Surveyor™ Nuclease: A New Rapid and Effective Strategy for Detection of Single Nucleotide Changes in Alpha Globin Genes.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3653-3653
Author(s):  
Mammen Chandy ◽  
Eunice E. Sindhuvi ◽  
R.V. Shaji ◽  
Vikram Mathews ◽  
Biju George ◽  
...  

Abstract Alpha thalassemia is the most common globin gene disorder in the world and the disease is caused by mutations in either the alpha2 or alpha1 genes. Deletions of one (-α) or both (--) of these genes are the most common cause of alpha-thalassemia, while point mutations and small insertions/deletions are present but at a much lower frequency (5%). The number of point mutations described in these genes has been steadily increasing, with greater than 40 identified to date. Identifying these point mutations acquires importance as patients with non-deletional hemoglobin (Hb) H disease are more severely affected. Comprehensive evaluation of α globin genes is also essential while determining the molecular basis of the thalassemia intermedia phenotype. Mutations in the alpha globin gene can be detected either by direct DNA sequencing or by screening methods. Although small (about 1kb, 3 exons and 2 introns), the alpha-globin genes are duplicate and highly G-C rich, which makes them difficult to denature and therefore reducing sequencing efficiency and causing frequent artifacts. We have developed a simple and robust method based on mismatch-specific DNA endonuclease, SurveyorTM Nuclease. Genomic DNA control samples (n=21) harboring 12 different nucleotide changes characterized by direct DNA sequencing in either the alpha2 or alpha1 samples were used to validate this method. These samples were heterozygous or homozygous for each point mutation, or compound heterozygous for a deletion and the point mutation. Controls were amplified by gene specific primers designed by Primer3 software followed by digestion with SurveyorTM Nuclease. This endonuclease is a member of the CEL nuclease family of mismatch-specific nucleases derived from celery. It recognizes all insertions, deletions and base substitutions, and cleaves the mismatch of any heteroduplex DNA. After digestion, cleavage products are analyzed by agarose gel electrophoresis. The size of the digestion products indicates the location of the mutation, which is then confirmed and characterized by sequencing. All the 12 different nucleotide changes [α1 CD 14 TàC, α2 CD 104 TàG, α2 IVS II-55 TàG, α1 IVS II 141 TàC, α1 IVS I 117 GàT, α2 IVS I 1 GàA, Poly A (-AA), α1 CD 119 CàT, α2 IVS I 116, α2 CD 22 CàT, α2 CD 29 TàC, α2 +15 CàG] in the alpha globin genes were detected by this assay indicating a high sensitivity and specificity of this method. Mutation screening by SurveyorTM Nuclease is rapid (~ 5 hours), cost effective ($8/sample) and sensitive (100%). This assay in combination with the multiplex-PCR for screening the common alpha globin gene deletions will be the most comprehensive and economical approach for genetic diagnosis of alpha thalassaemia. Mismatch specific nucleases may have increasing application as a mutation detection strategy for human genetic diseases.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1595-1595
Author(s):  
Feras M. Hantash ◽  
Monica V. Gallivan ◽  
Mikula Mario ◽  
Starn Kelsey ◽  
Sheng-Biao Wang ◽  
...  

