Improved Characterization of Complex ß-Globin Gene Cluster Structural Variants Using Long-Read Sequencing.

Complex insertion-deletion (indel) events in the globin genes manifest in widely variable clinical phenotypes. Many are incompletely characterized because of a historic lack of efficient methods. A more complete assessment enables improved prediction of clinical impact, which guides emerging therapeutic choices. Current methods have limited capacity for breakpoint assignment and accurate assessment of mutation extent, especially in cases containing duplications or multiple deletions and insertions. Technology, such as long-read sequencing, holds promise for significant impact in the characterization of indel events because of read lengths that span large regions, resulting in improved resolution. Four known complex ß-globin gene cluster indel types were assessed using single-molecule, real-time sequencing technology and showed high correlation with previous reports, including the Caribbean locus control deletion (g.5,305,478_5,310,336del), a large ß-gene duplication containing the Hb S mutation (g.4,640,335_5,290,171dup with g.5,248,232T>A, c.20A>T; variant allele fraction, 64%), and two nested variants (double deletions with intervening inversion): the Indian Gγ(Aγδß)0-thalassemia (g.5,246,804-5,254,275del, g.5,254,276_5,269,600inv, and g.5,269,601_5,270,442del) and the Turkish/Macedonian (δß)0 thalassemia (g.5,235,064_5,236,652del, g.5,236,653_5,244,280inv, and g.5,244,281_5,255,766del). Our data confirm long-read sequencing as an efficient and accurate method to identify these clinically significant complex events. Limitations include high-complexity sample preparation requirements, which hinder routine use in clinical laboratories. Continued improvements in sample and data workflow processes are needed to accommodate volumes in a tertiary clinical laboratory.

Interpreting sulfhemoglobin and methemoglobin in patients with cyanosis: An overview of patients with M-hemoglobin variants.

INTRODUCTION: Methemoglobin (MetHb) and sulfhemoglobin (SHb) measurements are useful in the evaluation of cyanosis. When one or both values are elevated, additional analysis is important to establish the etiology of the disorder. Methemoglobinemia occurs from acquired or hereditary causes with diverse treatment considerations, while true sulfhemoglobinemia is only acquired and treatment is restricted to toxin removal. Some toxic exposures can result in a dual increase in MetHb and SHb. Hereditary conditions, such as M-Hemoglobin variants (M-Hbs), can result in increased MetHb and/or SHb values but are clinically compensated and do not require treatment if they are cyanotic but otherwise clinically well. METHODS: Herein, we report 53 hemoglobin variant cases that have associated MetHb and SHb levels measured by an adapted Evelyn-Malloy laboratory assay method. RESULTS: Our data indicate M-Hbs cause variable patterns of MetHb and SHb elevation in a fairly reproducible pattern for the particular variant. In particular, α globin chain M-Hbs can mimic acquired sulfhemoglobinemia due to an isolated increased SHb value. CONCLUSION: If the patient appears clinically well other than cyanosis, M-Hbs should be considered early in the evaluation process to differentiate from acquired conditions to avoid unnecessary testing and treatment regimens and prompt genetic counseling.

Genotype-Phenotype Correlation of Hereditary Erythrocytosis Mutations, a single center experience.

