The T----C substitution at nucleotide + 1570 of the beta-globin gene is a polymorphism.
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Globins↗
Biomedical subjects
J S Waye
Publications and source records attributed to J S Waye.
Diagnosis of arylsulfatase A deficiency.
Metachromatic leukodystrophy (MLD) is a neurologically devastating autosomal recessive disorder in humans associated with deficient arylsulfatase A activity. However, clinically normal individuals described as being pseudo-arylsulfatase-A deficient also demonstrate the same deficiency. Genotypically, they may be homozygous for the pseudodeficiency mutation (associated with 2 A-->G transitions in the cDNA of arylsulfatase A) or heterozygous with one pseudodeficiency and one MLD allele. Using as examples 2 families in which the pseudo deficiency condition occurs either independently or together with MLD, we demonstrate the utility of a proposed diagnostic protocol to provide complete genotype identification of individuals suffering from arylsulfatase A deficiency. Patient fibroblasts are extracted for DNA and a cytoplasmic fraction, which is used for arylsulfatase A enzyme assay. This will identify an arylsulfatase A-deficient group, which is further analyzed electrophoretically. Cells from the clinically affected patients with MLD are completely deficient in arylsulfatase A activity, whereas those from the pseudodeficient individuals demonstrate a characteristic residual arylsulfatase A activity detectable only after electrophoresis. Within this pseudodeficient group, gene amplification of DNA specific for the A-->G mutations will distinguish between those who are homozygous for the pseudodeficiency allele and those who are compound heterozygous for the pseudodeficiency and MLD alleles. This protocol of complete genotype identification requires only about 10(6) fibroblasts (1 x 100 mm dish) and 2 days to complete. Such variant-specific genotype identification increases accuracy and prognostic value of the diagnosis. It will likely become the preferred choice for diagnosis of genetic disease in the future as more variant-specific mutations are identified at the molecular level.
Alleles↗
Human embryonic zeta-globin chain expression in deletional alpha-thalassemias.
zeta-Globin chain expression in carriers of a number of deletional alpha-thalassemias is investigated by radioimmunoassay. In a few cases, zeta-globin mRNAs are also studied. zeta-Globin chains are detected in (--SEA/), (--MED/), and (--SPAN/) deletions, but not in six other deletional mutations. These results suggest that the DNA element capable of suppressing zeta-globin expression in adult erythroid cells is present within the (--SPAN/) deletion, while the DNA fragment between the 5' breakpoints of the (--SA/) and the (--SEA/) deletions may contain sequences necessary for augmenting zeta-globin expression in adult erythroid cells. Furthermore, zeta-globin chains are shown by an immunocytologic technique to be present in all circulating erythrocytes in carriers of the (--SEA/) and (--MED/) deletions. This simple immunocytologic test is highly sensitive and specific to detect adult carriers of either the (--SEA/) or (--MED/) deletions, and can be used for the detection of couples at risk of pregnancies involving fetuses with homozygous alpha-thalassemia.
Chromosome Deletion↗
Two novel beta-thalassemia mutations in the 5' and 3' noncoding regions of the beta-globin gene.
Two novel beta-thalassemia mutations are described. The first mutation, found in an Italian family, is a G----A substitution in nucleotide (nt) +22 relative to the beta-globin gene Cap site. This mutation creates a cryptic ATG initiation codon, the utilization of which for translation would result in premature termination 36 bp 3' downstream. The second mutation, found in an Irish family, is a T----C substitution in nt +1570, or 12 bp 5' upstream of the AATAAA polyadenylation signal in the 3' noncoding region. It is postulated that this mutation leads to destabilization of the encoded beta-globin mRNA.
Adult↗
Clinical course and molecular characterization of a compound heterozygote for sickle hemoglobin and hemoglobin Kenya.
We describe a 25-year-old black woman who presented with a long history of anemia requiring transfusions during childhood and adolescence. Molecular analysis revealed her to be a compound heterozygote for the sickle mutation and the approximately 22.7 kb deletion associated with hemoglobin Kenya. This patient's clinical course was more severe than previously reported for the Hb S/Hb Kenya genotype, a probable consequence of concomitant iron deficiency.
Adult↗
Identification of an extensive zeta-alpha globin gene deletion in a Chinese individual.
