Guthrie cards for detection of point mutations in phenylketonuria

A methodological strategy for PAH genotyping in populations with a marked molecular heterogeneity of hyperphenylalaninemia

The elucidation of the molecular basis of hyperphenylalaninemia in various world populations (PKU Consortium Database: http://www.mcgill/ca/pahdb/) has revealed a remarkable molecular heterogeneity at the locus encoding for phenylalanine hydroxylase. As a consequence, genotyping of HPA patients has prompted the establishment of an impressive number of mutatIon detection protocols. In spite of the large variety of methods proposed so far, no comprehensive strategy has been yet developed for the detection of PAH gene mutations. Therefore, new approaches, combining the advantages of individual methods are required, especially in populations with a high number of PAH gene mutations. In this study, we propose the use of Reverse Dot Blot Analysis within a general mutation protocol to simplify the genotyping of hyperphenylalaninemics in the very heterogeneous population of Sicily (Italy).

Detection of mtDNA deletion in Pearson syndrome by two independent PCR assays from Guthrie card

Pearson syndrome is a multisystem juvenile condition associated with deletions in the mitochondrial genome. The most common 4977 bp deletion of mitochondrial DNA (mtDNA) can mainly be detected in the patients' peripheral blood. Here we report a child with a clinically unclarified diagnosis where molecular genetic results proved Pearson syndrome from stored dried blood sample 6 months after the patient's death. PCR amplification around the breakpoint of the most common mtDNA deletion could detect the presence of mutated mtDNA. Another polymerase chain reaction (PCR) assay indicated the low level of wild type mtDNA in patients' blood. We believe that this case shows the importance of storing Guthrie card and the availability of detection of Pearson syndrome from dried blood sample.

Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports

A simple and rapid method for the analysis of genetic polymorphisms has been developed using allele-specific oligonucleotide arrays bound to glass supports. Allele-specific oligonucleotides are covalently immobilized on glass slides in arrays of 3 mm spots. Genomic DNA is amplified by PCR using one fluorescently tagged primer oligonucleotide and one biotinylated primer oligonucleotide. The two complementary DNA strands are separated, the fluorescently tagged strand is hybridized to the support-bound oligonucleotide array, and the hybridization pattern is detected by fluorescence scanning. Multiple polymorphisms present in the PCR product may be detected in parallel. The effect of spacer length, surface density and hybridization conditions were evaluated, as was the relative efficacy of hybridization with single or double-stranded PCR products. The utility of the method was demonstrated in the parallel analysis of 5 point mutations from exon 4 of the human tyrosinase gene.

Detection of human T-cell lymphotropic virus type 1 infection by the polymerase chain reaction using dried blood specimens on filter papers

A simple method for detection of proviral DNA sequences of human T-cell lymphotropic virus type 1 (HTLV-1) was developed using dried blood specimens on filter papers. The whole blood was blotted onto the Guthrie paper. After the blood has dried, the blotted paper was punched out into small discs. The discs were then boiled to prepare the template for PCR (filter paper-PCR method). The filter paper-PCR method detected even a single HTLV-1-infected cell in three discs. The sensitivity of the filter paper-PCR method was equivalent to that of the method in which DNA was extracted with phenol and used as the template for PCR (DNA extraction-PCR method). In addition, DNA in the blotted filter paper was still utilizable as the template after the storage at 25 degrees C for at least 7 wk. A total of 53 clinical specimens from 30 seropositive and 23 seronegative individuals who were screened by particle agglutination (PA) test were analysed for HTLV-1 DNA by both PCR methods. Of 30 PA-positive specimens, 28 were also positive for HTLV-1 antibody by Western blot (WB) analysis, but two were indeterminate. The twenty eight WB-positive and one of the two indeterminate specimens were positive for HTLV-1 proviral DNA by both PCR methods. Of 23 PA-negative specimens, 22 were negative for HTLV-1 proviral DNA by both PCR methods. However, one PA-negative specimen was positive by both PCR methods. This patient was a 16-mth-old infant who was born to an HTLV-1 carrier mother and fed thereafter without her breast milk. In comparison to DNA extraction-PCR method, the sensitivity and specificity of the filter paper-PCR method was 100%, respectively.

Universal community carrier screening for cystic fibrosis?

