The haematology of Jamaicans: red cell indices in HbAA, HbAS, HbAC, and HbA-HPFH genotypes.

Based in the parish of Manchester in central Jamaica, the Manchester Project offered free detection of haemoglobin genotype to senior classes in 15 secondary schools between 2008 and 2013. Restricting the database to 15,103 students aged 15.0-19.9 years provided an opportunity to examine the red cell characteristics of the different haemoglobin genotypes, including normal (HbAA) in 85.0%, the sickle cell trait (HbAS) in 9.7%, HbC trait (HbAC) in 3.5% and hereditary persistence of foetal haemoglobin (HbA-HPFH) in 0.4%. Compared to the normal HbAA phenotype, HbAS had significantly increased mean cell haemoglobin concentration (MCHC), red cell count (RBC), and red cell distribution width (RDW) and decreased mean cell volume (MCV) and mean cell haemoglobin (MCH), these differences being even more marked in HbAC. Compared to HbAA, the HbA-HPFH had significantly increased RDW, but there were no consistent differences in other red cell indices, and there were no significant differences in haematological indices between the two common deletion HPFH variants, HPFH-1 and HPFH-2. Although these changes are unlikely to be clinically significant, they contribute to an understanding of the haematological spectrum of the common haemoglobin genotypes in peoples of African origin.

Next-generation sequencing as a tool for breakpoint analysis in rearrangements of the globin gene clusters.

INTRODUCTION: Next-generation sequencing (NGS), now embedded within genomic laboratories, is well suited to the detection of small sequence changes but is less well adapt for detecting structural variants (SV), mainly due to the relatively short sequence reads. Of the available target enrichment methods, bait capture or whole-genome sequencing appears better suited to detecting SV as there is less PCR amplification and is therefore more representative of the genome being sequenced. MATERIAL AND METHODS: In 2015, we described the first inversion/deletion causing εγδß- thalassemia using an NGS approach, with base-pair resolution. Bioinformatic processing of the sequencing data was manual and time-consuming. The methodology relied on detecting the presence or absence of the SV by assessing sequence coverage and then mapping the deletion by capturing and sequencing breakpoint spanning reads (split reads). In the period between developing more automated analytical methods, we identified the first duplication of the entire beta globin cluster. RESULTS: Detecting the presence of the SV is reliable but capturing the breakpoint spanning reads is challenging. Confirmation by Sanger sequencing a breakpoint spanning amplicon has confirmed the NGS results in all cases. CONCLUSIONS: We have now streamlined and automated the bioinformatic approach using Exome Depth to assess sequence coverage and Delly to detect split and discordant reads. The combined NGS and bioinformatic strategy has proven to be highly successful and applicable to routine diagnostics.

Venous thromboembolism in adults with sickle cell disease: experience of a single centre in the UK.

Venous thromboembolism (VTE) is a recognised complication of sickle cell disease (SCD), long considered to be a hypercoagulable state. While there is a good understanding of arterial thrombosis in SCD, the nature of VTE in SCD is less well-characterised. In this retrospective cohort study, we found that the incidence of VTE in our patient cohort was higher than in the non-SCD black population; patients of all SCD genotypes with VTE had significantly elevated steady-state platelet counts compared to those without. Recent hospitalisation (typically with acute sickle pain) was the commonest precipitating risk factor. These findings suggest consideration of longer VTE prophylaxis for acute hospital admissions in SCD.

Peak expiratory flow in Afro-Caribbean children with and without sickle cell anaemia.

AIMS: To create a reference range of peak expiratory flow (PEF) results of Afro-Caribbean children and determine whether interpretation of PEF results in children with sickle cell anaemia (SCA) differed according to whether comparison was made of results obtained from children of similar age or height. METHODS: A prospective observational study was carried out in two specialist sickle cell disease clinics. Seventy-eight nonasthmatic African and Caribbean (AC) controls (age range 2.6-17.8 years), and 99 nonasthmatic SCA children (age range 3.4-17.3 years) were recruited. PEF was measured using a dry rolling sealed spirometer before and after bronchodilator therapy. RESULTS: PEF results in the AC controls correlated with height (r = 0.88, p< 0.0001). Comparison of similarly aged children demonstrated that pre- (p = 0.02) and post- (p = 0.04) bronchodilator PEF results were lower in the SCA children, but comparison of children of similar height revealed no statistically significant differences in PEF results between children with SCA and controls. The SCA children tended to be shorter than the controls. CONCLUSION: The results suggest PEF measurements are not a useful method of monitoring the respiratory status of children with sickle cell disease.

