopathy with the presence (17%) of unstable Hasharon-Sinai-Sealy hemoglobin in a heterozygous form was verified during the preparation to RIT. The radionuclide therapy I131 with activity of 400 MBq was performed on 02.07.2019. The monthly monitoring of laboratory and instrumental indicants was carried out during the post-therapeutic period: the state of hypothyroidism was reached by the end of 2 months after RT, no episodes of significant increase in bilirubin levels were observed during the observation period; no side effects from RT were stated. It becomes possible based on the example of the above observation, to judge the safety of conducting RT for treatment of thyrotoxicosis in patients with similar hemoglobinopathy, without excluding, however, the need for an individual approach in each case.

A Wide Spectrum Study of α-Globin Chain Variants: Cases from the UK

Over many years, cases of suspected α-globin chain variants were collected from different parts of the UK. The suspicion was based on the clinical picture, high performance liquid chromatography (HPLC) variant percentage, retention time (RT) and isoelectric focusing (IEF). DNA sequencing and the restriction enzyme EaeI were used for definitive diagnosis. One hundred and forty-eight variants were confirmed on one or both of the two α-globin genes (HBA2, HBA1). These cases were identified as 46 different α-globin chain variants. The most common variants were Hb J-Meerut [HBA2: c.362C>A (or HBA1)] (10.1%) and Hb Q-India (HBA1: c.193G>C) (8.1%), followed by Hb J-Paris-I [HBA2: c.38C>A (or HBA1)] and Hb Manitoba II (HBA1: c.309C>A) (7.4% for each). Other α variants were detected at lower frequencies. Two novel alleles were also detected: Hb Walsgrave [α116(GH4)Glu→Val (HBA2: c.350A>T)] and Hb Coombe Park [α127(H10)Lys→Glu (HBA2: c.382A>G)]. The majority of the ethnic origin was Indian. The positive predictive value for α variant identification by HPLC-RT analysis was 65.9%, 41.9% by IEF, and using both RT and IEF, the value was 72.1%. The number of variants was higher in HBA1 than in HBA2 genes and in exons 1 and 2 than in exon 3. There was no clustering of mutations in consecutive codons. This study, the characterization of a wide spectrum of α-globin chain variants, can facilitate the presumptive diagnosis of these variants prior to screening by a panel of amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), and a definitive diagnosis by DNA sequencing.

In Silico Analysis of the Effects of Point Mutations on α-Globin: Implications for α-Thalassemia

Hemoglobinopathies are inherited diseases that impair the structure and function of the oxygen-carrying pigment hemoglobin (Hb). Adult Hb consists of two α and two β subunits. α-Thalassemia (α-thal) affects the genes that code for the α-globin chains, HBA1 and HBA2. Mutations can result in asymptomatic, mild or severe outcomes depending on several factors, such as mutation type, number of mutations and the location at which they occur. PredictSNP was used to estimate whether every possible single nucleotide polymorphism (SNP) would have a neutral or deleterious effect on the protein. These results were then used to create a plot of predicted tolerance to change for each residue in the protein. Tolerance to change was negatively correlated with the residue's sequence conservation score. The PredictSNP data were compared to clinical reports of 110 selected variants in the literature. There were 29 disagreements between the two data types. Some of these could be resolved by considering the role of the affected residue in binding other molecules. The three-dimensional structures of some of these variant proteins were modeled. These models helped explain variants which affect heme binding. We predict that where a point mutation alters a residue that is intolerant to change, is well conserved and or involved in interactions, it is likely to be associated with disease. Overall, the data from this study could be used alongside biochemical and clinical data to assess novel α-globin variants.

Impact of annotation error in α-globin genes on molecular diagnosis

Background

Recent studies on the variants in duplicated human alpha globin genes (HBA2 and HBA1) actively target the α-globin gene as molecular modulators for the treatment of β-thalassemia major. Identification of the exact position of variant in HBA1, HBA2 or its patchworks is mandatory to support the therapeutic aims in β-thalassemia major, by identifying specific modulators for the reactivation of fetal hemoglobin production. Hence, accurate identification of the variants in α-globin genes is crucial for the proper diagnosis, treatment and genetic counseling.

Method

The objective was to reveal the annotation errors produced in α-globin gene sequence analysis while using different analytic tools. An HBA2 gene sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert have been taken as examples to prove annotation error in α-globin gene from different analytic tools.