We describe a novel alpha-thalassaemia-1 deletion that removes the entire zeta-alpha globin gene cluster. A Chinese couple were referred for counselling after two consecutive pregnancies ended with fetal hydrops. Gene mapping was used to demonstrate that the mother is heterozygous for the South-east Asia alpha-thalassaemia-1 deletion (zeta zeta zeta alpha alpha/zeta zeta--SEA), while the father carries an alpha-thalassaemia-1 deletion of more than 100 kilobases (zeta zeta alpha alpha/----). This newly discovered deletion extends for unknown distances 3' and 5' of the zeta-alpha globin gene cluster and has been designated (--HW).
Chromosome Deletion↗
High hemoglobin A2 beta 0-thalassemia due to a 532-basepair deletion of the 5' beta-globin gene region.
We identify and characterize a novel beta 0-thalassemia mutation that is associated with an unusually high level of hemoglobin (Hb) A2 in the heterozygote. This newly discovered mutation is caused by a 532-basepair deletion that extends from positions -454 to + 78 relative to the mRNA cap site of the beta-globin gene. The propositi are 9-month-old fraternal twins. One of the twins is a compound heterozygote for the deletion and Hb S, the other is a compound heterozygote for the deletion and Hb C.
Base Sequence↗
Hb S/beta zero-thalassemia due to the approximately 1.4-kb deletion is associated with a relatively mild phenotype.
We report a relatively mild phenotype associated with two siblings who are compound heterozygotes for Hb S and a beta zero-thalassemia mutation due to a approximately 1.4-kb deletion of the 5' region of the beta-globin gene. Each is found to have unusually high levels of Hb A2 and Hb F, accounting for more than 20% of the total hemoglobin. These may interfere with intracellular Hb S polymerization, thus leading to a mild clinical course.
Adult↗
Fixed-bin analysis for statistical evaluation of continuous distributions of allelic data from VNTR loci, for use in forensic comparisons.
The detection of DNA polymorphisms by RFLP analysis is having a major impact on identity testing in forensic science. At present, this approach is the best effort a forensic scientist can make to exclude an individual who has been falsely associated with an evidentiary sample found at a crime scene. When an analysis fails to exclude a suspect as a potential contributor of an evidentiary sample, a means should be provided to assess suitable weight to the putative match. Most important, the statistical analysis should not place undue weight on a genetic profile derived from an unknown sample that is attributed to an accused individual. The method must allow for limitations in conventional agarose-submarine-gel electrophoresis and Southern blotting procedure, limited sample population data, possible subpopulation differences, and potential sampling error. A conservative statistical method was developed based on arbitrarily defined fixed bins. This approach permits classification of continuous allelic data, provides for a simple and portable data-base system, and is unlikely to underestimate the frequency of occurrence of a set of alleles. This will help ensure that undue weight is not placed on a sample attributed to an accused individual.
Alleles↗
Sensitive and specific quantification of human genomic deoxyribonucleic acid (DNA) in forensic science specimens: casework examples.
We describe the forensic science application of a method for quantification of human genomic deoxyribonucleic acid (DNA). The two cases cited in this report involve DNA samples extracted from skin tissue and bloodstained clothing recovered from different crime scenes. High-molecular-weight DNA was recovered from both specimens, and the concentrations of these DNAs were estimated to be approximately 0.5 microgram/microL by ethidium bromide/agarose gel electrophoresis. Using the human-specific DNA probe p17H8 (locus D17Z1) to quantify the amount of human genomic DNA in these samples, it is shown that less than 1% of the DNA isolated from the skin tissue is of human origin and that the DNA isolated from the bloodstained clothing is effectively devoid of human DNA sequences. These case examples illustrate the need to quantify not only the total amount of DNA recovered from forensic casework material, but also the proportion of the DNA that is of human origin.
Adult↗
High hemoglobin A2 beta-thalassemia.
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Chromosome Mapping↗
Identification of complex DNA polymorphisms based on variable number of tandem repeats (VNTR) and restriction site polymorphism.
Restriction fragment length polymorphisms (RFLPs) of genomic DNA are generally attributable to base changes that create or abolish restriction endonuclease sites or to nucleotide sequence insertions or deletions that alter the distance separating two restriction sites. Minisatellite or variable number of tandem repeats (VNTR) markers are prominent examples of the latter type of polymorphism. In this report, we describe complex DNA polymorphisms that are due both to the presence of VNTRs as well as to altered restriction endonuclease sites. A strategy for identifying such polymorphisms and resolving their component allelic fragments is demonstrated.
