Potential misdiagnosis of factor V Leiden: a comparison of two genotyping techniques.
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Factor V↗
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DNA-based genotyping techniques for the detection of point mutations associated with insecticide resistance in Colorado potato beetle Leptinotarsa decemlineata.
Three DNA-based genotyping techniques, bi-directional PCR amplification of specific allele (bi-PASA), single-stranded conformational polymorphism (SSCP) and minisequencing, have been developed and compared for the detection of the S291G (insensitive acetylcholinesterase) and L1014F (insensitive sodium channel) mutations associated with azinphos-methyl and permethrin resistance, respectively, in the Colorado potato beetle (Leptinotarsa decemlineata). Extraction of genomic DNA from individual neonates that were hatched from previously collected egg masses is the most efficient and reliable means to obtain suitable templates in terms of convenience, economy, speed and DNA quality. Bi-PASA, employing two allele-specific primers, appears to be the most efficient and rapid genotyping method for the simultaneous detection of both resistant/susceptible homozygous (SS, RR) and heterozygous (SR) alleles. Its resolution, however, is strongly dependent on the quality of template genomic DNA. SSCP also allows unambiguous genotyping, including the detection of heterozygous alleles, and is less dependent on template DNA quality, but requires a longer processing time. Minisequencing is amenable to a 96-well microtiter plate format for the processing of a large number of samples and allows direct detection of resistant/susceptible homozygous alleles but is not as efficient as the PASA and SSCP in detecting heterozygous alleles. In considering the advantages and disadvantages of each technique, DNA-based genotyping is best employed in combinations, with the bi-PASA as the primary method and the SSCP and minisequencing as the secondary validating methods. These methods are rugged, rapid, cost-effective and capable of resolving SS, RR and SR individuals. The availability of such DNA-based genotyping techniques, using neonate genomic DNA as templates, will enable the precise monitoring of the resistant and susceptible allele frequencies, including those of heterozygote individuals, in field populations of L. decemlineata.
Acetylcholinesterase↗
Comparison of five genotypic techniques for identification of optochin-resistant pneumococcus-like isolates.
Three PCR techniques (amplification of the psaA, ply, and lytA genes) and a commercial kit (AccuProbe [GenProbe, San Diego, Calif.], based on hybridization with the 16S rRNA gene), all four of which claimed to be specific for Streptococcus pneumoniae, were used to identify 49 alpha-hemolytic streptococcal isolates suspected of being pneumococci. The definite phenotypic identification of these organisms as S. pneumoniae was difficult when optochin susceptibility and the presence of a capsule were taken as markers. Furthermore, RsaI digestion of the amplified 16S rRNA gene was applied. All 49 strains were optochin resistant. Eleven of these were encapsulated and were identified as pneumococci by all tests. Twenty of the 38 unencapsulated strains were unambiguously identified as nonpneumococci by all tests. The identities of another 18 unencapsulated strains remained inconclusive due to highly variable reactions for all phenotypic and genotypic techniques applied. The AccuProbe test was positive for seven strains for which the results of the other tests were inconclusive. RsaI restriction of the amplified 16S rRNA gene confirmed the AccuProbe result for all strains, while the result of the psaA-specific PCR was in concordance with encapsulation for all strains. The results presented here indicate that identification problems continue to exist for some strains, despite the application of genotypic and phenotypic tests in combination. We found the psaA-specific PCR to be the genotypic technique best suited for the identification of genuine pneumococci and optochin-resistant pneumococci.
Bacterial Typing Techniques↗
Evaluation of Cryptosporidium parvum genotyping techniques.
We evaluated the specificity and sensitivity of 11 previously described species differentiation and genotyping PCR protocols for detection of Cryptosporidium parasites. Genomic DNA from three species of Cryptosporidium parasites (genotype 1 and genotype 2 of C. parvum, C. muris, and C. serpentis), two Eimeria species (E. neischulzi and E. papillata), and Giardia duodenalis were used to evaluate the specificity of primers. Furthermore, the sensitivity of the genotyping primers was tested by using genomic DNA isolated from known numbers of oocysts obtained from a genotype 2 C. parvum isolate. PCR amplification was repeated at least three times with all of the primer pairs. Of the 11 protocols studied, 10 amplified C. parvum genotypes 1 and 2, and the expected fragment sizes were obtained. Our results indicate that two species-differentiating protocols are not Cryptosporidium specific, as the primers used in these protocols also amplified the DNA of Eimeria species. The sensitivity studies revealed that two nested PCR-restriction fragment length polymorphism (RFLP) protocols based on the small-subunit rRNA and dihydrofolate reductase genes are more sensitive than single-round PCR or PCR-RFLP protocols.
