Quantitative analysis of human DNA sequences by PCR and solid-phase minisequencing

Reliable quantification by PCR requires careful experimental design and conditions, often involving sampling of the PCR reactions at different time points or amplifying multiple dilutions of a standard DNA. We describe here an accurate, quantitative and easily automatizable solid-phase method based on competitive PCR. The PCR products are analyzed by solid-phase mini-sequencing after capture of biotinylated PCR products in streptavidin-coated microtiter wells and single-nucleotide extension of a specific detection primer by a radioactively labelled nucleotide. The results are expressed as numeric cpm-values, and the incorporated label expresses the relative amount of sequence variants in the original template mixture. We have applied the method to determination of allele frequencies in pooled DNA samples, of mitochondrial heteroplasmy, of gene copy numbers, and to forensic DNA analysis.

Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 5'-nuclease TaqMan assay and Molecular Beacon probes

Homogeneous assays based on real-time fluorescence monitoring during PCR are relevant alternatives for large-scale genotyping of single-nucleotide polymorphisms (SNPs). We compared the performance of the homogeneous TaqMan 5'-nuclease assay and the Molecular Beacon assay using three SNPs in the human estrogen receptor gene as targets. When analyzing a panel of 90 DNA samples, both assays yielded a comparable power of discrimination between the genotypes of a C-to-T transition in codon 10 and a G-to-A transition in codon 594 of the estrogen receptor gene. The Molecular Beacon probes distinguished better than the TaqMan probes between homozygous and heterozygous genotypes of a C-to-G transversion in codon 325. The sensitivity of detecting one allele, present as a minority in a mixed sample, varied between the SNPs and was similar for both assays. With the Molecular Beacon assay, the measured signal ratios were proportional to the amount of the minor allele over a wider range than with the TaqMan assay at all three SNPs.

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem

There are great hopes that the most common form of human genetic variation, single nucleotide polymorphisms (SNPs), can be used to improve radically biological understanding and to advance medicine. However, considerable controversy exists over just how SNPs can be applied to gain these insights. The second international SNP meeting, held at Schloss Hohenkammer, Munich, Germany, brought together leading international scientists from academia and industry to look at these issues from a multidisciplinary perspective. Topics that were covered spanned SNP discovery, scoring technologies, population genetics, disease studies, commercial dimensions, pharmacogenomics, bioinformatics, and legal considerations. SNP discovery is picking up speed; The SNP Consortium (TSC) is set to produce 300,000 publicly available SNPs within 2 years. Improved technologies for scoring SNPs are reducing hands-on time and cost, although truly high-throughput methods are still lacking for genome-wide population-based studies. Large numbers of SNPs have already been analysed in diverse populations. The results emphasise the importance of considering population history when using SNPs to search for genetic risk factors. Opinions on the feasibility of extensive SNP-based analysis of complex disease vary. However, combining expertise from several fields will be key to achieving optimal utilization of SNPs.

Recurrence of Marfan syndrome as a result of parental germ-line mosaicism for an FBN1 mutation

Mutations in the FBN1 gene cause Marfan syndrome (MFS), a dominantly inherited connective tissue disease. Almost all the identified FBN1mutations have been family specific, and the rate of new mutations is high. We report here a de novo FBN1mutation that was identified in two sisters with MFS born to clinically unaffected parents. The paternity and maternity were unequivocally confirmed by genotyping. Although one of the parents had to be an obligatory carrier for the mutation, we could not detect the mutation in the leukocyte DNA of either parent. To identify which parent was a mosaic for the mutation we analyzed several tissues from both parents, with a quantitative and sensitive solid-phase minisequencing method. The mutation was not, however, detectable in any of the analyzed tissues. Although the mutation could not be identified in a sperm sample from the father or in samples of multiple tissue from the mother, we concluded that the mother was the likely mosaic parent and that the mutation must have occurred during the early development of her germ-line cells. Mosaicism confined to germ-line cells has rarely been reported, and this report of mosaicism for the FBN1 mutation in MFS represents an important case, in light of the evaluation of the recurrence risk in genetic counseling of families with MFS.

