Applications of DNA fingerprinting in pediatric practice

Pediatric cases have played historic and precedent-setting roles in DNA forensics. DNA fingerprinting is a powerful tool for the pediatrician in cases of physical and sexual abuse and when issues arise regarding identification and familial relationships. If this technology is to be utilized effectively, the physician must know how to collect and document specimens. The pediatrician needs to be cautious in making referrals for commercial DNA banking. Whereas well-maintained and protected DNA repositories can be extremely valuable when there are medical and other appropriate indications, there are very real concerns about commercial DNA banking solely for purposes of identification. Pediatricians should recognize that this technology can be applied in novel but important new ways in their practices. For example, at the first indication of a possible mix-up of babies in the nursery, this should be acknowledged and rapidly resolved through DNA profiling of the parents and the neonates.

Genotypic confirmation from the original dried blood specimens in a neonatal hemoglobinopathy screening program

Dried blood spots are used for newborn screening because of ease of sample collection, handling, and shipment. DNA is stable and accessible in the filter paper matrix. Genotypic confirmation using initial specimens is demonstrated for a regional screening program. Seventy-five blinded samples underwent DNA analysis after Hb electrophoresis. DNA was microextracted from a 1/2-inch semicircle (25 microL whole blood equivalent), amplified, and analyzed by four different methods. Direct amplification without microextraction and automated sequencing from microextracted DNA also was performed. All four analyses agreed for the A and S alleles in 70 of 75 specimens. Three disagreements were clarified by the other semicircle from the original sample: two were due to polymerase chain reaction contamination and one to contamination of one of four analytical tests. Two would have required analysis of a second specimen, one because of polymerase chain reaction failure and the second because the patient had S/beta-thalassemia. Direct amplification without microextraction was successful in an additional 77 of 78 specimens for analysis of the A, S, C, and E alleles. Automated direct sequencing from microextracted DNA was demonstrated for the A, S, and C alleles. Analysis of microextracted DNA from dried blood specimens for A and S alleles reduced the need for and costs of obtaining a second specimen for confirmation by 97%. Direct amplification without microextraction for analysis of A, S, and C alleles permits additional reduction in personnel time and costs. We have demonstrated that microextracted DNA is amenable to automated sequencing after asymmetric polymerase chain reaction. Direct genotypic confirmation can facilitate diagnosis and initiation of medical intervention.

Developmental expression of hexokinase 1 in the rat

Hexokinase 1 (HK1) activity varies in a developmental stage- and tissue-specific manner and is a key step in glucose homeostasis and energy metabolism. We conducted studies to determine if HK1 expression is regulated at the transcriptional level. Expression of HK1 was examined in selected pre- and postnatal rat tissues using Northern blot analyses and RNAase protection assays. We found that brain and kidney exhibited significantly higher expression than heart, lung, spleen and skeletal muscle. Brain HK1 expression was constant prenatally, peaked at 7 days of age and reached a constant level after weaning. In kidney, HK1 expression was essentially constant or perhaps gradually decreased after weaning. HK1 transcription in heart, skeletal muscle and liver was higher during fetal stages than postnatally. Lung expression was essentially constant except in the adult. HK1 mRNA levels were compared to phosphoglycerate kinase (PGK) mRNA. PGK steady state mRNA levels were relatively constant in all tissues and developmental stages, except in skeletal muscle where there was a postnatal rise. The developmental profiles of HK1 and PGK mRNA expression are not consistent with enzyme activity measurements in all the tissues examined. We conclude that regulation of HK1 expression involves both transcriptional and posttranscriptional mechanisms that are tissue and stage specific.

Rapid mapping of Escherichia coli::Tn5 insertion mutations by REP-Tn5 PCR

We describe a novel method to map chromosomal Escherichia coli::Tn5 insertion mutations rapidly. This method utilizes the ends of Tn5 and the E. coli REP sequence as primer binding sites for the polymerase chain reaction (PCR). The unique E. coli chromosomal sequence located between these primer binding sites is amplified by PCR and used as a probe to identify the recombinant clones from the Kohara phage ordered E. coli miniset bank that contains the Tn5 mutated loci. We used this approach to map two Tn5 insertion mutations previously identified by their effect on glycerol metabolism. The insertion mutations mapped to glpD, the aerobic sn-glycerol-3-phosphate dehydrogenase gene. Phenotypic analysis of the mutant strains revealed one with partial GlpD activity, suggesting transposon-mediated alteration of promoter activity. This mapping method should be applicable to the rapid physical mapping of any insertion mutation in the E. coli chromosome.