Abstract The alpha globin gene cluster contains two highly homologous alpha globin genes, HBA1 and HBA2, that code for identical proteins. Mutations in the alpha globin gene cluster are predominantly large deletions causing the loss of either one copy of the alpha-globin gene (e.g. -α3.7 and -α4.2 deletions) or both copies (e.g. --THAI, --FIL or --MED). A few large deletions encompassing the regulatory HS-40 region have also been described in alpha-thalassaemia patients. Point mutations and small base pair insertions or deletions have also been detected in HBA1 and HBA2 genes. Seven common large deletions in the alpha globin gene cluster are detected by a gapped-PCR assay. These common mutations and some other types of rearrangements can be detected by Southern blot, a laborious and time consuming method. However, these methods may not accurately identify the total number of copies of alpha globin like genes. We designed a single-tube alpha globin gene dosage assay (αGDA) using semi-quantitative fluorescent PCR (SQF PCR) for detecting the total number of alpha globin genes. Primers that amplify specific fragments from HBA1 and HBA2 genes, a fragment between the alpha globin pseudogenes, and three fragments flanking and including the HS-40 regulatory region were included in a single PCR reaction together with primers that amplify fragments from 3 different normalization genes. Using the αGDA, we were able to detect in patient samples varying copy numbers of alpha globin genes and to identify the nature of DNA rearrangements between HBA1 and HBA2. We also identified novel alpha globin conversion events that were verified by DNA sequencing. We also designed a complimentary comprehensive DNA sequencing assay to detect point mutations and small base pair insertions or deletions in the HBA1 and HBA2 genes. Using this method, and in combination with cation exchange HPLC and agarose gel electrophoresis, novel mutations in alpha globins were identified and submitted to the globin gene server, including Hb Linwood (α2 40 Lys>Gln), Hb Creve Coeur (α2 24 Tyr>Asp), and Hb Westborough (α-3.7 130 Ala>Val). The simplicity of αGDA will allow the replacement of the laborious Southern blot analysis to detect large deletions in the alpha globin gene cluster and to provide accurate information of total a-globin gene dosage, while the DNA sequencing assay will allow the detection of known and novel variants.


Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1846-1851 ◽  
Author(s):  
J Chang ◽  
RH Lu ◽  
SM Xu ◽  
J Meneses ◽  
K Chan ◽  
...  

We have disrupted the 5′ locus of the duplicated adult alpha-globin genes by gene targeting in the mouse embryonic stem cells and created mice with alpha-thalassemia syndromes. The heterozygous knockout mice (.alpha/alpha alpha) are asymptomatic like the silent carriers in humans whereas the homozygous knockout mice (.alpha/.alpha) show hemolytic anemia. Mice with three dysfunctional alpha-globin genes generated by breeding the 5′ alpha-globin knockouts (.alpha/alpha alpha) and the deletion type alpha-thalassemia mice (../alpha alpha) produce severe hemoglobin H disease and they die in utero. These results indicate that the 5′ alpha-globin gene is the predominant locus in mice, and suggest that it is even more dominant than its human homologue.


Blood ◽  
1979 ◽  
Vol 54 (6) ◽  
pp. 1407-1416 ◽  
Author(s):  
LE Lie-Injo ◽  
AM Dozy ◽  
YW Kan ◽  
M Lopes ◽  
D Todd

Abstract Two Chinese patients with HbQ-alpha 2 74 Asp replaced by His beta 2- alpha-thalassemia, one HbQ-alpha 2 74 or 75 Asp replaced by His beta 2 carrier, and one HbG-alpha 2 30 Glu replaced by Gln beta 2 carrier were studied to determine the number of alpha-globin genes in their chromosomes. DNA was isolated from white blood cells and bone marrow cells and studied by liquid hybridization and by hybridization of DNA fragments obtained by restriction enzyme endonuclease digestion (Ecr to nitrocellulose filters. The liquid hybridization analysis showed that in HbQ-alpha 2 74 Asp replaced by His beta 2-alpha-thalassemia, as in HbH disease, only one-fourth of the usual number of alpha-globin genes is present. Hybridization patterns of DNA restriction enzyme fragments showed that in HbQ-alpha 2 74 Asp replaced by His beta 2-alpha- thalassemia one chromosome has both alpha-globin genes deleted and the other chromosome, which carries the alpha-mutant gene, has one alpha- globin gene deleted. Our results show that the HbQ-alpha 74 Asp replaced by His structural gene is located adjacent to a deleted alpha- globin gene, whereas the alpha-globin gene adjacent to HbG-alpha 30 Glu replaced by Gln gene is not deleted.


Blood ◽  
1983 ◽  
Vol 62 (1) ◽  
pp. 226-229 ◽  
Author(s):  
MA Melis ◽  
M Pirastu ◽  
R Galanello ◽  
M Furbetta ◽  
T Tuveri ◽  
...  