Evidence for involvement of the type 1 angiotensin II receptor locus in essential hypertension

Components of the renin-angiotensin system play an important role in the normal regulation of blood pressure. We carried out a comprehensive genetic linkage study of the genes involved in the renin-angiotensin cascade in Finnish hypertensive twins and their affected siblings. We found no evidence for linkage between essential hypertension and the genes coding for renin, angiotensinogen, angiotensin-converting enzyme, or kallikrein 1 in the 329 hypertensive individuals of 142 families studied. In contrast, two intragenic markers for the type 1 angiotensin II receptor (AT1) showed some evidence for linkage in the total sample. A closer examination of this gene locus was carried out using subgroups of nonobese sibpairs with early onset of hypertension and uniform geographical origin. These stratifications yielded suggestive evidence for linkage of hypertension to the genetic area containing the AT1 gene, with a maximal multipoint logarithm of the odds (LOD) score of 2.9. A genetic association study carried out in an independent series of 50 hypertensive cases and 122 normotensive controls showed an increase in the frequency of the A1166-->C allele of the AT1 gene in the hypertensive individuals. In a novel variant of model-free multipoint linkage analysis allowing linkage disequilibrium in the calculations, an LOD score of 5.13 was obtained. Sequence analyses of the entire coding region and 848 bp of promoter region in the DNA sample on 8 index samples did not reveal previously unpublished sequence variations. The data provide evidence that a common genetic variant of the AT1 gene locus influences the risk of essential hypertension in the Finnish population.

Experimentally observed germline mutations at human micro- and minisatellite loci

We have analysed close to 30,000 human germline transmission events at five microsatellite loci (D3S1359, HumTH01, HumvWA, HumTPO and HumFES) and four minisatellite loci (D1S80, ApoB, Col2A1 and D17S30). At these loci the mutation rates are similar at the microsatellite and the minisatellite loci, varying from 0.2 x 10(-3) to < 3.3 x 10(-3) and from 0.5 x 10(-3) to 1.5 x 10(-3), respectively. Interestingly, paternal mutations appeared to be dominant at the microsatellite loci, whilst maternal mutations are dominant at minisatellite loci. Based on our data, no unequivocal support for a strict strand-slippage mutation mechanism (gain or loss of a single repeat) was found, although the vast majority of the mutational events were small gains or losses of one to three repeats, and only few unequivocal large gains or losses were observed.

Quantitative analysis of human DNA sequences by PCR and solid-phase minisequencing

The PCR technique provides highly specific and sensitive means for analyzing nucleic acids, but it does not allow their direct quantification. This limitation originates from the fact that the efficiency of PCR depends on the amount of template sequence present in the sample, and the amplification is exponential only at low template concentrations (1). Because of this "plateau effect" of the PCR, the amount of the amplification product does not directly reflect the original amount of the template. Moreover, subtle differences in the reaction conditions, such as material from biological samples, might cause significant sample to sample variation in the final yield of the PCR product.

Ethnic differences in catechol O-methyltransferase pharmacogenetics: frequency of the codon 108/158 low activity allele is lower in Kenyan than Caucasian or South-west Asian individuals

Catechol O-methyltransferase (COMT) inactivates neurotransmitters, hormones and drugs such as levodopa. COMT activity is inherited in an autosomal recessive manner and individuals with low activity have thermolabile COMT protein. A low activity allele has been demonstrated at codon 108/158 of the soluble and membrane bound COMT protein, respectively, whereby a G to A transition results in a valine to methionine substitution, rendering the protein more thermolabile. As ethnic differences in erythrocyte COMT activity have been previously demonstrated, the frequency of low activity alleles were investigated in 265 British Caucasian, 99 British South-west Asian and 102 Kenyan individuals. Genotyping of COMT codon 108/158 was performed using a minisequencing method. Erythrocyte COMT activity was measured in 60 British Caucasian individuals by radiochemical assay. The frequency of low activity alleles was 0.54 in Caucasians, 0.49 in South-west Asians, and 0.32 in Kenyans. There was a much lower frequency of individuals with homozygous low activity allele in the Kenyan population (9%) than in Caucasians (31%) or South-west Asians (27%). Erythrocyte COMT activity was lower and less thermostable in individuals with homozygous low activity alleles. The data provide molecular evidence that low COMT is less common in African individuals than the Caucasian population.

Contribution of the CCR5 and MBL genes to susceptibility to HIV type 1 infection in the Finnish population

Homozygosity for a variant of a chemokine receptor gene (CCR5) has been shown to protect from HIV-1 infection. Variants of the mannose-binding lectin (MBL) gene have been suggested to predispose to HIV-1 infection. These genetic variants and their possible role in susceptibility to HIV-1 infection were studied in sample material from more than 300 Finnish HIV-infected and control individuals. The genotyping was carried out efficiently using a novel, primer extension assay in a miniaturized oligonucleotide array format. Homozygotes for the protective deletion allele of the CCR5 gene were found only in the control group, and the frequency of the allele was high in the Finnish population. Homozygosity for the MBL variant alleles was enriched significantly in the HIV-1-infected group, thus providing further evidence for the harmfulness of MBL variant homozygosity in HIV-1 transmission.