Hereditary erythrocytosis is associated with high oxygen affinity hemoglobin variants (HOAs), 2,3-bisphosphoglycerate deficiency and abnormalities in EPOR and the oxygen-sensing pathway proteins PHD, HIF2α, and VHL. Our laboratory has 40 years of experience with hemoglobin disorder testing and we have characterized HOAs using varied protein and molecular techniques including functional assessment by p50 analysis. In addition, we have more recently commenced adding the assessment of clinically relevant regions of the VHL, BPGM, EPOR, EGLN1 (PHD2), and EPAS1 (HIF2A) genes in a more comprehensive hereditary erythrocytosis panel of tests. Review of our experience confirms a wide spectrum of alterations associated with erythrocytosis which we have correlated with phenotypic and clinical features. Through generic hemoglobinopathy testing we have identified 762 patients with 81 distinct HOA Hb variants (61 ß, 20 α), including 12 that were first identified by our laboratory. Of the 1192 cases received for an evaluation specific for hereditary erythrocytosis, approximately 12% had reportable alterations: 85 pathogenic/likely pathogenic mutations and 58 variants of unknown significance. Many have not been previously reported. Correlation with clinical and phenotypic data supports an algorithmic approach to guide economical evaluation; although, testing is expanded if the suspected causes are negative or of uncertain significance. Clinical features are similar and range from asymptomatic to recurrent headaches, fatigue, restless legs, chest pain, exertional dyspnea and thrombotic episodes. Many patients were chronically phlebotomized with reported relief of symptoms. This article is protected by copyright. All rights reserved.

A Novel ß-Globin Chain Hemoglobin Variant, Hb Allentown [ß137(H15)Val→Trp (GTG>TGG) HBB: c.412_413delinsTG, p.Val138Trp], Associated with Low Oxygen Saturation, Intermittent Aplastic Crises and Splenomegaly.

Hemoglobin (Hb) variants may be associated with low oxygen saturation and exacerbated episodes of anemia from common stressors such as viral infections. These attributes frequently cause increased clinical concern and unnecessary and expensive testing if not considered early in the evaluation of the patient. Some clinically significant Hb variants result in a normal Hb electrophoresis result, which can be method-dependent. Herein we describe a patient with low oxygen saturation and a history of hemolytic anemia who was subsequently found to carry a novel, unstable ß-globin variant that we have named Hb Allentown [ß137(H15)Val→Trp (GTG>TGG) HBB: c.412_413delinsTG, p.Val138Trp] for the place of identification of the variant. Hb Allentown is formed by a rare double nucleotide substitution within the same codon. Additionally, positive identification of rare Hb variants characterized by a single method is discouraged, as the Hb variant was misclassified as Hb S-South End or ß6(A3)Glu→Val;ß132(H10)Lys→Asn (HBB: c.[20A > T;399A > C]) by the initial laboratory.

ß-Thalassemia major resulting from compound heterozygosity for HBB: c.92+2T>C [formerly known as IVS-I-2 (T>C)] and a novel ß(0)-thalassemia frameshift mutation: HBB: c.209delG; p.Gly70Valfs*20.

A novel ß(0)-thalassemia (ß-thal) frameshift mutation, HBB: c.209delG; p.Gly70Valfs*20, is described in a 21-year-old African American female with ß-thalassemia major (ß-TM) due to compound heterozygosity for the ß(0)-thal mutation HBB: c.92+2T>C [formerly known as IVS-I-2 (T>C)] and HBB: c.209delG. The combination of these mutations demonstrates a complete lack of ß-globin chain synthesis, evidenced by the proband having no Hb A present.

Hb Manukau [ß67(E11)Val → Gly; HBB: c.203T>G]: the role of genetic testing in the diagnosis of idiopathic hemolytic anemia.

The increasing availability of DNA sequencing of globin genes has improved our ability to detect conditions that were presumed to be extremely rare. These conditions may remain undiagnosed due to unfamiliarity with clinical presentation, relative unavailability of advanced diagnostic alternatives, or may defy detection by being electrophoretically silent or extreme instability rendering their presence to be below detection level. Genetic studies were pursued in a mother and daughter with severe hemolytic anemia as initial testing failed to be diagnostic. DNA sequence analysis of the ß-globin gene identified Hb Manukau [ß67(E11)Val → Gly; HBB: c.203T > G], an extremely unstable hemoglobin (Hb) variant. This is the second family described with this condition (first in the western hemisphere). An astute clinician may benefit from being persistent and pursuing additional testing including molecular genetic characterization where clinical suspicion remains high.