In this study, we carried out restriction endonuclease mapping in order to characterize the alpha-globin genotype of 10 Sardinian beta 0- thalassemia heterozygotes, all of whom presented with normal red blood cell indices and increased HbA2 levels. In 8 of these subjects, we found the deletion of two alpha-globin genes (-alpha/-alpha), and in the remaining two the deletion of a single alpha-globin gene (- alpha/alpha alpha). In three of these carriers with the (-alpha/-alpha) alpha-globin genotype and in one with the (-alpha/alpha alpha) genotype, we also found the glucose-6-phosphate dehydrogenase (G6PD) defect of the Mediterranean type. On the basis of these findings, we may conclude that the interaction of heterozygous beta 0-thalassemia with alpha-thalassemia, due to the deletion of either one or two alpha- globin genes, may lead to the production of red blood cells with normal indices. The association of the G6PD defect with this thalassemia gene complex may eventually contribute to this effect. We suggest, therefore, that screening programs for heterozygous beta-thalassemia in populations where alpha-thalassemia is also prevalent, should incorporate the determination of HbA2 in the first set of tests.


Blood ◽  
1990 ◽  
Vol 76 (1) ◽  
pp. 221-227
Author(s):  
CS Hatton ◽  
AO Wilkie ◽  
HC Drysdale ◽  
WG Wood ◽  
MA Vickers ◽  
...  

We describe a family in which alpha-thalassemia occurs in association with a deletion of 62 kilobases from a region upstream of the alpha globin genes. DNA sequence analysis has shown that the transcription units of both alpha genes downstream of this deletion are normal. Nevertheless, they fail to direct alpha globin synthesis in an interspecific hybrid containing the abnormal (alpha alpha)RA chromosome. It seems probable that previously unidentified positive regulatory sequences analogous to those detected in a corresponding position of the human beta globin cluster are removed by this deletion.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 6-7
Author(s):  
Christopher C Denton ◽  
Payal Shah ◽  
Silvie Suriany ◽  
Honglei Liu ◽  
Wanwara Thuptimdang ◽  
...  

Introduction Absence of alpha globin genes has long been known to influence the physiology of sickle cell disease (SCD). Individuals with SCD who are missing one or two alpha globin genes have decreased rates of cerebral vasculopathy, stroke, acute chest syndrome, and leg ulcers (Bernaudin, Blood 2008; Flanagan, Blood 2011; Nolan, Br J Haematol 2006). Although there is laboratory evidence of decreased hemolytic rate in these patients (Higgs, N Engl J Med 1982), the mechanism for their improved clinical outcomes has not been identified. Recently, the alpha globin protein has been shown to be present in the endothelial wall of human arterioles, where it modulates nitric oxide (NO) scavenging during vasoconstriction (Straub, Nature 2012). In mice, pharmacological inhibition of alpha globin leads to increased endothelial NO activity, independently of NO production, and results in increased blood perfusion, reduced systemic hypertension, and increased pulmonary artery vasodilation (Keller, Hypertension 2016; Alvarez, Am J Respir Cell Mol Biol 2017). The relationship between absence of alpha globin and arterial vasodilation, and the role of alpha globin in NO-mediated vascular signaling are potential mechanisms that could explain the beneficial effect of missing alpha globin genes in SCD. Using alpha thalassemia as a naturally occurring human model of alpha globin gene knockout, we hypothesized that loss of alpha globin genes leads to improvement in microvascular blood flow in thalassemia trait subjects without hemolysis. Methods Alpha thalassemia trait subjects missing one or two alpha globin genes, and healthy controls were recruited to the study, which was approved by the Children's Hospital Los Angeles Institutional Review Board. Blood samples were obtained from all subjects to test for hemoglobin, mean corpuscular volume (MCV), reticulocyte count, plasma hemoglobin, lactate dehydrogenase, and alpha globin genotype. We assessed flow-mediated dilation (FMD) of the brachial artery following distal forearm occlusion (Detterich, Blood 2015) simultaneously with laser Doppler flowmetry (LDF) and photoplethysmography (PPG) in the fingertip. We also measured the increase in microvascular perfusion with a thermal stimulus. The maximal change in vascular perfusion after provocation indicates vasodilatory capacity. Statistical analysis was performed in JMP® version 14 (SAS Institute Inc., USA). Results Twenty-seven subjects were enrolled, including 12 controls (4 alpha globin genes), 10 patients with 3 alpha globin genes and 5 with 2. The mean MCV was lower in subjects missing alpha globin genes than in controls (p=0.0099). Importantly, hemoglobin levels and markers of hemolysis were normal in both groups. There was no detectable difference in FMD between individuals missing one and two alpha globin genes; thus, these groups were combined and labeled as alpha trait for further analyses. FMD was significantly higher in alpha trait subjects after adjusting for age (Figure 1, p=0.0357). Missing alpha globin genes had no effect on microvascular flow by LDF or PPG (data not shown). Discussion FMD is an established and specific predictor of NO bioavailability (Thijssen, Am J Physiol Heart Circ Physiol 2011), and, in addition to shear-mediated NO circulation in conduit vessels, it reflects the sum of flow in multiple arteriolar networks downstream of the conduit artery. Using this method, a difference in endothelial function between control and alpha thalassemia trait was easily detected (Figure 1). Because endothelial alpha globin is present in arterioles rather than conduit vessels (Butcher, Free Radic Biol Med 2014), we measured microvascular flow in a 1-mm3 volume in the skin using a laser Doppler sensor, and in the fingertip by PPG, but were unable to detect an effect of alpha trait. As none of the subjects had anemia or evidence of hemolysis, the significantly increased FMD associated with loss of alpha globin genes is most likely due to increased NO as a result of decreased scavenging by alpha globin. The finding reported here that lower alpha globin gene number is associated with increased NO-related perfusion in humans may explain the beneficial effect of alpha thalassemia trait in SCD and suggests that the presence of alpha thalassemia trait may also play a role in other types of vascular disease. Disclosures Wood: BiomedInformatics: Consultancy; Imago Biosciences: Consultancy; BluebirdBio: Consultancy; Celgene: Consultancy; WorldcareClinical: Consultancy; Philips Medical Systems: Research Funding. Coates:apo pharma (Chiesi Pharma): Consultancy, Honoraria; Sangamo: Honoraria, Membership on an entity's Board of Directors or advisory committees; Agios pharma: Consultancy, Honoraria; Vifor Pharma: Consultancy, Honoraria; Celgene, BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Bluebird Pharma: Honoraria, Membership on an entity's Board of Directors or advisory committees.