Results and discussion

Although various bioinformatics tools used to predict variants are usually of high reliability, the current study using the an alpha globin 2 sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert, has showcased ambiguous outputs among the three bioinformatics tools used and against the manual analytical method adopted.

Conclusions

This report emphasizes the necessity for caution in the usage of DNA sequence analysis tools during molecular diagnosis and the importance of the selection of more appropriate tools for analysis. Furthermore, ethnic specific sequences should be considered as reference sequence for the analysis to bypass sequence dissimilarities among diverse populations.

Hb Bakersfield (HBA1: c.151_152insGGAGCC): The Insertion of Arg-His Between Codons 49 and 50 of the α1-Globin Chain Leads to Increased Oxygen Affinity

We describe an insertion variant on the α1-globin gene (HBA1) identified in a 49-year-old woman of Jurassian ancestry presenting with macrocytosis and erythrocytosis. The variant resulted in a peak of 15.5% of the total hemoglobin (Hb) on high performance liquid chromatography (HPLC). Stability and oxygen affinity testing revealed that the variant was stable and had an increased oxygen affinity. Molecular genetic testing detected the heterozygous sequence variant Hb Bakersfield [α50(CE8)His→0; Arg-Ser-His- inserted between 49(CE7) and 51(CE9) of α1; HBA1: c.151_152insGGAGCC (p.Ser50_His51insArgSer)] in the index patient, one of her sons, as well as in two of her grandchildren, who showed a similar hematological pattern.

Ten Years of Routine α- and β-Globin Gene Sequencing in UK Hemoglobinopathy Referrals Reveals 60 Novel Mutations

We review and report here the genotypes and phenotypes of 60 novel thalassemia and abnormal hemoglobin (Hb) mutations discovered following the adoption of routine DNA sequencing of both α- and β-globin genes for all UK hemoglobinopathy samples referred for molecular investigation. This screening strategy over the last 10 years has revealed a total of 11 new β chain variants, 15 α chain variants, 19 β-thalassemia (β-thal) mutations and 15 α(+)-thalassemia (α(+)-thal) mutations. The large number of new thalassemia alleles confirms the wide racial heterogeneity of mutations in the UK immigrant population. Eleven of the new variants ran with Hb A on high performance liquid chromatography (HPLC), demonstrating the value of routine sequencing of both α- and β-globin genes for all hemoglobinopathy investigations. The new β chain variants are: Hb Bury [β22(B4)Glu  →  Asp (HBB: c.69A > T)], Hb Fulwood [β35(C1)Tyr → His (HBB: c.106T > C)], Hb Little Venice [β42(CD1)Phe → Cys (HBB: c.128T > G)], Hb Cork [β57(E1)Asn → Ser (HBB: c.173A > G), Hb Basingstoke [β118(GH1)Phe → Ser (HBB: c.356T > C)], Hb Howden [β20(B2)Val → Ala (HBB: c.62T > C)], Hb Wilton [β41(C7)Phe → Leu (HBB: c.126C > A)], Hb Belsize Park [β120(GH3)Lys → Asn (HBB: c.363A > T)], Hb Hampstead Heath [β2(NA2)His → Gln;β26(B8)Glu → Lys (HBB: c.[6C > G;79G > A])], Hb Grantham [β85(F1)Phe → Cys (HBB: c.257T > G)] and Hb Calgary [β64(E8)Gly → Val (HBB: c.194G > T). The new α chain variants are: Hb Edinburgh [α70(E19)Val → Gly (HBA2: c.212T > G)], Hb Walsgrave [α116(GH4)Glu → Val (HBA2: c.350A > T)], Hb Wexham [α117(GH5) and 118(H1) insertion Ser (HBA1: c.354-355insTCA)], Hb Coombe Park [α127(H10)Lys → Glu (HBA2: c.382A > G)], Hb Oxford [α17(A15)Val → Asp (HBA2: c.53T > A)], Hb Bridlington [α32(B13)Met → Thr (HBA1: c.98T > C), Hb Wolverhampton [α81(F2)Ser → Tyr (HBA2: c.9245C > A)], Hb Little Waltham [α13(A11)Ala → Asp (HBA2: c.41C > A)], Hb Derby [α61(E10)Lys → Arg (HBA1: c.185A > G)], Hb Uttoxter [α74(EF3)Tyr → Asp (HBA2: c.223G > T)], Hb Harehills [α124(H7)Ser → Cys (HBA1: c.374C > G)], Hb Hekinan II [α27(B8)Glu → Asp (HBA1: c.84G > T)], Hb Manitoba IV [α102(G9)Ser → Arg (HBA1: c.307A > C), Hb Witham [α139(HC1)Lys → Arg (HBA2: c.419A > G) and Hb Farnborough [α9(A7)Asn → Asp (HBA1: c.28A > G). In addition, 10 more paralogous α-globin chain variants have been discovered. The novel β-thal alleles are: HBB: c.-138C > G, HBB: c.-121C > T, HBB: c.-80T > G, HBB: c.18_19delTG, HBB: c.219_220insT, HBB: c.315 + 2_315 + 13delTGAGTCTATGGG, HBB: c.316-70C > G, HBB: c.345_346insTGTGCTG, HBB: c.354delC, HBB: c.376-381delCCAGTG, HBB: c.393T > A, HBB: c.394_395insA, HBB: c.375_376insA, HBB: c.*+95_*+107delTGGATTCTinsC, HBB: c.* + 111_*+112delAA, HBB: c.*+112A > T, HBB: c.394C > T, HBB: c.271delG and HBB: c.316-3C > T. The novel α (+ )-thal alleles are: HBA1: c.95+1G > C, HBA1: c.315C > G [Hb Donnington, α104(G11)Cys → Trp], HBA1: c.327delC, HBA1: c.333_345del, HBA1: c.*+96G > A, HBA2: c.2T > G, HBA2: c.112delC, HBA2: c.143delA, HBA2: c.143_146delACCT, HBA2: c.156_157insG, HBA2: c.220_223delGTGG, HBA2: c.305T > C [Hb Bishopstown, α101(G8)Leu → His], HBA2: c.169_170delAA, HBA2: c.1A > T and HBA2: c.-3delA.

