Direct Solid-phase Sequencing Research Articles

Dynamics of hepatitis C virus quasispecies turnover during interferon-alpha treatment.

Interferon-alpha (IFN) has been shown to accelerate the evolution of hepatitis C virus (HCV) variants (quasispecies) in nonresponder patients. Different sensitivities of HCV variants to IFN are discussed as a possible mechanism. In the present study, quasispecies were investigated in detail by a newly established and validated direct solid-phase sequencing of the hypervariable region 1 (HVR1), during the initial 3 months of IFN therapy. According to single strand conformation polymorphism (SSCP) analysis, 14 of 26 (54%) virologic nonresponders with quasispecies evolution were identified. Six representative patients with SSCP changes were selected for frequent HVR1 sequencing. Pre-existing variants were identified by cloning and sequencing of the pretreatment serum HCV sample. In one patient the major type was substituted by a minor variant within 3 days of treatment while in the majority of patients the pretreatment major type did not decline before days 26-57 of treatment. Total serum HCV RNA levels remained constant in all patients. In conclusion, although quasispecies evolution during IFN therapy is common, it occurs after a wide range of time intervals after initiation of therapy. Thus, nonresponse to IFN cannot exclusively be explained by changes in the quasispecies.

Acute intermittent porphyria: novel missense mutations in the human hydroxymethylbilane synthase gene

PurposeTo identify mutations in families with acute intermittent porphyria, an autosomal dominant inborn error of metabolism that results from the half-normal activity of the third enzyme in the heme biosynthetic pathway, hydroxymethylbilane synthase. MethodsMutations were identified by direct solid phase sequencing. ResultsTwo novel missense mutations E80G and T78P and three previously reported mutations, R173W, G111R, and the splice site lesion. IVS1 +1, were detected, each in an unrelated proband. The causality of the novel missense mutations was demonstrated by expression studies. ConclusionThese findings provide for the precise diagnosis of carriers in these families and further expand the molecular heterogeneity of AIP.

Fabry disease: comparison of enzymatic, linkage, and mutation analysis for carrier detection in a family with a novel mutation (30delG).

Fabry disease (FD) is an X-linked recessive disorder caused by the deficient activity of the lysosomal enzyme alpha-galactosidase A (alpha-Gal A). Affected males are reliably diagnosed by demonstration of deficient alpha-Gal A activity in plasma or leukocytes. However, identification of female carriers is problematic due to Lyonization, requiring mutation identification and/or linkage studies for accurate carrier detection. Here, we describe a large Brazilian kindred with Fabry disease that permitted comparison of biochemical and molecular diagnostic techniques. Initially, the plasma alpha-Gal A activities were determined in at-risk affected males and potential female carriers; affected males were readily diagnosed, while the females had variable results. To detect carrier females, haplotype analysis using 10 polymorphic markers adjacent to the gene was performed. Subsequently, solid-phase direct sequencing of the alpha-Gal A gene demonstrated a novel single base deletion in exon 1 (30delG). Discrepancies were observed between the enzymatic and molecular diagnoses in two at-risk females. These findings emphasize the need for precise heterozygote diagnosis by mutation and/or haplotype analyses in all families with Fabry disease.

Comparison of the LiPA HIV-1 RT test, selective PCR and direct solid phase sequencing for the detection of HIV-1 drug resistance mutations

The performance to detect drug resistence mutations in the reverse transcriptase gene of HIV-1 was compared for direct solid phase sequencing, selective polymerase chain reaction (PCR) using the amplification refractory mutation system (ARMS) and the new line probe assay (LIPA) HIV-1 RT™. The three tests were undertaken on 50 plasma samples from 25 treatment-experienced patients under combination therapy with dideoxynucleoside analogues. LiPA HIV-1 RT gave interpretable results in 80 to 96% of the samples depending on the codon of interest. In 2% of the samples a failure to amplify resulted in uninterpretable results for sequencing. ARMS gave no result in seven samples (14%). Overall, there was a 73 to 100% concordance between the three methods. In this study, LiPA HIV-1 RT proved to be an accurate and reliable alternative to DNA sequencing for the detection of drug resistance mutations in patient samples.