Animals↗
PCR-CTPP: a new genotyping technique in the era of genetic epidemiology.
A new PCR method, PCR-CTPP (polymerase chain reaction with confronting two-pair primers) was invented to genotype a relatively large number of samples in a cost-effective and time-saving manner. In this method, allele-specific DNA products are amplified by means of applying appropriately designed two-pair primers (four primers) into an ordinary PCR tube. Single genotyping for G2886T at L-myc, Arg72Pro of p53 and Glu487Lys of ALDH2 as well as duplex genotyping for C-31T of IL-1B with VNTR of IL-1RN and A385T of secretor gene with se5, are demonstrated as examples with the primers and PCR conditions.
DNA Primers↗
Endocarditis of native aortic and mitral valves due to Corynebacterium accolens: report of a case and application of phenotypic and genotypic techniques for identification.
Endocarditis of native aortic and mitral valves due to an organism identified as Corynebacterium accolens developed in a 73-year-old patient without predisposing factors. The organism was identified as C. accolens by biochemical identification, amplified rRNA gene restriction analysis, and DNA-DNA hybridization. This is the first case of C. accolens endocarditis reported, adding to the increasing number of Corynebacterium-related cases of endocarditis.
Aged↗
The application of genotyping techniques to the epidemiological analysis of Campylobacter jejuni.
Campylobacter jejuni serogroup reference strains and collections of sporadic and outbreak-associated isolates were examined for restriction fragment length polymorphisms (RFLPs), using C. jejuni random chromosomal and 16S rRNA gene probes. A collection of 48 Penner (HS) and 14 Lior (HL) serogroup reference strains, plus 10 clinical isolates, generated 35 RFLP and 26 ribotype patterns. In combination the two loci generated 48 distinct genotypes. Both probes were able to differentiate between certain random isolates of the same HS/HL serogroups but greater discrimination was obtained with RFLP than with ribotyping. Genotyping distinguished accurately between related and unrelated strains when applied to several outbreaks. Genotypic analysis of C. jejuni by restriction fragment length polymorphisms is a valuable technique for epidemiological typing. Chromosomal variation detected by the two unlinked probe loci provides some information about the genetic relationship between isolates.
Campylobacter Infections↗
Orogenital transmission of Neisseria meningitidis serogroup C confirmed by genotyping techniques.
Urethritis caused by Neisseria meningitidis in heterosexual patients is presumed to occur via orogenital contact, but confirmation has not been possible in most cases. Presented here is a case of urethritis caused by N. meningitidis, serogroup C, and the isolation of the same microorganism from the nasopharynx and endocervix of the patient's sexual partner. The similarity of the urethral and nasopharyngeal isolates' electrophoretic patterns, obtained using pulsed-field gel electrophoresis, proves the infection was transmitted via orogenital contact.
Adult↗
Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli.
Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. We used identification systems based on cellular fatty acid profiles (Sherlock; MIDI, Inc., Newark, Del.), carbon source utilization (Microlog; Biolog, Inc., Hayward, Calif.), and 16S rRNA gene sequence (MicroSeq; Perkin-Elmer Applied Biosystems Division, Foster City, Calif.) to evaluate 72 unusual aerobic gram-negative bacilli isolated from clinical specimens at the Mayo Clinic. Compared to lengthy conventional methods, Sherlock, Microlog, and MicroSeq were able to identify 56 of 72 (77.8%), 63 of 72 (87.5%), and 70 of 72 (97.2%) isolates to the genus level (P = 0.002) and 44 to 65 (67.7%), 55 of 65 (84.6%), and 58 of 65 (89.2%) isolates to the species level (P = 0.005), respectively. Four Acinetobacter and three Bordetella isolates which could not be identified to the species level by conventional methods were identified by MicroSeq. In comparison to the full 16S rDNA sequences, the first 527 bp provided identical genus information for all 72 isolates and identical species information for 67 (93.1%) isolates. These data show that MicroSeq provides rapid, unambiguous identification of clinical bacterial isolates. The improved turnaround time provided by genotypic identification systems may translate into improved clinical outcomes.