Understanding the contrasting spatial haplotype patterns of malaria-protective β-globin polymorphisms

The malaria-protective β-globin polymorphisms, sickle-cell (β(S)) and β(0)-thalassaemia, are canonical examples of human adaptation to infectious disease. Occurring on distinct genetic backgrounds, they vary markedly in their patterns of linked genetic variation at the population level, suggesting different evolutionary histories. β(S) is associated with five classical restriction fragment length polymorphism haplotypes that exhibit remarkable specificity in their geographical distributions; by contrast, β(0)-thalassaemia mutations are found on haplotypes whose distributions overlap considerably. Here, we explore why these two polymorphisms display contrasting spatial haplotypic distributions, despite having malaria as a common selective pressure. We present a meta-population genetic model, incorporating individual-based processes, which tracks the evolution of β-globin polymorphisms on different haplotypic backgrounds. Our simulations reveal that, depending on the rate of mutation, a large population size and/or high population growth rate are required for both the β(S)- and the β(0)-thalassaemia-like patterns. However, whilst the β(S)-like pattern is more likely when population subdivision is high, migration low and long-distance migration absent, the opposite is true for β(0)-thalassaemia. Including gene conversion has little effect on the overall probability of each pattern; however, when inter-haplotype fitness variation exists, gene conversion is more likely to have contributed to the diversity of haplotypes actually present in the population. Our findings highlight how the contrasting spatial haplotype patterns exhibited by β(S) and β(0)-thalassaemia may provide important indications as to the evolution of these adaptive alleles and the demographic history of the populations in which they have evolved.

Distribution of alpha-thalassemia mutations in Iranian population

BACKGROUND

Alpha-thalassemia as one of the most common monogenetic disorders is widely spread over the Mediterranean, Southeast Asian, and Middle Eastern populations, including Iran. Although beta-thalassemia is much more common than alpha-thalassemia, alpha-thalassemia is still one of the main health problems in Iran with different mutation frequencies in various ethnic groups. So the evaluation of alpha-thalassemia mutations could be helpful to detect carriers as well as prevention strategy in Iranian population.

OBJECTIVES

The aim of this study was to investigate the spectrum and frequencies of alpha-globin mutations in different ethnic groups of southern Iran.

MATERIALS AND METHODS

Common alpha-globin mutations were evaluated in 4010 Iranian population using a reverse dot blot for all point mutations and gap-polymerase chain reaction.