Evolution of HIV drug Resistance in Zidovudine/Zalcitabine- and Zidovudine/ Didanosine-Experienced Patients Receiving Lamivudine-Containing Combination Therapy

Drug resistance patterns and their correlation to treatment response 24 weeks after addition of lamivudine to a previous zidovudine/zalcitabine or zidovudine/ didanosine combination treatment, or after substitution of lamivudine for the zalcitabine or didanosine in these combinations, were evaluated in 21 patients with CD4 counts between 50 and 300 cells/mm3. Clinical, immunological and virological outcomes were measured at baseline and at weeks 4, 12 and 24. Drug resistance was assessed using the recombinant virus assay and direct solid-phase sequencing of the reverse transcriptase gene. Viral load decreased by an average of 0.78 log RNA copies/ml at week 4, but returned to baseline at week 24 for most patients. CD4 cell counts increased in all treatment groups without reaching statistical significance. Resistance to lamivudine was readily acquired in all four treatment groups and was often associated with a partial reversal of phenotypic zidovudine resistance and a moderate increase in the 50% inhibitory concentrations for didanosine and zalcitabine. One patient receiving the zidovudine/didanosine combination treatment harboured multi-nucleoside analogue-resistant virus. A poor response to lamivudine tended to be related to the extent of pre-existing zidovudine resistance.

Quantification and genotyping of serum HCV-RNA in patients with chronic hepatitis C undergoing interferon treatment.

Quantification of serum HCV-RNA and HCV genotyping was studied in 27 patients with chronic hepatitis C undergoing interferon treatment. Pretreatment serum HCV-RNA levels were quantified using competitive RT-PCR and compared to a quantitative RT-PCR assay based on co-amplification of HCV-RNA with a synthetic RNA standard. HCV genotyping was performed using a line probe reversed hybridisation assay or direct solid-phase sequencing. This study shows the feasibility of performing HCV-RNA quantification. RT-PCR based on co-amplification HCV-RNA titer less than 6 x 10(4) genome equivalents/ml serum did correlate with a complete sustained response to alpha interferon in chronic hepatitis C. HCV genotype 1b was alpha predominantly associated with a high non-responder rate. Future prospective trials will be required to evaluate quantitative HCV-RNA levels and HCV genotyping as response predicting parameters for interferon-treatment.

Fabry Disease: Thirty-Five Mutations in the α-Galactosidase A Gene in Patients with Classic and Variant Phenotypes

Fabry disease, an X-linked inborn error of glycosphingolipid catabolism, results from mutations in the alpha-galactosidase A (alpha-Gal A) gene located at Xq22.1. To determine the nature and frequency of the molecular lesions causing the classical and milder variant Fabry phenotypes and for precise carrier detection, the alpha-Gal A lesions in 42 unrelated Fabry hemizygotes were determined. Genomic DNA was isolated from affected probands and their family members. The seven alpha-galactosidase A exons and flanking intronic sequences were PCR amplified and the nucleotide sequence was determined by solid-phase direct sequencing. Two patients with the mild cardiac phenotype had missense mutations, I9IT and F113L, respectively. In 38 classically affected patients, 33 new mutations were identified including 20 missense (MIT, A31V, H46R, Y86C, L89P, D92Y, C94Y, A97V, R100T, Y134S, G138R, A143T, S148R, G163V, D170V, C202Y, Y216D, N263S, W287C, and N298S), two nonsense (Q386X, W399X), one splice site mutation (IVS4 + 2T-->C), and eight small exonic insertions or deletions (304del1, 613del9, 777del1, 1057del2, 1074del2, 1077del1, 1212del3, and 1094ins1), which identified exon 7 as a region prone to gene rearrangements. In addition, two unique complex rearrangements consisting of contiguous small insertions and deletions were found in exons 1 and 2 causing L45R/H46S and L120X, respectively. These studies further define the heterogeneity of mutations causing Fabry disease, permit precise carrier identification and prenatal diagnosis in these families, and facilitate the identification of candidates for enzyme replacement therapy.