Linkage of familial combined hyperlipidaemia to chromosome 1q21-q23

More than half of the patients with angiographically confirmed premature coronary heart disease (CHD) have a familial lipoprotein disorder. Familial combined hyperlipidaemia (FCHL) represents the most common genetic dyslipidemia with a prevalence of 1.0-2.0%. FCHL is estimated to cause 10-20% of premature CHD and is characterized by elevated levels of cholesterol, triglycerides, or both. Attempts to characterize genes predisposing to FCHL have been hampered by its equivocal phenotype definition, unknown mode of inheritance and genetic heterogeneity. In order to minimize genetic heterogeneity, we chose 31 extended FCHL families from the isolated Finnish population that fulfilled strictly defined criteria for the phenotype status. We performed linkage analyses with markers from ten chromosomal regions that contain lipid-metabolism candidate genes. One marker, D1S104, adjacent to the apolipoprotein A-II (APOA2) gene on chromosome 1, revealed a lod score of Z = 3.50 assuming a dominant mode of inheritance. Multipoint analysis combining information from D1S104 and the neighbouring marker D1S1677 resulted in a lod score of 5.93. Physical positioning of known genes in the area (APOA2 and three selectin genes) outside the linked region suggests a novel locus for FCHL on 1q21-q23. A second paper in this issue (Castellani et al.) reports the identification of a mouse combined hyperlipidaemia locus in the syntenic region of the mouse genome, thus further implicating a gene in this region in the aetiology of FCHL.

Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays

We describe a method for multiplex detection of mutations in which the solid-phase minisequencing principle is applied to an oligonucleotide array format. The mutations are detected by extending immobilized primers that anneal to their template sequences immediately adjacent to the mutant nucleotide positions with single labeled dideoxynucleoside triphosphates using a DNA polymerase. The arrays were prepared by coupling one primer per mutation to be detected on a small glass area. Genomic fragments spanning nine disease mutations, which were selected as targets for the assay, were amplified in multiplex PCR reactions and used as templates for the minisequencing reactions on the primer array. The genotypes of homozygous and heterozygous genomic DNA samples were unequivocally defined at each analyzed nucleotide position by the highly specific primer extension reaction. In a comparison to hybridization with immobilized allele-specific probes in the same assay format, the power of discrimination between homozygous and heterozygous genotypes was one order of magnitude higher using the minisequencing method. Therefore, single-nucleotide primer extension is a promising principle for future high-throughput mutation detection and genotyping using high density DNA-chip technology.

No evidence of linkage between familial combined hyperlipidemia and genes encoding lipolytic enzymes in Finnish families

Familial combined hyperlipidemia (FCHL) is characterized by different lipid phenotypes (IIa, IIb, IV) and elevated apolipoprotein B (apo B) levels in affected family members. Despite intensive research, the genes involved in the expression of this complex disorder have not been identified, probably because of problems associated with phenotype definition, unknown mode of inheritance, and most probably genetic heterogeneity. To explore the genetics of FCHL in the genetically homogeneous Finnish population, we collected 14 well-documented Finnish pedigrees with premature coronary heart disease and FCHL-like dyslipidemia. The lipolytic enzymes lipoprotein lipase (LPL), hepatic lipase (HL), and hormone-sensitive lipase (HSL) were selected as initial candidate genes because of their central roles in apo B and triglyceride metabolism. On the basis of the pedigree structures, a dominant mode of inheritance was adopted for linkage analyses, and serum total cholesterol and/or triglyceride levels exceeding the 90th percentile level were set as diagnostic criteria (criterion 1). In pairwise linkage analyses with intragenic markers, no evidence for linkage was found. Instead, the significantly negative LOD scores suggested exclusion of all three loci for single major gene effect. LOD scores were -14.63, -5.03, and -5.70 for the three LPL polymorphisms (theta=0.00); -9.40, -6.30, and -4.74 for the three HL polymorphisms (theta=0.00); and -15.29 for the HSL polymorphism (theta=0.00). The results were very similar when apo B levels over the 90th percentile were used as criteria for affected status (criterion 2). Also, when linkage calculations were carried out using an intermediate or recessive mode of inheritance, the results of pairwise linkage analysis remained negative. Furthermore, when haplotypes were constructed from multiple polymorphisms of the LPL and HL genes, no segregation with the FCHL phenotype could be observed in the 14 Finnish families. Data obtained by the affected sib-pair method supported these findings, suggesting that the LPL, HL, or HSL genes do not represent major loci influencing the expression of the FCHL phenotype.