RESULTS

Out of all individuals, 3993 were distinguished as carriers of alpha-thalassemia mutations. Thirteen types of alpha-thalassemia mutations were discovered. Allele of α(3.7) mutation was the most prevalent (43.84%) followed by the α(IVS1/-5NT) allele with the prevalence of 4.91%. The less frequent alleles were Hb ICARIA and α(codon16) with the prevalence of 0.04 and 0.01%, respectively.

CONCLUSION

Our findings are essential for carrier screening, genetic counseling, and prenatal diagnosis in order to decrease the prevalence of α-thalassemia in Iran which is one of the goals of the national screening program.

Interaction of hemoglobin Grey Lynn (Vientiane) with a non-deletional α(+)-thalassemia in an adult Thai proband

Hemoglobin (Hb) Grey Lynn is a Hb variant caused by a substitution of Phe for Leu at position 91 of α1-globin chain, originally described in individual of unknown ethnic background. This article addresses the interaction of Hb Grey Lynn with a non-deletional α⁺-thalassemia found in Thailand, a hitherto un-described condition. The proband was adult Thai woman referred for investigation of mild anemia with Hb 90 g/L. Hb analyses using low pressure liquid chromatography raised a suspicion of abnormal Hb presence, which was failed to demonstrate by cellulose acetate electrophoresis and capillary electrophoresis. DNA sequencing identified a CTT (Leu) to TTT (Phe) mutation at codon 91 corresponding to the Hb Grey Lynn (Vientiane) [α91(FG3)Leu>Phe (α1) on α1-globin gene and a C deletion between codons 36 and 37 on α2-globin gene causing α⁺-thalassemia. As compared to those observed in a compound heterozygote for Hb Grey Lynn / α⁰-thalassemia reported previously, higher MCV (81.7 fL) and MCH (26.3 pg) values with a lower level of Hb Grey Lynn (19.7%) were observed in the proband. The normochromic normocytic anemia observed could be due to the interaction of Hb Grey Lynn with α⁺-thalassemia. The two mutations could be identified using PCR-RFLP and allele-specific PCR assays developed.

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for α-, and β-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.

Alpha chain hemoglobins with electrophoretic mobility similar to that of hemoglobin S in a newborn screening program

Objective

To characterize alpha-chain variant hemoglobins with electric mobility similar to that of hemoglobin S in a newborn screening program.

Methods

β^S allele and alpha-thalassemia deletions were investigated in 14 children who had undefined hemoglobin at birth and an electrophoretic profile similar to that of hemoglobin S when they were six months old. Gene sequencing and restriction enzymes (DdeI, BsaJI, NlaIV, Bsu36I and TaqI) were used to identify hemoglobins. Clinical and hematological data were obtained from children who attended scheduled medical visits.

Results

The following alpha chain variants were found: seven children with hemoglobin Hasharon [alpha2 47(CE5) Asp>His, HbA2:c.142G>C], all associated with alpha-thalassemia, five with hemoglobin Ottawa [alpha1 15(A13) Gly>Arg, HBA1:c.46G>C], one with hemoglobin St Luke's [alpha1 95(G2) Pro>Arg, HBA1:c.287C>G] and another one with hemoglobin Etobicoke [alpha212 84(F5) Ser>Arg, HBA212:c.255C>G]. Two associations with hemoglobin S were found: one with hemoglobin Ottawa and one with hemoglobin St Luke's. The mutation underlying hemoglobin Etobicoke was located in a hybrid α212 allele in one child. There was no evidence of clinically relevant hemoglobins detected in this study.

Conclusion

Apparently these are the first cases of hemoglobin Ottawa, St Luke's, Etobicoke and the α212 gene described in Brazil. The hemoglobins detected in this study may lead to false diagnosis of sickle cell trait or sickle cell disease when only isoelectric focusing is used in neonatal screening. Additional tests are necessary for the correct identification of hemoglobin variants.

Hb Treviso [α91(FG3)Leu→Phe (α2)]: a new slightly unstable hemoglobin variant with moderately decreased oxygen affinity

We report a new hemoglobin (Hb) variant, found in a North-East Italian family living in the city of Treviso. The proband, a non anemic 60-year-old male with a history of chronic rhinitis, allergy to Parietaria and suspected obstructive sleep apnea syndrome, was referred for blood gas analysis. Determination of the oxygen affinity revealed a p50 of 32.5 mmHg (control 27.5 mmHg) indicating a moderate decrease in oxygen affinity. An abnormal pattern compatible with an α Hb variant was observed on high performance liquid chromatography (HPLC); direct sequencing revealed a transition at codon 91 of the α2 gene (HBA2: c.274C>T) changing leucine into phenylalanine. Characterization and phenotype studies are reported.