Sickle liver disease--an unusual presentation in a compound heterozygote for HbS and a novel beta-thalassemia mutation.

A 38-year-old Ghanaian man presented with a 6-month history of worsening pruritus, jaundice, and ascites. He was previously fit and well and rarely drank alcohol. Screening tests for chronic liver disease including viral, autoimmune, and other metabolic causes including iron overload were unremarkable. A liver biopsy performed at the referring hospital demonstrated intralobular cholestasis and cirrhosis. He was listed for liver transplantation but subsequently developed sepsis with multiple organ failure and died. The sickle solubility test was positive. Blood smear showed cells consistent with liver failure and no sickle cells. Hemoglobin electrophoresis revealed HbA2 2.8%, HbF 0.5%, and HbS greater than HbA (49.6% vs. 41.3%) in the absence of blood transfusion. Sequence analysis of the beta-globin genes showed he was a compound heterozygote for the Hbs mutation at codon 6 (CAG --> GTG) and a novel mutation at position 844 of intron 2 (betaIVS2-844 C --> A). A diagnosis of sickle hepatopathy causing decompensated cirrhosis was made. This case is unusual insomuch as this patient was asymptomatic for over 35 years and represents a novel presentation of sickle cell disease. Sickle cell disease should be considered in appropriate patients when unusual presentations of liver disease arise.

Computed tomography and pulmonary function abnormalities in sickle cell disease.

The aim of this study was to determine whether patients with sickle cell disease (SCD) in steady state had pulmonary abnormalities seen on high-resolution computed tomography (HRCT) and whether any abnormalities correlated with contemporaneously diagnosed lung function abnormalities. A subsidiary question was whether the results of a noninvasive measure of haemolysis (end-tidal carbon monoxide (ETCO) levels) correlated with pulmonary function abnormalities. Thirty three patients with SCD, median (range) age 36 yrs (17-67 yrs) were examined. The degree of lobar volume loss and ground-glass opacification and prominence of central vessels on HRCT were quantitatively assessed. Pulmonary function was assessed by measurements of lung volumes, spirometry, gas transfer and oxygen saturation. ETCO levels were measured using an end-tidal CO monitor. Forced expiratory volume in one second (FEV1), forced vital capacity and total lung capacity significantly correlated with HRCT findings, particularly lobar volume loss. ETCO levels significantly negatively correlated with FEV1, vital capacity measured using a plethysmograph, specific airway conductance and arterial oxygen saturation measured by pulse oxymetry. In conclusion, the present results suggest that high-resolution computed tomography noninvasive assessment of haemolysis might be useful to identify sickle cell disease patients with respiratory function impairment.

Interaction between two quantitative trait loci affects fetal haemoglobin expression.

The biological mechanisms controlling complex quantitative traits are likely to be affected by interactions between genetic factors, sometimes referred to as epistasis. The identification of interacting loci through genetic analyse faces many challenges, and few examples of replicated findings of interaction exist for humans and model system organisms. The replication of an interaction, or the non-independence, of two quantitative trait loci (QTL) affecting the developmental switch from the expression of fetal to adult haemoglobin is reported here. Fetal haemoglobin expression in adults is a highly heritable, yet complex, phenotype. Using a sample of 874 dizygotic twin pairs of European descent, we found linkage to a QTL on chromosome 8 to be conditional on the twin pairs' genotypes at a polymorphism in the beta-globin complex; an interaction originally identified in a large Asian Indian kindred. The beta-globin polymorphism has been previously shown to be associated with fetal haemoglobin levels in adults. This study reports the first known replication of a genetic interaction between QTLs influencing a complex human trait.