Targeting of hexokinase 1 to liver and hepatoma mitochondria

The proportion of hexokinase (HK; EC 2.7.1.1) isozyme 1 (HK1) that is bound to the outer mitochondrial membrane is tissue specific and developmentally regulated. HK activity is known to be markedly elevated in many cancer cells and a significant fraction is mitochondrial bound. This study examined the role of the 15-amino acid N-terminal domain of HK1 in binding to liver and hepatoma mitochondria. A chimeric reporter construct, pCMVHKCAT, encoding this HK1 domain coupled to the chloramphenicol acetyltransferase (CAT) gene was electroporated into mouse Hepa 1-6 hepatoma cells. After digitonin treatment, cell fractions were assayed for HK, lactate dehydrogenase, and CAT activities. Digitonin (75 micrograms/mg of protein) caused cytosolic leak but 70% of HK remained with the pellet. HKCAT, like HK, remained predominantly with the pellet; CAT form the control, pCMVCAT, remained mostly unbound. Binding of membrane-free cell extracts to rat liver mitochondria in vitro showed 91% of the HKCAT bound, whereas only 12% of CAT bound. Specificity of HKCAT binding to mitochondria was demonstrated by competition of HK1 for HKCAT binding sites on rat liver mitochondria as well as by blockage of HKCAT binding by N,N'-dicyclohexylcarbodiimide, which covalently binds to porin and blocks HK1 binding. Deletional mutant constructs of HKCAT showed reduced binding with increasing deletion size. In summary, these studies demonstrate that the 15-amino acid N-terminal domain of HK1 is necessary and sufficient to confer mitochondrial binding properties to CAT and that there is specificity for this binding to the mitochondria.

Mammalian hexokinase 1: evolutionary conservation and structure to function analysis

We have amplified and sequenced the complete coding region of bovine hexokinase isoenzyme 1 (HK1) from brain RNA with PCR primers selected for sequence conservation. The sequence information was analyzed to evaluate the evolutionary and structure-function relationships among the mammalian and yeast HK isoenzymes. Structure to function analysis identified an unduplicated, invariant N-terminal domain involved in HK1 outer mitochondrial membrane targeting, as well as putative carbohydrate and nucleotide-binding sites in the regulatory and catalytic halves of HK1 essential to enzyme function. The ATP-binding site in the catalytic half of the HK1 protein resembles nucleotide-binding regions from protein kinases, with the single amino acid replacement (lysine to glutamate) in the ATP-binding site of the amino half explaining the loss of HK1 catalytic function in the regulatory domain. Sequence comparisons suggest that the 50-kDa mammalian and yeast glucokinases arose separately in evolution. In addition to providing valuable phylogenetic and structure-function insights, this work provides an efficient strategy for rapid cloning and sequencing of the coding regions for other HKs and related proteins.

San Luis Valley recombinant chromosome 8 and tetralogy of Fallot: a review of chromosome 8 anomalies and congenital heart disease

Tetralogy of Fallot, the most common cyanotic heart defect, has not been closely associated with a specific chromosome defect. The San Luis Valley Recombinant Chromosome 8 [SLV Rec(8)] syndrome is strongly associated with congenital heart disease, particularly tetralogy of Fallot. This article reviews SLV Rec(8) syndrome and other chromosome 8 aberrations to suggest locations for cardiogenic genes. SLV Rec(8) [rec(8),dup q,inv(8)(p23q22)] syndrome has been found in Hispanic families in the southwestern United States. Congenital heart disease is found in 93.3% of SLV Rec(8) individuals (n = 45), with tetralogy of Fallot constituting 40.5% of all lesions and conotruncal defects, 55.6%. These frequencies exceed the incidence of tetralogy of Fallot (10%) and conotruncal defects (20%) among all children with heart defects (P less than 0.003 for both). Review of patients with deletion 8p (n = 13) showed heart defects in 84.6% with 27.3% being conotruncal defects. Among duplication 8q patients (n = 20), 45% had heart defects with conotruncal defects constituting 44%. Neither group differed significantly from expected in its incidence of conotruncal defects. Among patients with mosaic trisomy 8 (n = 47), 12 had heart abnormalities including one conotruncal defect. Among 3 patients with other rec(8) chromosomes, one had a ventricular septal defect. The cause of heart defects in SLV Rec(8) cannot be assigned to either the deletion of 8p or the duplication of 8q. The lack of an association between other chromosome 8 abnormalities and tetralogy of Fallot suggests that genes at the SLV Rec(8) breakpoints or an interaction between genes on both arms of chromosome 8 are important.