Alleles↗
A case of 46,XX,r(X) (p1q1) diagnosed by in situ hybridization.
A small marker chromosome was identified as an X-derived ring chromosome by in situ hybridization with a biotinylated X-chromosome specific a-satellite DNA probe. This procedure clearly determined the chromosomal origin of the marker chromosome, which had been impossible to define by conventional cytogenetic techniques including high resolution banding.
Centromere↗
Hae III--a suitable restriction endonuclease for restriction fragment length polymorphism analysis of biological evidence samples.
Hae III has been selected by our laboratories as the restriction endonuclease of choice for restriction fragment length polymorphism analysis of forensic science samples. The enzyme is compatible with the D2S44 probe system and generates relatively small DNA fragments for that marker system. Similarly, Hae III is compatible with several other independent polymorphic loci, including D1S7, D4S139, D16S85, D17S74, D17S79, D14S13, and D20S15. Hae III is functional under a variety of adverse conditions for DNA digestion and is not affected by the methylation pattern in mammals. Finally, Hae III is a relatively inexpensive restriction endonuclease.
Base Sequence↗
Agarose gel electrophoresis of linear genomic DNA in the presence of ethidium bromide: band shifting and implications for forensic identity testing.
We demonstrate that agarose gel electrophoresis of linear duplex DNA in the presence of ethidium bromide has a marked effect on the mobility of genomic DNA fragments detected by Southern hybridization. Mobility shifts of greater than 6% of the actual molecular weight were detected when different amounts of the same DNA sample were analyzed in 1.0% agarose gels containing 0.5 micrograms ml-1 ethidium bromide. For forensic applications, shifts of this magnitude could complicate the task of comparing restriction fragment length polymorphism profiles and introduce a degree of uncertainty to allele frequency population databases.
DNA↗
Discussion of "Recent application of DNA analysis to issues of paternity".
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DNA↗
Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3.
The human alpha satellite DNA family, like many highly repeated satellite DNAs in eukaryotic genomes, is organized in distinct chromosome-specific subsets. As part of investigations into the molecular and evolutionary basis for the chromosome-specific nature of such subsets, we report the isolation and characterization of alpha satellite sequences specific for human chromosome 3. This subset is characterized by a predominant tandemly arranged approximately 2.9 kb higher-order repeat unit which, in turn, consists of 17 tandem diverged monomer repeat units of approximately 171 bp. Nucleotide sequence analysis reveals that the chromosome 3 higher-order repeat units are comprised, at least in part, of diverged dimeric (approximately 340 bp) sub-repeats and that this divergence accounts for the chromosome-specific behavior of this subset. Pulsed-field gel electrophoresis demonstrates that the chromosome 3 higher-order repeat units are localized in large domains, at least 1000 kb in length. Familial restriction fragment length polymorphisms associated with the satellite subset can be detected by pulsed-field gel electrophoresis and may facilitate molecular analysis of interchromosomal variation.
Base Sequence↗
Concerted evolution of alpha satellite DNA: evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates.
We investigated relationships among alpha satellite DNA families in the human, gorilla, chimpanzee, and orangutan genomes by filter hybridization with cloned probes which correspond to chromosome-specific alpha satellite DNAs from at least 12 different human chromosomes. These include representatives of both the dimer-based and pentamer-based subfamilies, the two major subfamilies of human alpha satellite. In addition, we evaluated several high-copy dimer-based probes isolated from gorilla genomic DNA. Under low stringency conditions, all human probes tested hybridized extensively with gorilla and chimpanzee alpha satellite sequences. However, only pentameric and other non-dimeric human alphoid probes hybridized with orangutan alpha satellite sequences; probes belonging to the dimer subfamily did not cross-hybridize detectably with orangutan DNA. Moreover, under high stringency conditions, each of the human probes hybridized extensively only with human genomic DNA; none of the probes cross-hybridized effectively with other primate DNAs. Dimer-based gorilla alpha satellite probes hybridized with human and chimpanzee, but not orangutan, sequences under low stringency hybridization conditions, yet were specific for gorilla DNA under high stringency conditions. These results indicate that the alpha satellite DNA family has evolved in a concerted manner, such that considerable sequence divergence is now evident among the alphoid sequences of closely related primate species.
Animals↗