Sequence Polymorphisms of the Control Region of Human Mitochondrial DNA in Japanese Population

Nucleotide sequences of 2 hypervariable regions (HV1, HV2) within the control region of human mitochondrial DNA (mtDNA) were analyzed from 55 unrelated Japanese. About 700 nucleotides were sequenced by using the nested PCR and the solid-phase direct sequencing methods. Comparison of these sequences with Anderson's reference sequence revealed 97 mutation types within 93 positions, and 11 positions of them were novel. Fifty five samples analyzed were classified into 52 different sequences, while 3 pairs have shown the same sequences. Comparison of the Japanese sequences to those reported from other populations indicated many differences in such a point that the substitutions at 16,223 and 73 in Japanese were more frequent than those in Caucasian, while the substitutions at 16,126 and 16,311 in Japanese were less frequent than those in Caucasian. Twenty one of 55 samples analyzed showed a T-to-C transition at the position 16,189 of the C-stretch region in the HV1 region. This replacement caused the blurred bands on the sequence image, which resulted in the ambiguity of exact number of cytosine in the C-stretch region of HV1. For this ambiguity, the number of cytosine in the C-stretch region should not be currently taken into account in forensic practices of individualization of evidence samples. Regardless of such problem, the polymorphisms of HV1 and HV2 regions are highly useful for individual identification.

Characterization of human immunodeficiency virus type 1 p17 matrix protein motifs associated with mother-to-child transmission

In order to determine if viral selection occurs during mother-to-child transmission of human immunodeficiency virus type 1 (HIV-1), we used a direct solid-phase sequencing method to sequence the p17 matrix protein-encoding regions of viral isolates from 12 HIV-1-infected mother-and-child pairs, 4 infected infants, 4 transmitting mothers, and 22 nontransmitting mothers and compared the sequences. The blood samples were collected during the delivery period for the mothers and during the first month of life for most of the children. The p17 nucleic sequences were distributed among several clades corresponding to the HIV-1 A, B, and G subtypes. At the amino acid level, no significant differences within the known p17 functional regions were observed among the subtypes. Statistical analyses could be performed with the B subtype. Within the major p17 antibody binding site, a constant KIEEEQN motif (amino acids 103 to 109) was found in all mother-and-child isolates from the B subtype. On the other hand, 9 of 17 nontransmitting mother isolates were variable in this 103 to 109 region. Thus, this motif was significantly associated with the transmitting status (chi square, P = 0.0034). A valine residue at position 104 was significantly associated with the nontransmitting phenotype (chi square, P = 0.014), suggesting that it has a protective role during vertical transmission. The C-terminal end of p17 was globally conserved among nontransmitting mother isolates (chi square, P = 0.0037). These results might improve the understanding of the pathogenesis of HIV-1 vertical transmission and might allow the screening of seropositive mothers by a rapid molecular or peptide test.

HIV-1 D subtype viruses in Finland

Background: Human immunodeficiency virus (HIV)-1 strains are divided into seven genetic subtypes based on their gag sequences (A, B, C, D, F, G and H). Strains that have appeared in Finland show unusual heterogeneity compared to most industrialized countries, up to 25% of the strains belong to non-B subtypes (Liitsola et al., 1996). Three D subtype viruses have so far been identified in Finland. All patients were men, one Kenyan immigrant and two Finnish men, who had been infected in Africa. Here we describe some of the characteristics of the genomic diversity of these strains. Method: The genotype was determined by direct solid-phase sequencing of the p7 gag region. Phylogenetic analysis was done using standard methods. Results: The analysis showed that the D subtype sequences clustered clearly distinctly from the other non-B strains, but did not suggest any transmission links between the three cases. From one case both cerebrospinal fluid (CSF) and blood leukocyte virus isolates were studied. The analysis revealed significant differences between the blood and CSF viruses. A four amino acid duplication and other differences were observed between the strains. Conclusion: The results confirm that D subtype viruses do indeed occur in Finland and they represent quite heterogenic strains within the D cluster.