Blood ◽  
1991 ◽  
Vol 78 (10) ◽  
pp. 2740-2746 ◽  
Author(s):  
G Lacerra ◽  
G Fioretti ◽  
M De Angioletti ◽  
L Pagano ◽  
E Guarino ◽  
...  

Abstract A novel 5.3-kb deletion of the alpha-globin gene cluster was observed in a family from Naples, Southern Italy. It removes the 5′ end of the alpha 2-globin gene, causing an alpha (+)-thalassemia defect. Because of the presence of the residual 3′ end of the alpha 2-globin gene, we indicated this new haplotype with the symbol (alpha)alpha 5.3. The 5′ breakpoint, the first to be reported in the intergene region of the psi alpha 2- and psi alpha 1-globin genes, is located 822 bp upstream of the cap site of the psi alpha 1-gene and about 150 bp upstream of a 300- nt Alu family member. The 3′ breakpoint is located in the IVS-1 nt 58 of the alpha 2-globin gene. The 5.3-kb deleted fragment shows particular characteristics: it contains four Alu sequences having long regions 80% complementary and the 5′-GGCC-3′ short repeat at both ends. The sequences spanning across the breakpoints on the same strand and containing this repeat on their 3′ and 5′ ends, respectively, are 17 of 25 base complementary. These particular features led us to assume the formation of a multistem-loop due to the intrastrand interaction between the complementary regions as intermediate to the deletion. The unusual localization of the 5′ breakpoint suggests that even the intergene region of the psi alpha 2- and psi alpha 1-globin genes may function as a deletion target.


Blood ◽  
1987 ◽  
Vol 69 (1) ◽  
pp. 341-344 ◽  
Author(s):  
GJ Dover ◽  
VT Chang ◽  
SH Boyer ◽  
GR Serjeant ◽  
S Antonarakis ◽  
...  