Hb Stanleyville-II [α78(EF7)Asn→Lys (α2); HbA2: c.237C>A]: incidence of 1:11,500 in a newborn screening program in Brazil

Almost 3 million babies were tested in a newborn screening program in Minas Gerais, Brazil (1998-2008); 128 who have S-like hemoglobins (Hbs) were tested for the β(S) allele and 112 were identified through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or sequencing. Hb Stanleyville-II [α78(EF7)Asn→Lys (α2); HbA2: c.237C>A] was present in 96 children (85.7%), two in a homozygous state and 94 in a heterozygous state. Its estimated prevalence was 1:11,500. Hbs Hasharon [α47(CE5)Asp→His, GAC>CAC (α2)], Ottawa [α15(A13)Gly→Arg (GGT>CGT) (α2 or α1)], G-Ferrara [β57(E1)Asn→Lys (AAC>AAA or AAG)], St. Luke's [α95(G2)Pro→Arg, C CG>C GG (α1)], Maputo [β47(CD6)Asp→Tyr (GAT>TAT)] and Etobicoke [α84(F5)Ser→Arg (AG C>AG G or CGC or AGA) (α2 or α1)] were also identified. Many children with Hbs Stanleyville-II and Hasharon also co-inherited the -α(3.7) thalassemia gene. African ancestry was recognized by parents of all 31 children with Hb Stanleyville-II who were interviewed. Mean corpuscular volume (MCV) and mean corpuscular Hb (MCH) values were significantly lower in children with α-thalassemia (α-thal). We came to the conclusion that Hb Stanleyville-II is not so uncommon in Brazil and seems to have originated from the African slave trade. This study reinforces the importance of an accurate diagnosis of variants that have electrophoretic mobility similar to Hb S [β6(A3)Glu→Val, GAG>GTG] so that false diagnoses are avoided.

Identical mutations in the paralogous human γ-globin genes leading to hemoglobin variants and nondeletional hereditary persistence of fetal hemoglobin

The human fetal globin genes are highly similar at the DNA sequence level, resulting in a single amino acid difference between the (G)γ- and (A)γ-globin chains. A large proportion of hemoglobin (Hb) variants of the (G)γ- and (A)γ-globin chains result from an identical mutation in the HBG2 and HBG1 genes, respectively, while the same is true for a fraction of mutations leading to nondeletional hereditary persistence of fetal Hb (HPFH). In particular, 11 different Hb variants result from identical mutations on either one of the two human γ-globin paralogous genes, while seven other promoter substitutions result either in nondeletional HPFH or are benign polymorphisms. In the former case, the percentage of the Hb variants due to an HBG2 gene mutation was significantly higher than the percentage of Hb variants due to the same HBG1 gene mutation, following the (G)γ/(A)γ-globin chain ratio seen in wild-type individuals. These γ-globin chain variants have most likely occurred via recurrent mutations, gene conversion events or both and, contrary to the situation observed in the human α-globin genes, these mutations lead to distinct variant Hb molecules.

Homozygous Hb Stanleyville-II [alpha2 78(EF7) Asn>Lys; HBA2:c.237C>A, not C>G] associated with genotype -α 3.7/-α 3.7 in two Brazilian families

INTRODUCTION

Several hemoglobin variants have electrophoretic behavior similar to hemoglobin S, which may lead to false diagnosis for sickle-cell disorders in newborn screening programs. A homozygous hemoglobin with S mobility was detected in two unrelated babies in Brazil.

METHODS

Isoelectric focusing and high-performance liquid chromatography assays, gene sequencing, and restriction fragment length polymorphism with AfeI were used to characterize the hemoglobin.

RESULTS

Hb Stanleyville-II and -α(3.7) /-α(3.7) type I deletion in the α-globin gene was diagnosed. Parents were heterozygous for both Hb Stanleyville-II and α-thalassemia. Hypochromia and microcytosis were probably due to the homozygous α-thalassemia.

CONCLUSION

Stanleyville-II gene mutation is HBA2:c.237C>A, or C>G, and this information on the Globin Gene Server should be updated; AfeI test is a fast and accurate method to detect it; NBS programs should consider the possibility of Hb Stanleyville-II whenever IEF shows one band in the HbS position, and another one between S and C.