The genetic basis of the interaction between pyrimidine 5' nucleotidase I deficiency and hemoglobin E.

We have previously described a family in which the interaction between pyrimidine 5' nucleotidase I (P5N-I) deficiency and hemoglobin E resulted in severe haemolytic anaemia. In this study we explored the genetic basis of the severe clinical phenotype and look for evidence of the interaction between these conditions. A P5N-I gene mutation (IVS8 + 1-2delGT) was found in the family, confirming that the severe phenotype results from the interaction between two genetic diseases.

Molecular diagnosis of haemoglobin disorders.

The haemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassaemias) or the synthesis of a structurally abnormal haemoglobin (Hb). In prevalent regions, the thalassaemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and haematological phenotypes. An appreciation of these phenotypes is needed to facilitate the definitive diagnosis of the causative mutations to inform management and counselling. Haematological and biochemical investigations, and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. With the exception of a few rare deletions and rearrangements, the molecular lesions causing haemoglobinopathies are all identifiable by PCR-based techniques. Although a full spectrum of >1000 mutations causing haemoglobinopathies has been documented, in practice only a limited number are associated with disease states and clinical significance. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassaemia mutations. Prior identification of the ethnic origin is thus an important part of the diagnostic strategy which becomes less reliable in the UK because of the large ethnic mix. Although the current approach using a combination of different PCR-based techniques seems to work in most laboratories, practice pressures with the imminent implementation of universal antenatal screening for clinically significant Hb disorders in the UK will require a higher throughput approach for DNA diagnostics in the near future. The complex mutational spectrum and the compactness of the globin genes places them in an ideal position for the different non-gel based analytical platforms.

Pulmonary function abnormalities in children with sickle cell disease.

BACKGROUND: Adults with sickle cell disease (SCD) have restrictive lung function abnormalities which are thought to result from repeated lung damage caused by episodes of pulmonary vaso-occlusion; such episodes start in childhood. A study was therefore undertaken to determine whether children with SCD have restrictive lung function abnormalities and whether the severity of such abnormalities increases with age. METHODS: Sixty four children with SCD aged 5-16 years and 64 ethnic matched controls were recruited. Weight and sitting and standing height were measured, and lung function was assessed by measurement of lung volumes and forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and peak expiratory flow (PEF) before and after bronchodilator. RESULTS: Compared with the control subjects, the children with SCD had lower mean (SD) sitting height (69 (6.3) cm v 73 (7.7) cm; p=0.004), sitting:standing height ratio (0.50 (0.02) v 0.51 (0.01); p<0.0001), weight (33 (10.9) kg v 41 (14.9) kg; p=0.001), functional residual capacity measured by a helium gas dilution technique (1.2 (0.3) l v 1.3 (0.4) l; p=0.04), FEV1 (1.5 (0.5) l v 1.9 (0.7) l; p=0.0008), FVC (1.7 (0.6) l v 2.1 (0.8) l; p=0.001), and PEF (3.9 (1.3) l/s v 4.8 (1.5) l/s; p=0.0004). The effect of age on lung function differed significantly between the children with SCD and the controls for total lung capacity and vital capacity measured by plethysmography and functional residual capacity measured by helium gas dilution. CONCLUSION: Lung function differs significantly in children with SCD compared with ethnic matched controls of a similar age. Our results suggest that restrictive abnormalities may become more prominent with increasing age.

Genetic basis of hemolytic anemia caused by pyrimidine 5' nucleotidase deficiency.