Use of the polymerase chain reaction for physical mapping of Escherichia coli genes

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Prevalence of K329E mutation in medium-chain acyl-CoA dehydrogenase gene determined from Guthrie cards

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is an autosomal recessive disorder that has been associated with sudden infant death syndrome and a condition resembling Reye's syndrome. The point mutation K329E is thought to be the commonest mutation causing MCAD deficiency in caucasian patients. The prevalence of this mutation was determined by use of dried blood spots on Guthrie cards obtained during neonatal screening programmes. 12 carriers were identified among 479 newborn babies in Britain, 5 among 353 in Australia, and 5 among 536 in North America but none among 500 in Japan. Since presymptomatic diagnosis and appropriate dietary management can prevent life-threatening episodes in MCAD deficiency, population-based DNA screening for this potentially fatal disorder might be justified in countries with a high frequency of this mutation.

Screening for cystic fibrosis: feasibility of molecular genetic analysis of dried blood specimens

Direct genotypic analysis for the common Caucasian cystic fibrosis mutation (delta F508) was performed using dried blood specimens in a filter paper matrix (neonatal screening blotter). DNA was obtained from dried and liquid blood samples, amplified, and analyzed by polyacrylamide gel electrophoresis. Additionally, intact 4-mm-diameter punched discs from blotters containing dried blood specimen were used in the amplification reactions and analyzed by electrophoresis. The results agreed completely between these three sample types, demonstrating the feasibility of molecular genetic confirmation of the delta F508 mutation from the neonatal screening blotter among those with positive CF screening results. Such a program could reduce follow-up testing by at least 50% in a CF newborn screening program and would identify immediately those families who would benefit from carrier detection for the delta F508 allele.

Isodicentric X chromosome in a patient with Turner syndrome--implications for localization of the X-inactivation center

Cytogenetic analyses have previously shown that the region Xq11.2-q21 is retained in all structurally abnormal X chromosomes. From these observations the conclusion has been drawn that this "critical region" on the proximal long arm of the X chromosome contains the locus controlling X-inactivation. Structurally abnormal X chromosomes without the X-inactivation center would allow nullisomy, disomy, or trisomy for genes on the X chromosome, and this condition is presumed nonviable. We studied a 28-year-old woman with primary amenorrhea and features of Turner syndrome who had an unusual isodicentric chromosome of the short arm of X. This patient provided us with the opportunity to more closely define the location of the X-inactivation center. High resolution chromosome analysis showed a 46,X,idic(X)(pter----q13.2::q13.2----pter) chromosome pattern in 94% of her cells and a 45,X complement in 6%. Replication studies showed this derivative X chromosome to be late-replicating (inactive) in all cells analyzed. DNA analysis confirmed the breakpoint of the isodicentric chromosome to be proximal to PGK1. Based on these results, the locus for the X-inactivation center can be refined to be within Xq11.2-q13.2.

Protein kinase activity of rat brain hexokinase

Hexokinase 1 (HK1) purified from rat brain exhibits protein kinase activity, including autophosphorylation and phosphorylation of histone H2A. This protein kinase activity is observed only in the absence of the HK1 carbohydrate substrate, glucose. Analysis of the ATP-binding domains of the mammalian HK1 protein sequences shows significant homology with other mammalian protein kinases.

Porin interaction with hexokinase and glycerol kinase: metabolic microcompartmentation at the outer mitochondrial membrane

Porin is the pore-forming protein involved in the movement of adenine nucleotides across the outer mitochondrial membrane (OMM). Hexokinase and glycerol kinase interact with porin on the outer surface of the OMM in a manner which provides these enzymes with preferred access to the ATP generated in the mitochondrion. We review recent evidence which permits refinement of our knowledge of these proteins and their interactions at the OMM. The involvement of this system in metabolic microcompartmentation is discussed, as well as possible pathological consequences of its disruption in malignancy and genetic deficiencies of hexokinase, glycerol kinase, and porin.

Genetic screening for the next decade: application of present and new technologies

Molecular genetic technology is diffusing from the research laboratory to the clinical laboratory, where it has already begun to influence prenatal diagnosis and counseling. In the very near future, this technology will be applied more generally, using population-based screening strategies. Pilot programs are beginning to evaluate the technical feasibility and efficacy of recombinant DNA techniques for newborn screening follow-up. DNA-based population screening is being considered for heterozygous carriers of an autosomal recessive disorder such as cystic fibrosis in order to identify carrier couples at risk of having an affected child. We will review the current DNA methodologies in the context of three genetic disorders: sickle-cell disease, Duchenne muscular dystrophy, and cystic fibrosis. We will then consider the requirements for implementation of these new technologies. We will conclude that implementation will require two key factors: machines and people. Machines are required to automate molecular genetic procedures, which are currently personnel-intensive, so that the expense can be reduced and the procedures made more cost-effective. The people who are required are health professionals knowledgeable in the clinical aspects of the target disorders, as well as in the DNA laboratory testing. These professionals will be able to facilitate sample acquisition and information exchange among the laboratory, the primary health care provider, and the families requesting consultation.