Sequence-Based Analysis of Properdin Deficiency: Identification of Point Mutations in Two Phenotypic Forms of an X-Linked Immunodeficiency

Properdin deficiency is an inherited X-linked disorder causing increased susceptibility to meningococcal disease. Here, underlying genetic defects in the properdin gene were identified for the first time. Samples from individuals with type I deficiency, defined as complete absence of properdin in serum, and individuals with type II deficiency, characterized by low concentrations of properdin in serum, were analyzed by direct chromosome sequencing of overlapping PCR products. The complete gene, including 10 exons and 9 introns, covering 6460 bases of the region Xp11, was investigated by direct solid-phase sequencing. In the related individuals with type I deficiency a C to T mutation in exon 5 was identified, which gives rise to a stop codon TGA and thus a truncated gene product. In addition, point mutations were found in 4 introns and a silent mutation in exon 10. In the properdin gene from related individuals with type II deficiency two point mutations were found, one in intron 3 and one in exon 4. The latter mutation yields a substitution of arginine to tryptophan, which may affect folding, secretion, and/or turnover of the protein. The genetic and biochemical implications of these mutations are discussed.

Acute intermittent porphyria: A single‐base deletion and a nonsense mutation in the human hydroxymethylbilane synthase gene, predicting truncations of the enzyme polypeptide

Acute intermittent porphyria (AIP) is an autosomal-dominant inborn error of metabolism that results from the half-normal activity of the third enzyme in the heme biosynthetic pathway, hydroxymethylbilane synthase (HMB-synthase). AIP is an ecogenetic condition, since the life-threatening acute attacks are precipitated by various factors, including drugs, alcohol, fasting, and certain hormones. Biochemical diagnosis is problematic, and the identification of mutations in the HMB-synthase gene provides accurate detection of presymptomatic heterozygotes, permitting avoidance of the acute precipitating factors. By direct solid-phase sequencing, two mutations causing AIP were identified, an adenine deletion at position 629 in exon 11(629delA), which alters the reading frame and predicts premature truncation of the enzyme protein after amino acid 255, and a nonsense mutation in exon 12 (R225X). These mutations were confirmed by either restriction enzyme analysis or family studies of symptomatic patients, permitting accurate presymptomatic diagnosis of affected relatives.

Dynamic analysis of heterogeneous hepatitis C virus populations by direct solid-phase sequencing

In the present study, we used a semiautomated solid-phase direct sequencing method to analyze sequence diversity and variation of the hypervariable E2/NS1 region in the hepatitis C virus (HCV) genome in isolates from patients seropositive for HCV. A total of 24 isolates of various origins were sequenced. Six of the patients, not subject to any antiviral therapy, were monitored longitudinally, and rapid sequence variations were observed over a period of 14 months. The nucleotide change rate was found to be 0.1 to 0.2 nucleotide substitution per genome site per year. Furthermore, isolates from five of the patients were used for a comparative study of the direct solid-phase sequencing approach versus the frequently used approach of sequencing individual reverse transcriptase PCR clones. The advantage of direct solid-phase sequencing for studying dynamic changes in heterogeneous populations of HCV is discussed.

Mutations in the low density lipoprotein receptor gene of familial hypercholesterolemic patients detected by denaturing gradient gel electrophoresis and direct sequencing.

Familial hypercholesterolemia (FH) results from mutations in the low density lipoprotein receptor (LDLR) gene. We applied denaturing gradient gel electrophoresis (DGGE) to screen for sequence variations in the coding and splice site consensus sequences of the LDLR gene. For amplification of each exon by the polymerase chain reaction (PCR), optimal pairs of primers were designed by the MELT 87 computer algorithm. To increase the sensitivity, an artificial GC-clamp was included in either the 5'- or the 3'-end of each fragment. DGGE screening of 32 apparently unrelated heterozygous FH patients revealed 16 unique different aberrant DGGE patterns in 27 patients, while in a group of 32 normal subjects none of these DGGE patterns could be observed, suggesting that the aberrant patterns represent disease-causing mutations. Interestingly, 16 out of 27 patients showed an aberrant DGGE pattern in the part of the gene encoding the ligand binding domain (exons 2-6). Direct solid-phase sequencing of the corresponding exon-specific PCR products revealed the nature of the mutations: three nonsense, four splicing, two frameshift, one silent, and six missense mutations. Six of the mutations have been previously reported, while ten are novel mutations. These results indicate that DGGE provides a reliable method for the detection of the presence of point mutations in the LDLR gene of FH patients, thereby facilitating the introduction of rapid DNA diagnosis for this common and genetically heterogeneous disorder.