Approximately 5% of the Caucasian North European and North American populations are carriers of the gene defect causing cystic fibrosis (CF). Since the CF gene was isolated in 1989 and the common mutations identified, there has been debate as to whether community-wide screening for CF carriers should be offered. Pilot studies and new discussions are leading to a consensus that screening is now possible and will not lead to undue anxiety, but there is still no agreement as to cost, or how it will be used by those screening positive.

Differentiation of homozygous hemoglobin E from compound heterozygous hemoglobin E-beta O-thalassemia by hemoglobin E mutation analysis

OBJECTIVES

To facilitate the differential diagnosis of hemoglobin FE in newborn infants (homozygous hemoglobin E vs hemoglobin E-beta O-thalassemia).

METHODS

The beta-globin gene in DNA from infants found to have hemoglobin FE in the California newborn screening program was amplified by the polymerase chain reaction, and the product was digested with Mnl I, which fails to cut the product when the hemoglobin E mutation is present. When both amplified alleles fail to be cut, homozygous EE is diagnosed. If only one allele is cut, a beta-globin allele without the E mutation is present (non-E), which is most likely a gene with a beta O-thalassemia mutation.

RESULTS

Samples from 18 infants revealed an EE genotype, and from two samples a non-E/E genotype was determined. Clinical examination of these two patients confirmed a diagnosis of hemoglobin E-beta O-thalassemia. An independent clinical diagnosis agreed with DNA analysis for all 17 of the 20 infants for whom follow-up and family studies were available. The DNA results were obtained within a week, but the clinical diagnoses often could not be resolved unequivocally for months.

CONCLUSIONS

The direct analysis of patient DNA samples for the hemoglobin E mutation allowed rapid and accurate diagnosis in this sample of infants with hemoglobin FE on the newborn screen. This rapid discriminatory test should reduce cost and simplify the diagnostic approach for these patients, which currently consists of expensive and lengthy follow-up until clinical data and family studies result in a diagnosis.

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.

The application of PCR amplification and the polymorphic marker KM.19 to dried blood spots: comparison with deletion 508 for the confirmation of the neonatal screening test for cystic fibrosis

Cystic fibrosis (CF) screening by measurement of immunoreactive trypsin (IRT) lacks specificity: only 9% of hypertrypsinemic neonates have CF. We have studied retrospectively 114 hypertrypsinemic samples (including 37 CF) for KM.19 polymorphic DNA marker and made risk calculations. If the neonate is homozygous for KM.19 allele 2, the risk of CF rises to 55%; if homozygous for allele 1, the risk is very low (less than 1%) and if heterozygous, the risk is intermediate (4%). In a prospective study including 28,000 IRT tests, 76 neonates with IRT greater than 800 micrograms/L have been identified: 16 were homozygous for allele 2 (8 CF), 30 for allele 1 (1 CF), and 30 were heterozygotes (no CF). Deletion 508 was present in 10 neonates: 4 homozygotes (4 CF) and 6 heterozygotes (3 CF). Two CF did not carry any copy of deletion 508. We have studied 181 (presumably non-CF) neonates with IRT greater than 600 micrograms/L. The KM.19 genotypes distribution is significantly different from the one expected in the French population: homozygotes for allele 2 are more numerous. Furthermore, heterozygotes for deletion 508 are 1 in 15 (expected: 1 in 42). In conclusion, molecular biology in dried blood spots can enhance the specificity of CF neonatal screening, but IRT and genotype may not be independent.

Mapping of acute (type I) spinal muscular atrophy to chromosome 5q12-q14. The French Spinal Muscular Atrophy Investigators

Linkage analysis in twenty-five families with acute (type I) spinal muscular atrophy (SMA) showed that the mutant gene responsible for the disorder is tightly linked to the D5S39 locus. The mutation(s) causing the intermediate (type II) and juvenile chronic (type III) forms of SMA were also mapped to DNA marker D5S39 on chromosome 5 (5q12-q14). Thus, the three forms, which have been differentiated clinically on the basis of age of onset and clinical course, are most probably due to different mutations at a single locus on chromosome 5. Prenatal diagnosis of SMA type I will now be possible.