Tissue distribution and levels of gelsolin mRNA in normal individuals and patients with gelsolin-related amyloidosis

We measured quantitatively the mRNA levels of intracellular and secretory forms of gelsolin, an actin-modulating protein, in human tissues from subjects of different ages. The intracellular gelsolin mRNA constituted the major type of gelsolin steady-state mRNA in all tissues analyzed. Both forms of gelsolin were expressed in most adult tissues, with particularly high mRNA levels in all types of muscle and interestingly in skin. Between the adult and infantile tissues the most striking difference in expression levels was found in liver, as the adult liver contained only a subtle amount of gelsolin mRNA. Skin and muscle samples from patients with gelsolin-related amyloidosis (FAF), with significantly increased concentrations of serum gelsolin, did not reveal an increased expression of the gene, and both mutant and wild-type alleles were expressed in equal amounts. The high level of expression of the gelsolin gene in the skin in general could locally contribute to the characteristic skin amyloidosis in FAF patients.

A colorimetric minisequencing assay for the mutation in codon 506 of the coagulation factor V gene

We describe a colorimetric screening method for the mutation in codon 506 of the coagulation factor V gene. The nucleotide at the site of the FV:Q506 mutation is identified in an immobilized amplified DNA template by extension of a primer with a hapten-labelled dNTP using a DNA polymerase. The incorporated hapten is detected by an antibody-alkaline phosphatase conjugate that catalyses the formation of a coloured end product. The assay is carried out in a microtiter plate format, and the procedure is identical to that of enzyme immunoassays. It unequivocally identifies the FV:Q506 mutation in heterozygous and homozygous form. The colorimetric minisequencing method gave the same result as a 3H-based minisequencing assay and restriction site analysis with Mn11 used as reference methods. Because of its simple format and numeric result, the novel colorimetric minisequencing method should be an attractive alternative for screening for the FV:Q506 mutation in clinical laboratories.

DNA diagnosis and identification of carriers of infantile and juvenile neuronal ceroid lipofuscinoses

The recent identification of the genes and the mutations underlying infantile neuronal ceroid lipofuscinosis and juvenile onset neuronal ceroid lipofuscinosis facilitates specific DNA-based diagnostics for the disorders. We have developed a solid-phase minisequencing test for the identification of the major Finnish INCL mutation, an A to T transversion at nucleotide position 364 of the palmitoyl protein thioesterase gene on chromosome 1. This test has been applied for prenatal diagnosis and for identification of disease carriers in INCL families. For population-based screening for INCL carriers the coverage of the test would be 98%. In addition, by combining the solid-phase minisequencing test with whole genome preamplification, we have developed a procedure that allows reliable identification of the INCLFin-mutation in single blastomeres from in-vitro-fertilized embryos. This method is applicable for preimplantation diagnosis, and thus it offers an alternative to early prenatal diagnosis in the prevention of INCL. A modification of the solid-phase minisequencing test was devised for detection of the major INCL mutation, a 1.02 kb deletion in the CLN3 gene on chromosome 16. The coverage of this test for diagnosis of INCL and identification of carriers is 90% in Finland and > 80% worldwide.

Genetic polymorphism of catechol-O-methyltransferase (COMT): correlation of genotype with individual variation of S-COMT activity and comparison of the allele frequencies in the normal population and parkinsonian patients in Finland

The catechol-O-methyltransferase (COMT) gene occurs as two polymorphic alleles, which code for a high activity thermostable and low activity thermolabile form of the enzyme. We devised a fast solid-phase minisequencing assay for genotyping the COMT gene at nucleotide position 544 encoding amino acid residue 158. The method was applied to correlate the genotype of the COMT gene with the biological activity of the COMT enzyme. In red blood cells from individuals homozygous for G at nucleotide position 544 coding for Val-158, the activity of COMT ranged from 0.55-1.03 pmol min-1 mg-1 protein, and in individuals homozygous for A at position 544 coding for Met-158, the activity ranged from 0.21-0.43 pmol min-1 mg-1. Heterozygotes showed intermediate activities of 0.20-0.88 pmol min-1 mg-1. The thermostability (heated/unheated) at 48 degrees C of the high activity form was shown to be about two-fold compared to that of the low activity form of the enzyme. By analysing 76 individual samples and three pooled samples representing altogether 3140 individuals using the solid-phase minisequencing method, the two COMT alleles were shown to be equally distributed in the Finnish population. No statistically significant difference in the frequencies of the COMT alleles was found when comparing the normal population with a sample of 158 Finnish patients with Parkinson's disease.