Identification of the causative agent of granulocytic ehrlichiosis in Swedish dogs and horses by direct solid phase sequencing of PCR products from the 16S rRNA gene

Seven Swedish isolates of Ehrlichia species from the blood of four dogs and three horses with clinical granulocytic ehrlichiosis, were identified by direct solid phase DNA sequencing of polymerase chain reaction (PCR) products from the 16S rRNA gene. The amplified DNA fragments were produced with primers complementary to the universal regions, Ul, U2, U5 and U8 of the 16S rRNA molecule. Identical sequences were obtained from all seven isolates. This nucleotide sequence was similar to the sequences deposited in GenBank for Ehrlichia phagocytophila and E equi. The sequence of the Swedish ehrlichiae differed in two nucleotide positions from the E phagocytophila sequence and in three positions from the E equi sequence, and it is tentatively proposed that it is a subspecies of one of these two. The alignment of the sequence of the Swedish isolates with a recently deposited sequence from human cases of ehrlichiosis in the USA revealed 100 per cent identity in a segment of about 1400 bp.

In Vivo Genetic Variability of the HIV-1 vif Gene

The human immunodeficiency virus type 1 (HIV-1) vif gene encodes a 23-kDa protein (viral infectivity factor) whose exact mechanism of action is not entirely clear, Vif is believed to be highly conserved among different HIV-1 strains. We have analyzed the proviral vif sequences of 61 peripheral blood mononuclear cell samples from HIV-1 positive patients by direct solid phase sequencing and temperature gradient gel electrophoresis of polymerase chain reaction products. Inter- and intraindividual sequence variations, conserved motifs, and prevalent vif subtypes were investigated. The consensus proviral vif DNA sequence of the 61 samples as well as the consensus sequence of the 61 deduced vif amino acid sequences were found to be less conserved than previously thought. The vif proviral sequences were 58% conserved, with the 5′ end of the vif gene being the most conserved region (84%). Of the vif amino acids only 45% were absolutely conserved in the 61 samples, i.e., the absolutely conserved and as such possibly functionally important domains of the vif protein comprised less than half of the vif amino acids. In two-thirds of the variable positions residues belonging to different amino acid groups were found. In individual patients the prevalent vif sequence changed with the course of disease, but the differences found in two serial samples of a patient were ⩽ 10%. Phylogenetic analysis revealed that one African vif subtype had been introduced in the investigated population.

The phylogeny of Neospora caninum and Toxoplasma gondii based on ribosomal RNA sequences.

Neospora caninum is a newly described cyst-forming coccidium which is the cause of severe neurological disease in dogs. The parasite is morphologically similar to Toxoplasma gondii, but the two species can be differentiated serologically. In order to define the phylogenetic position of N. caninum, we have determined 16S-like rRNA sequences from three members of the family of Sarcocystidae: N. caninum, T. gondii, and Sarcocystis fusiformis. The 16S-like rRNA genes from the three parasites were amplified by polymerase chain reaction and the sequences were determined by direct solid-phase sequencing. The sequences derived were computer aligned with several other 16S-like rRNA sequences from protozoan parasites to construct phylogenetic trees. The study confirmed that N. caninum should be classified as a member of the family Sarcocystidae. However, because of the close relationship to T. gondii it seems questionable that N. caninum should be placed in a new genus.