A consortium approach to molecular genetic services. Scottish Molecular Genetics Consortium

The four Scottish university medical genetics centres formed a consortium in 1985 to provide a DNA based service in prenatal diagnosis, carrier detection, and predictive testing for a range of Mendelian disorders. Each centre took sole responsibility for laboratory analyses of an assigned set of disorders, while families continued to be investigated and patients counselled within their own areas. DNA was extracted from relevant tissues in the centre most convenient to the family member and then dispatched to the appropriate laboratory for analysis. Results were interpreted and risks assessed by discussion between laboratory staff and the clinical geneticist in charge of the case. In the first three years of the consortium 92 prenatal diagnoses or exclusion tests were carried out, the majority being for cystic fibrosis (35), Duchenne muscular dystrophy (21), and Huntington's disease (11). Carrier testing was carried out in 271 X linked recessive disorders, the most common indications being Duchenne and Becker muscular dystrophies (198) and haemophilias A and B (48). Predictive testing was attempted in 41 consultants at risk for Huntington's disease, 37 at risk for myotonic dystrophy, and 32 at risk for developing adult polycystic kidney disease. The total of all carrier tests, including those for autosomal recessives, was 543. A consortium or supraregional approach to molecular genetics services has a number of advantages. Constituent laboratories need hold only those probes and enzymes relevant to their assigned disorders and can gain maximum experience with these systems. Scattered families may often be linked into single kinships, thus allowing rapid confirmation of diagnosis when an urgent request is made for a prenatal diagnosis.(ABSTRACT TRUNCATED AT 250 WORDS)

Heterogeneity of phenylketonuria at the clinical, protein and DNA levels

The cloning of the phenylalanine hydroxylase gene and cDNA has potentially allowed the complete characterization of patients with phenylketonuria and already many mutations have been defined. Parents of patients now have the option of prenatal diagnosis. The 18 mutations defined so far indicate enormous heterogeneity not only within particular populations but also between populations. These mutations give little indication as to the locations of the amino acid residues important in enzyme function but one-third of the mutations are in exon 7 which may be indicating the importance of the region coded by this exon in the protein.

CpG dinucleotides are mutation hot spots in phenylketonuria

The coding region of the phenylalanine hydroxylase (PAH) gene contains 22 CpG dinucleotides, including five doublets in the seventh exon of the gene. We hypothesized that CpG doublets could represent mutation hot spots in PAH deficiencies and we carried out the systematic sequence analysis of exon 7 in 20 unrelated PAH-deficient kindreds of Mediterranean ancestry. This procedure resulted in the detection of two novel missense mutations whose location and nature (CG to CA and CG to TG) were consistent with the accidental deamination of a 5-methylcytosine in a CpG doublet (codon 261arg----gln and codon 252arg----trp). Moreover, the codon 261 mutation was found to be associated with mutant restriction fragment length polymorphism (RFLP) haplotype 1, the most frequent mutant RFLP haplotype at the PAH locus in the studies reported thus far. However, since the mutation was detected in only 36% of haplotype 1 mutant alleles, it appears that this haplotype at the PAH locus is genotypically heterogeneous in Mediterranean countries.

Polymerase chain reaction

The PCR, like recombinant DNA technology, has had an enormous impact in both basic and diagnostic aspects of molecular biology because it can produce large amounts of a specific DNA fragment from small amounts of a complex template. Recombinant DNA techniques create molecular clones by conferring on a specific sequence the ability to replicate by inserting it into a vector and introducing the vector into a host cell. PCR represents a form of "in vitro cloning" that can generate, as well as modify, DNA fragments of defined length and sequence in a simple automated reaction. In addition to its many applications in basic molecular biological research, PCR promises to play a critical role in the identification of medically important sequences as well as an important diagnostic one in their detection.

The polymerase chain reaction

The polymerase chain reaction (PCR) is a powerful new method for 'in vitro cloning'. It can selectively amplify a single molecule of template DNA several millionfold in a few hours and has made possible new approaches to problems in molecular genetics, evolutionary biology, and development.

Molecular genetic diagnosis of sickle cell disease using dried blood specimens on blotters used for newborn screening

The protein-based technologies used to screen newborns for sickle cell disease require confirmation with a liquid blood specimen. We have developed a strategy for rapid and specific genotypic diagnosis using DNA extracted from a dried blood spot on the filter paper blotter used to screen newborns. DNA could be microextracted from a specimen as small as a 1/8 inch diameter punched disc representing the dried equivalent of approximately 3 microliters of whole blood. We utilized the DNA from a 1/4 inch diameter specimen (12 microliters equivalent) for polymerase chain reaction amplification of the beta-globin region spanning the sickle cell mutation with detection by allele-specific oligonucleotide probes. Molecular confirmation of genotype from the original blotter would reduce the personnel costs associated with obtaining follow-up liquid blood specimens and would provide information to the family in a more timely and less equivocal manner.