Neuropsychology of early-treated phenylketonuria: specific executive function deficits

This study explored the hypothesis that children with early-treated phenylketonuria (PKU) are selectively impaired on executive function measures, even when still on diet. The rationale for this hypothesis is that even mild elevations in phenylalanine (Phe) can lead to lower central levels of biogenic amines, including dopamine (DA). We hypothesize that this mild DA depletion causes subtle prefrontal dysfunction, which in turn affects executive functions such as set maintenance, planning, and organized search. 11 preschool early-treated PKU children (M age = 4.64) and a sample of age- and IQ-matched unaffected peers (n = 11) were evaluated on a battery of executive function (EF) measures. In addition, a "non-executive function" task, recognition memory, was administered to all subjects. Group comparisons demonstrated that PKU children were significantly impaired on an executive function composite score; there were no group differences, however, in recognition memory. These results supported the hypothesized specific deficit in executive function. Furthermore, within the PKU group the executive function composite score was significantly negatively correlated with concurrent phenylalanine levels, even after controlling for the correlation between IQ and executive function skills. This second finding provides support for the proposed biochemical mechanism underlying the specific cognitive deficits.

Deletion mapping of Aland Island eye disease to Xp21 between DXS67 (B24) and Duchenne muscular dystrophy

Aland Island Eye Disease (AIED) is an X-linked form of ocular hypopigmentation--also known as Forsius-Eriksson, or type 2, ocular albinism--in which affected males demonstrate subnormal visual acuity, protanomalous red-green colorblindness, axial myopia, astigmatism, hypoplasia of the fovea, and hypopigmentation of the fundus. A patient has previously been described who, in addition to AIED, manifested a contiguous gene syndrome which included congenital adrenal hypoplasia (AHC), glycerol kinase deficiency (GKD), and Duchenne muscular dystrophy (DMD). In the present paper report we report the molecular genetic analysis of his deletion. Initially, multiplex polymerase-chain-reaction amplification was used to screen for a DMD-locus deletion which was then further characterized, using DMD cDNA and genomic probes, via Southern blot analysis. The deletion includes the region encompassed by probes C7 (DXS28) and DMD cDNA 8. Probes B24 (DXS67) and DMD cDNA 5b-7 show normal hybridization patterns and appear to flank the deletion, while the DMD cDNA 8 detects a junction fragment. Molecular genetic techniques have mapped the deletion in this patient to the subbands Xp21.3-21.2, between DXS67 and DMD.

Mutational analysis of the Escherichia coli glpFK region with Tn5 mutagenesis and the polymerase chain reaction

Transposon Tn5 mutagenesis of the Escherichia coli chromosome was used to isolate 21 independent insertion mutations conferring an altered colony color phenotype on MacConkey-glycerol plates. The polymerase chain reaction was used to map 16 of these Tn5 insertions within the glpFK region at 88 min. The most polar Tn5 insertion was shown by nucleotide sequencing to be in the proposed glpF open reading frame. The data suggest that the glpF and glpK genes are in an operon with a bent DNA segment (BENT-6) involved in transcriptional regulation of this operon.

DXS28 (C7) maps centromeric to DXS68 (L1-4) and DXS67 (B24) by deletion analysis

Complex glycerol kinase deficiency (CGKD) is a contiguous gene syndrome consisting of glycerol kinase deficiency together with Duchenne muscular dystrophy (DMD), congenital adrenal hypoplasia, and/or Aland Island eye disease. Deletion mapping of genomic DNA from patients with CGKD was carried out and allowed definitive ordering of loci DXS28 (C7), DXS68 (L1-4), and DXS67 (B24). Most reports have placed DXS68 centromeric to DXS28 and DXS67 on the basis of the initial mapping of the Iowa patient 3, but others have presented evidence consistent with the placement of DXS28 telomeric to DXS68 and DXS67. Through the use of DNA from CGKD patients with a variety of genomic deletions, this controversy is resolved and the order Xcen...DMD-DXS28-DXS68-DXS67...pter is definitively demonstrated.

Overo lethal white foal syndrome: equine model of aganglionic megacolon (Hirschsprung disease)

The lethal white foal syndrome (LWFS) is a congenital abnormality of overo spotted horses which is a model for human aganglionic megacolon or Hirschsprung disease. Foals with LWFS have an all white, or nearly all white, coat. They also present clinically with an intestinal obstruction that proves fatal within the first few days of life. The LWFS involves both melanocytes and intestinal ganglion cells, and appears to result from a genetic defect involving neural crest cells. This report describes pathologic studies of two recent cases of LWFS. Two different hypothetical models of inheritance of LWFS are presented and discussed.