Pyrimidine 5' nucleotidase (P5'N-1) deficiency is an autosomal recessive condition causing hemolytic anemia characterized by marked basophilic stippling and the accumulation of high concentrations of pyrimidine nucleotides within the erythrocyte. It is implicated in the anemia of lead poisoning and is possibly associated with learning difficulties. Recently, a protein with P5'N-1 activity was analyzed and a provisional complementary DNA (cDNA) sequence published. This sequence was used to study 3 families with P5'N-1 deficiency. This approach generated a genomic DNA sequence that was used to search GenBank and identify the gene for P5'N-1. It is found on chromosome 7, consists of 10 exons with alternative splicing of exon 2, and produces proteins 286 and 297 amino acids long. Three homozygous mutations were identified in this gene in 4 subjects with P5'N-1 deficiency: codon 98 GAT-->GTT, Asp-->Val (linked to a silent polymorphism codon 92, TAC-->TAT), codon 177, CAA-->TAA, Gln-->termination, and IVS9-1, G-->T. The latter mutation results in the loss of exon 9 (201 bp) from the cDNA. None of these mutations was found in 100 normal controls. The DNA analysis was complicated by P5'N-1 pseudogenes found on chromosomes 4 and 7. This study is the first description of the structure and location of the P5'N-1 gene, and 3 mutations have been identified in affected patients from separate kindreds. (Blood. 2001;97:3327-3332)

Gene regulation and deregulation: a beta globin perspective.

The study of the beta globin gene has provided great insights into the mechanisms of gene regulation and expression. In this review, we consider the normal regulation and expression of the beta globin gene and illustrate how the various steps may be affected, providing a basis for understanding the molecular pathophysiology of beta thalassemia. Mutations causing beta thalassemia can be classified as beta0 or B+ according to whether they abolish or reduce the production of beta globin chains. The vast majority of beta thalassemia is caused by point mutations, mostly single base substitutions, within the gene or its immediate flanking sequences. Rarely, beta thalassemia is caused by major deletions of the beta globin cluster. All these mutations behave as alleles of the beta locus but in several families the beta thalassemia phenotype segregates independently of the beta globin complex, and are likely to be caused by mutations in trans-acting regulatory factors.

An integrated map of human 6q22.3-q24 including a 3-Mb high-resolution BAC/PAC contig encompassing a QTL for fetal hemoglobin.

Genetic studies have previously assigned a quantitative trait locus (QTL) for hemoglobin F and F cells to a region of approximately 4 Mb between the markers D6S408 and D6S292 on chromosome 6q23. An initial yeast artificial chromosome contig of 13 clones spanning this region was generated. Further linkage analysis of an extended kindred refined the candidate interval to 1-2 cM, and key recombination events now place the QTL within a region of <800 kb. We describe a high-resolution bacterial clone contig spanning 3 Mb covering this critical region. The map consists of 223 bacterial artificial chromosome (BAC) and 100 P1 artificial chromosome (PAC) clones ordered by sequence-tagged site (STS) content and restriction fragment fingerprinting with a minimum tiling path of 22 BACs and 1 PAC. A total of 194 STSs map to this interval of 3 Mb, giving an average marker resolution of approximately one per 15 kb. About half of the markers were novel and were isolated in the present study, including three CA repeats and 13 single nucleotide polymorphisms. Altogether 24 expressed sequence tags, 6 of which are unique genes, have been mapped to the contig.

Genetic influences on F cells and other hematologic variables: a twin heritability study.

To assess the relative contribution of genetic factors in the variation of F cells (FC) and other hematologic variables, we conducted a classical twin study in unselected twins. The sample included 264 identical (monozygotic [MZ]) twin pairs and 511 nonidentical (dizygotic [DZ]) same-sex twin pairs (aged 20 to 80 years) from the St. Thomas' UK Adult Twin Register. The FC values were distributed continuously and positively skewed, with values ranging from 0.6% to 22%. FC values were higher in women than in men and decreased with age, with the variables accounting for 2% of the total FC variance. The intraclass correlations of FC values were higher in MZ (rMZ = 0.89) than in DZ (rDZ = 0.49) twins. The XmnI-(G)gamma polymorphism in the beta-globin gene cluster had a significant effect on FC levels, accounting for approximately 13% of the total FC variance. Variance components analysis showed that the FC values were accounted for predominantly by additive genetic and nonshared environmental influences, with an estimate of heritability of 0.89. Hemoglobin levels and red blood cell, white blood cell, and platelet numbers were also substantially heritable, with heritability estimates of 0.37, 0.42, 0.62, and 0.57, respectively. Previously, studies of sib pairs with sickle cell disease and isolated family studies showed that high levels of Hb F and FC tend to be inherited. Here, our classical twin study demonstrated that the variance of FC levels in healthy adults is largely genetically determined. (Blood. 2000;95:342-346)

Determinants of iron status and bilirubin levels in congenital dyserythropoietic anaemia type I.