Solid-phase cloning to create sublibraries suitable for DNA sequencing

A solid-phase method is described to create subclones, suitable for DNA sequencing, from lambda or cosmid libraries. The purified target DNA is sonicated and two linkers, with one oligonucleotide biotinylated in the 5′-end, are ligated to the ends of the fragments produced by sonication. After size separation, the fragments are immobilised onto a solid support and the non-biotinylated strand of each immobilised fragment is eluted. In this way, a library of single-stranded fragments is obtained. All fragments contain ‘universal’ flanking sequences of 22 bases introduced by the linker ligation. These flanking sequences can subsequently be used for solid-phase cloning into a single-stranded vector containing the complementary sequences. Thus, cloning can be achieved without the use of ligase or restriction enzymes. The resulting subclones are used for direct solid-phase sequencing and the immobilised strand can be used to selectively remove homologous DNA from the library of single-stranded fragments. Thus, a sublibrary of non-sequenced fragments can be created. Here, we show that a library of clones, suitable for direct solid-phase sequencing, can be obtained starting with lambda DNA. The efficiency of selective hybridisation of homologous and non-homologous fragments was investigated. The possibility of using this approach for automated cloning strategies for large-scale genomic and cDNA sequencing is discussed.

Mutation specific PCR and direct solid phase sequencing assay for the detection of hepatitis B virus pre-C/C mutants in anti-HBe-positive, chronic hepatitis B.

Sequence analysis of the HBV DNA from patients with anti-HBe+, chronic hepatitis B revealed that the lack of HBeAg is mostly due to a single G-->A transition at nucleotide position 1896, resulting in a translational stop codon. A point mutation-specific polymerase chain reaction (msPCR) for the detection of this genetic variant was established. Two serologically defined groups of patients with symptomatic chronic hepatitis B (HBeAg+ n = 14, anti-HBe+ n = 11) were included in this study. Viral DNA from 43 sera (26 eAg+/17 anti-HBe+) was amplified twice, using two different sets of PCR primers. Each set contained the same -strand primer, but the +strand primers differed at their 3'-end, thus being complementary only to the wild-type or to the mutant DNA. Unspecific amplification was ruled out by choosing high annealing temperatures (66 degrees C) and cloned HBV-DNA as specificity controls. Furthermore, the results were compared to our findings obtained with direct solid-phase sequencing of the amplified viral DNA. Using msPCR, we found the mutation in four of 26 of the eAg+ sera and in 17 of 17 of our anti-HBe+ samples. Mixed virus populations were identified in 13 of 21 cases. Compared to the sequencing results, msPCR is more sensitive and less time consuming for the detection of the stop codon and thus is suitable as a rapid and specific screening method.

Altered CYP21 genes in HLA-haplotypes associated with congenital adrenal hyperplasia (CAH): a family study

Disorders of the CYP21 gene, which is located within the major histocompatibility complex on the short arm of chromosome 6, are the leading causes of congenital adrenal hyperplasia (CAH). The coding gene and a highly homologous pseudogene are tandemly arranged with the two genes for the fourth component of complement (C4A and C4B). To analyse the prevalence rates of mutations of the CYP21 genes and the segregation of the CYP21 genes with their corresponding human leucocyte antigen (HLA)-haplotypes, 21 families with one or two children with the severe form of 21-hydroxylase deficiency were studied. Mutations of the CYP21 gene on their corresponding HLA-haplotype were detected by hybridisation of polymerase chain reaction (PCR)-amplified genomic DNA with sequence-specific oligonucleotides and solid phase direct sequencing. Our study has shown the following. (1) A single basepair mutation (A-->G or C-->G) within the second intron is the most frequent mutation leading to impaired 21-hydroxylase activity. This mutation is only detected in HLA-haplotypes associated with the salt-wasting form of CAH. (2) A large deletion of part or all of the CYP21 gene is associated with the HLA-haplotype A3, BW47, C6, DR7, DR53, DQ2 but is also observed in other HLA-haplotypes and can be detected by a simple rapid PCR restriction fragment length polymorphism method. (3) Two alleles of the coding CYP21 gene differing in a leucine codon within the first exon, (formerly described as a mutation associated with 21-hydroxylase deficiency) have been found with an equal distribution in patients with 21-hydroxylase deficiency, non-disease HLA-haplotypes and the local healthy controls.