Fetal hemoglobin (HbF) levels vary widely among individuals with sickle cell anemia (SS). Previous studies have suggested that HbF levels in SS individuals with alpha-thalassemia (two or three functional alpha- globin genes) are lower than HbF levels in SS individuals with four normal alpha-globin genes. Using immunocytochemical techniques, we studied F cell production as measured by % F reticulocytes, the amount of HbF per F cell, and the preferential survival of F cells versus non- F cells in 51 subjects with four alpha genes, 32 subjects with three alpha genes, and 18 subjects with two alpha genes. Comparison between alpha-globin gene groups was performed for the total sample as well as for a subset of 82 individuals who had replicate samples and a further subset of 39 age-matched individuals. %HbF levels were 6.8, 4.9, and 4.5 percent for the total four-, three-, and two-alpha-globin-gene groups, respectively. The percentage of F reticulocytes, percentage HbF per F cell, and the enrichment ratio (% F cell/% F reticulocytes) did not change significantly with alpha-globin gene number. Moreover, no correlation existed between alpha-globin gene number and the absolute number of F cells in any group studied. However, there was a strong inverse correlation (r = -0.407, P = .0001) between non-F cell levels (1.7 +/- 2, 2.2 +/- 5, 3.0 +/- 1.0 X 10(12)/L) and decreasing alpha- globin gene number. These data suggest that falling HbF levels among SS individuals with lessened numbers of alpha-globin genes reflect prolonged survival of non-F cells and are not due to intrinsic differences in F cell production or in the amount of HbF per F cell. The improved survival of non-F cells in SS alpha-thalassemia is presumed to be due to the lower MCHC observed in such individuals.


Blood ◽  
1987 ◽  
Vol 69 (1) ◽  
pp. 341-344 ◽  
Author(s):  
GJ Dover ◽  
VT Chang ◽  
SH Boyer ◽  
GR Serjeant ◽  
S Antonarakis ◽  
...  

Abstract Fetal hemoglobin (HbF) levels vary widely among individuals with sickle cell anemia (SS). Previous studies have suggested that HbF levels in SS individuals with alpha-thalassemia (two or three functional alpha- globin genes) are lower than HbF levels in SS individuals with four normal alpha-globin genes. Using immunocytochemical techniques, we studied F cell production as measured by % F reticulocytes, the amount of HbF per F cell, and the preferential survival of F cells versus non- F cells in 51 subjects with four alpha genes, 32 subjects with three alpha genes, and 18 subjects with two alpha genes. Comparison between alpha-globin gene groups was performed for the total sample as well as for a subset of 82 individuals who had replicate samples and a further subset of 39 age-matched individuals. %HbF levels were 6.8, 4.9, and 4.5 percent for the total four-, three-, and two-alpha-globin-gene groups, respectively. The percentage of F reticulocytes, percentage HbF per F cell, and the enrichment ratio (% F cell/% F reticulocytes) did not change significantly with alpha-globin gene number. Moreover, no correlation existed between alpha-globin gene number and the absolute number of F cells in any group studied. However, there was a strong inverse correlation (r = -0.407, P = .0001) between non-F cell levels (1.7 +/- 2, 2.2 +/- 5, 3.0 +/- 1.0 X 10(12)/L) and decreasing alpha- globin gene number. These data suggest that falling HbF levels among SS individuals with lessened numbers of alpha-globin genes reflect prolonged survival of non-F cells and are not due to intrinsic differences in F cell production or in the amount of HbF per F cell. The improved survival of non-F cells in SS alpha-thalassemia is presumed to be due to the lower MCHC observed in such individuals.


Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1846-1851 ◽  
Author(s):  
J Chang ◽  
RH Lu ◽  
SM Xu ◽  
J Meneses ◽  
K Chan ◽  
...  

Abstract We have disrupted the 5′ locus of the duplicated adult alpha-globin genes by gene targeting in the mouse embryonic stem cells and created mice with alpha-thalassemia syndromes. The heterozygous knockout mice (.alpha/alpha alpha) are asymptomatic like the silent carriers in humans whereas the homozygous knockout mice (.alpha/.alpha) show hemolytic anemia. Mice with three dysfunctional alpha-globin genes generated by breeding the 5′ alpha-globin knockouts (.alpha/alpha alpha) and the deletion type alpha-thalassemia mice (../alpha alpha) produce severe hemoglobin H disease and they die in utero. These results indicate that the 5′ alpha-globin gene is the predominant locus in mice, and suggest that it is even more dominant than its human homologue.


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