Seven untransfused patients with congenital dyserythropoietic anaemia type I were investigated to assess the determinants of both iron overload and serum bilirubin levels. The serum ferritin concentration was increased in all patients and non-transferrin-bound iron (NTBI) was increased in all but one patient. None of the patients showed the C282Y mutation in the hereditary haemochromatosis gene, HFE. One patient was homozygous for the H63D mutation in this gene. The data indicated that differences in the extent of iron overload were not mediated by co-inheritance of the C282Y mutation in the HFE gene but could largely be explained by differences in the severity of anaemia and ineffective erythropoiesis, and in the age of the patient. In one patient an unusually high plasma bilirubin level was associated with the variant A[TA]7TAA configuration in the TATA box of the uridine diphosphate glucuronosyltransferase (UGT-1A) gene promoter, the mutation found in most patients with mild Gilbert's syndrome.

An in vitro system for expression analysis of mutations of the beta-globin gene: validation and application to two mutations in the 5' UTR.

We describe the setting up of an in vitro expression system for the analysis of mutations of the beta-globin gene. The system is based on the stable transfection of a normal or mutated beta-globin gene into mouse erythroleukaemia (MEL) cells. The expression construct contains an Agamma gene as an internal control and both globin genes are under the control of the HS2 element of the beta LCR. The system enables analysis of transcription, RNA processing and transport, as well as mRNA stability. With non-mutant genes, high-level expression of both beta and Agamma genes is seen and both mRNAs are stable. The system was validated by comparing the expression of the beta654 thalassaemia splicing mutation in MEL cells with its well-characterized expression in vivo. The level of the initial transcript, the proportion of abnormally spliced mRNA and its instability during erythroid cell maturation were all faithfully reproduced. The system was used to examine the mechanism by which two mutations in the beta-globin 5' untranslated region (5' UTR) result in beta thalassaemia. Surprisingly, the mechanism appeared to differ in the two cases, with the C-G substitution at position +33 affecting transcription, whereas the -T deletion at position +10 resulted in a translational defect. The stably transfected MEL cells, with an internal control and an endogenous enhancer, appear to be a valid and realistic experimental model, superior to transient expression studies. This system should find wide application in the analysis of the effects and mechanisms of gene inactivation in mutations affecting the beta-globin as well as other genes.

Genetics of Hb F/F cell variance in adults and heterocellular hereditary persistence of fetal hemoglobin.

Hb F and F cell values in normal adults vary considerably with a continuous distribution that is substantially skewed to the right implicating a polygenic influence. The high values of Hb F and F cells are transmitted in the condition referred to as heterocellular hereditary persistence fetal hemoglobin which should be regarded as a multifactorial quantitative trait, quite distinct from the classical pancellular hereditary persistence of fetal hemoglobins. Several factors have been shown to influence F cell/Hb F levels in normal adults including age, gender, genetic determinants linked and unlinked to the beta-globin locus on chromosome 11p. Two trans-acting quantitative trait loci for F cell variance have been mapped, one on 6q and the other on Xp, with at least one other implicated. As an initial step towards hunting for the other quantitative trait loci we have carried out a preliminary analysis of F cell variance in 182 pairs of monozygotic and 373 pairs of dizygotic twins. The correlation coefficient of F cell variance in monozygotic twins was 0.89, while that in the dizygotic twins was 0.51. Overwhelming evidence for a strong genetic component in the control of Hb F/F cell levels is provided by a heritability of 0.87. However, the role and extent of contribution from the quantitative trait loci on 6q and Xp are still not known.