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

Gene conversion in human genetic disease

Gene conversion is a specific type of homologous recombination that involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a highly homologous ‘acceptor’. We have recently reviewed the molecular mechanisms underlying gene conversion, explored the key part that this process has played in fashioning extant human genes, and performed a meta-analysis of gene-conversion events known to have caused human genetic disease. Here we shall briefly summarize some of the latest developments in the study of pathogenic gene conversion events, including (i) the emerging idea of minimal efficient sequence homology (MESH) for homologous recombination, (ii) the local DNA sequence features that appear to predispose to gene conversion, (iii) a mechanistic comparison of gene conversion and transient hypermutability, and (iv) recently reported examples of pathogenic gene conversion events.

Neonatal screening for hemoglobinopathies: results of a public health system in South Brazil

AIM

The aim of this study was to estimate the prevalence of hemoglobinopathies in South Brazil.

METHODS

Samples of dried blood spots collected by heel prick in neonates were evaluated by isoeletric focusing and/or high-performance liquid chromatography techniques. All variants were characterized at the molecular level.

RESULTS

A total of 437,787 samples were evaluated. Among these, 6391 showed an abnormal hemoglobin pattern. These included 48 cases (0.01%) of sickle cell disorders (33 hemoglobin SS [Hb SS], 7 Hb SC, 7 Hb S/beta thalassemia, 1 Hb SD), 1 neonate who was homozygous for beta thalassemia, 6272 (1.4%) newborns who were heterozygous for Hb S, C, or D, and 71 (0.02%) neonates who were carriers for rare hemoglobin variants. Most of these rare variants were identified for the first time in Brazil.

CONCLUSIONS

Comparing these results with those obtained in other Brazilian regions, we observe a highly heterogeneous distribution. This knowledge is useful in healthcare planning and allocation of resources, as well as identifying at-risk couples, which will assist with disease prevention.

Unexpectedly low pulse oximetry measurements associated with variant hemoglobins: a systematic review

Pulse oximetry estimates arterial blood oxygen saturation based on light absorbance of oxy- and deoxy-hemoglobin at 660 and 940 nm wavelengths. Patients with unexpectedly low SpO₂ often undergo cardio-pulmonary testing to ascertain the cause of their hypoxemia. However, in a subset of patients, a variant hemoglobin is responsible for low SpO₂ measurements. The extent of this problem is unclear. We performed a systematic literature review for reports of low SpO₂ associated with variant hemoglobins. We also reviewed unpublished cases from an academic hemoglobin diagnostic reference laboratory. Twenty-five publications and four unpublished cases were identified, representing 45 patients with low SpO₂ and confirmed variant hemoglobin. Fifty-seven family members of patients had confirmed or suspected variant hemoglobin. Three low oxygen affinity variant hemoglobins had concordantly low SpO₂ and SaO₂. Eleven variant hemoglobins were associated with unexpectedly low SpO₂ measurements but normal SaO₂. Hemoglobin light absorbance testing was reported in three cases, all of which showed abnormal absorption spectra between 600 and 900 nm. Seven other variant hemoglobins had decreased SpO₂, with unreported or uncertain SaO₂. Twenty-one variant hemoglobins were found to be associated with low SpO₂. Most variant hemoglobins were associated with spuriously low SpO₂. Abnormal absorption spectra explain the discrepancy between SpO₂ and SaO(2) for some variants. The differential diagnosis of possible variant hemoglobin ought to be considered in asymptomatic patients found to have unexpectedly low SpO₂. The correct diagnosis will help to spare patients from unnecessary investigations and anxiety.

A new stable alpha chain variant: Hb Basel [alpha14(A12)Trp-->Leu (alpha1)]

We describe a heterozygosity for a new missense mutation on the alpha1-globin gene of an 18-year-old woman of Portuguese ancestry with severe hypochromic anemia and iron deficiency. Hemoglobin (Hb) analysis by high performance liquid chromatography (HPLC) found a prominent peak constituting about 12% of total Hb. Sequencing of the globin genes of the index patient found the mutation alpha14(A12)Trp-->Leu (alpha1), HBA1:c.44G<T. We identified the same mutation in blood and DNA of the mother, which provides evidence that the variant is stable and does not have direct pathophysiological or hematological consequences.