Rapid diagnostic test for the major mutation underlying Batten disease

Batten disease is the most common progressive neurodegenerative disorder of childhood in western countries. A novel cDNA responsible for Batten disease has recently been identified. We have developed a rapid diagnostic solid phase minisequencing test to detect the major 1.02 kb deletion which is responsible for 81% of affected chromosomes in Batten disease worldwide. In Finland, 90% of Batten chromosomes carry the major deletion owing to the enrichment of the CLN3 gene in the isolated Finnish population.

A chimeric disposition of the elongation factor genes in Rickettsia prowazekii

An exceptional disposition of the elongation factor genes is observed in Rickettsia prowazekii, in which there is only one tuf gene, which is distant from the lone fus gene. In contrast, the closely related bacterium Agrobacterium tumefaciens has the normal bacterial arrangement of two tuf genes, of which one is tightly linked to the fus gene. Analysis of the flanking sequences of the single tuf gene in R. prowazekii shows that it is preceded by two of the four tRNA genes located in the 5' region of the Escherichia coli tufB gene and that it is followed by rpsJ as well as associated ribosomal protein genes, which in E. coli are located downstream of the tufA gene. The fus gene is located within the str operon and is followed by one tRNA gene as well as by the genes secE and nusG, which are located in the 3' region of tufB in E. coli. This atypical disposition of genes suggests that intrachromosomal recombination between duplicated tuf genes has contributed to the evolution of the unique genomic architecture of R. prowazekii.

Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation

We developed a multiplex, solid-phase minisequencing method to detect multiple single-nucleotide polymorphisms in an undivided sample. The amplified DNA templates are first captured on a manifold. Then, with multiple minisequencing primers of various sizes, single-nucleotide extension reactions are carried out simultaneously with fluorescently labeled dideoxynucleotides. The size of the extended product, determined by using a DNA sequencing instrument, defines the site of the polymorphisms, and the incorporated nucleotide gives the identity of the nucleotide at each site. HLA-DQA1 typing was used as a model system to evaluate the method. The DR2 subgroup of the HLA-DRB1 gene was typed along with the DQA1 gene to demonstrate the feasibility of the method in analyzing multiple genes at multiple sites simultaneously. The method is generally applicable for screening any single-nucleotide polymorphisms or point mutations, and its manifold format allows practical handling of large numbers of samples.

Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA

We have developed a new method for preimplantation diagnosis of inherited diseases. Our procedure for the identification of point mutations in single cells combines whole-genome amplification using 15-mer random primers (primer extension preamplification, PEP) with a single locus-specific PCR amplification, followed by detection of the mutation by solid-phase minisequencing. The procedure was evaluated by detecting three disease-causing mutations and seven polymorphic nucleotides located on different human chromosomes from single granuloma and blastomere cells. The correct genotype of the cell was identified at 96% of the nucleotide positions analyzed, showing that a representative part of the genome is amplified during PEP. We estimate that PEP yielded at least 1000 copies of the genome. The quantitative nature of the solid-phase minisequencing method allowed us to notice that preferential amplification of one allele occurs at heterozygous loci during PEP, which is a potential problem in preimplantation diagnosis.

DNA-based carrier screening in primary healthcare: screening for aspartylglucosaminuria mutations in maternity health offices

Large-scale genetic screening programs are complex enterprises in which ethical, technical, medical, and socioeconomic aspects have to be handled with professional expertise. Establishment of automated, relatively robust, and inexpensive laboratory techniques is one step of this path. Here a pilot carrier-screening program for the mutations causing aspartylglucosaminuria was carried out for pregnant women in primary care maternity health offices. Women (1975) were tested before their 12th week of pregnancy, and 31 heterozygotes were detected. The sampling was based on dried blood strips, facilitating convenient handling and inexpensive mailing to the laboratory. The mutation detection technique, solid-phase mini-sequencing simplified by the use of scintillation microplates and automated equipment, proved to be rapid, simple, inexpensive, and reliable, with a low repeat rate (2.5%). In conclusion, we found that good collaboration between the primary healthcare unit, the laboratory, and counseling experts, combined with modern laboratory technology, facilitate reliable low-cost genetic testing.