Hb Memphis [HBA2: c.70G>C (or HBA1)] in a Turkish child: a case report and comparison to Hb Q-Thailand (HBA1: c.223G>C).

Hb Memphis [α23(B4)Glu→Gln; HBA2: c.70G > C (or HBA1)] is a stable hemoglobin (Hb) variant caused by a substitution of glutamine for glutamic acid at residue 23 of the α2- or α1-globin chain. Heterozygous Hb Memphis has no known clinical or hematological effect, and all prior reports have resulted from observations in persons of African descent with sickle cell disease and an unusually mild clinical course. Family studies suggest that Hb Memphis may modulate sickling. Only brief characterizations of Hb Memphis trait in the absence of Hb S are present in the current literature. We report isolated Hb Memphis trait in Turkish individuals in whom the initial laboratory incorrectly identified the α variant as Q-Thailand [α74(EF3)Asp→His; HBA1: c.223G > C]. In one case, a heterozygous -3.7 kb α gene deletion was also present, which increased the variant Hb level to a percentage similar to that of the more common Hb Q-Thailand, which may have led to the misidentification. Herein, we discuss the characterization and comparison of these variants and underscore the necessity of confirming characterization by more than one method prior to assigning Hb variant identification.

Hb Grand Junction (HBB: c.348_349delinsG; p.His117IlefsX42): a new hyperunstable hemoglobin variant.

Hyperunstable hemoglobinopathy (HUH) [dominantly inherited ß-thalassemia (ß-thal)] is a relatively rare form of congenital hemolytic anemia in which mutations occur in the genes encoding for α and ß chains, or both chains of the hemoglobin (Hb) molecule. We describe two Hispanic adolescents with a new unstable Hb variant (HBB: c.348_349delinsG; p.His117IlefsX42), resulting from a frameshift mutation at codons 115/116 of the ß-globin gene. Both patients also have a 3.7 kb deletion on one α gene, leading to a decreased imbalance between α and ß chain formation, and subsequently a milder phenotype than that seen in other hyperunstable Hb variants.

Hb Grove City [ß38(C4)Thr→Ser, ACC>AGC; HBB: c.116C>G]: a new low oxygen affinity ß chain variant.

A previously unreported ß chain hemoglobin (Hb) variant, Hb Grove City [ß38(C4)Thr→Ser, ACC>AGC; HBB: c.116C>G], was discovered in a woman who presented with hypoxia and mild anemia. Her young daughter also tested positive for the variant and displayed similar symptoms. Hemoglobin-oxygen dissociation testing confirmed right-shifted oxygen dissociation curves. A corresponding Hb variant was detected by high performance liquid chromatography (HPLC) and intact mass spectrometry (MS) but was not detected by capillary electrophoresis (CE), isoelectrofocusing (IEF) or alkaline or acid electrophoresis. DNA sequencing analysis confirmed a ß-globin gene mutation. All three previous mutations at this locus affect oxygen affinity, as does this new variant. This newly described variant showed variable stability results and therefore may be mildly unstable but is not associated with microcytosis, significant hemolysis or clinically evident cyanosis. It is important to consider hemoglobinopathies in patients who are anemic and have unexplained hypoxia. Arterial blood gas and p50 evaluations may prevent unnecessary diagnostic interventions. Additionally, Hb variants with altered oxygen affinity can be electrophoretically silent; therefore, multiple methods including MS and/or DNA sequencing are warranted when clinical suspicion is high.

Homozygous hemoglobin Abruzzo in a North American child.

Hemoglobin Abruzzo is a stable hemoglobin variant with increased oxygen affinity, clinically causing compensatory erythrocytosis in affected patients. Heterozygosity of this variant with or without beta-thalassemia has been previously described in three Italian families, thereby suggesting a single origin of the mutation. The authors report the first case of homozygosity in a North American female infant, born to heterozygous parents as a product of consanguineous marriage.