Carbon↗
Streptococcus cristatus isolated from a resected heart valve and blood cultures: case reports and application of phenotypic and genotypic techniques for identification.
BACKGROUND: Viridans streptococci are known as an important cause of endocarditis, but at present no cases of endocarditis caused by Streptococcus cristatus have been published, probably because phenotypic identification of viridans streptococci is tedious. Using tDNA-PCR, it is possible to identify to species level and to differentiate between species of the viridans group.
Adult↗
The mutagenically separated polymerase chain reaction is a rapid and reliable method for genotyping of the tumour necrosis factor-alpha promoter polymorphism (-308 G/A).
BACKGROUND: The tumour necrosis factor-alpha (TNF alpha) promoter polymorphism (-308 G/A) has been shown to be associated with the susceptibility to and/or the severity of diverse diseases such as infections, autoimmunity, and malignancies. We developed a genotyping technique based on the mutagenically separated polymerase chain reaction (MS-PCR) which may be useful in the clinical risk assessment. METHODS: Different length allele-specific primers and an unspecific complementary strand primer were used in a one-tube assay. At least one PCR product was generated in a single reaction obviating the need for an internal control amplification. Introduction of additional base substitutions into the allele-specific primers led to a clear-cut separation between the alleles through the reduction of cross-reactions during amplification. The only post-PCR step required was the separation of allelic PCR products by size upon agarose gel electrophoresis. RESULTS: The allele frequencies in 300 German healthy Caucasians were 0.84 for TNF1 (-308 G) and 0.16 for TNF2 (-308 A) in accordance with published data obtained with the conventional RFLP method. No significant deviation from Hardy-Weinberg equilibrium was observed. The specificity of MS-PCR was confirmed by sequence-based typing. CONCLUSIONS: MS-PCR is a rapid, reliable, and cost-effective technique for genotyping of the TNF alpha promoter polymorphism (-308 G/A).
Adult↗
Multiplexing schemes for generic SNP genotyping assays.
Association studies in populations relate genomic variation among individuals with medical condition. Key to these studies is the development of efficient and affordable genotyping techniques. Generic genotyping assays are independent of the target SNPs and offer great flexibility in the genotyping process. Efficient use of such assays calls for identifying sets of SNPs that can be interrogated in parallel under constraints imposed by the genotyping technology. In this paper, we study problems arising in the design of genotyping experiments using generic assays. Our problem formulation deals with two main factors that affect the genotyping cost: the number of assays used and the number of PCR reactions required for sample preparation. We prove that the resulting computational problems are hard, but provide approximate and heuristic solutions to these problems. Our algorithmic approach is based on recasting the multiplexing problems as partitioning and packing problems on a bipartite graph. We tested our algorithmic approaches on an extensive collection of synthetic data and on data that was simulated using real SNP sequences. Our results show that the algorithms achieve near-optimal designs in many cases and demonstrate the applicability of generic assays to SNP genotyping.
Algorithms↗
[Progress and prospects of HLA genotyping technology].
Over a long period of time, studies on HLA structure and function have been the research hotspots. for it is very important to understand the essential of life science and disease mechanism. With the rapid development of molecular biology, HLA typing makes great progress. It has changed from traditional serological typing to DNA-based typing. More and more HLA genotyping methods have been developed and applied. In this essay, the author reviewed and appraised all kinds of HLA genotyping techniques and introduced two new techniques.
DNA Primers↗
Hepatitis C virus genotyping versus serotyping in Egyptian patients.
BACKGROUND: The RNA genome of hepatitis C virus (HCV) displays extensive sequence variation. In this study, serotyping and genotyping techniques were applied to assess this variability by comparing the performance of the serotyping assay with a panel of well-characterized HCV strains isolated from chronic active hepatitis (CAH) patients. PATIENTS AND METHODS: 60 serum samples from CAH patients were analyzed. All isolates were genotyped by a line probe assay and the results of genotyping and serotyping were evaluated. RESULTS: The overall sensitivity of the serotyping and genotyping techniques was 81.16% with a concordance of 73.3%. Type 4 was detected in 73.3% of cases and it was highly heterogeneous. CONCLUSION: Type 4 HCV is the most prevalent type in Egyptian CAH patients and there is a high concordance between the results of serotyping and genotyping techniques.
Egypt↗
Comparison of genotypic and phenotypic techniques for assessing the variability of the fungus Epicoccum nigrum.
AIMS: The diversity within a collection of worldwide isolates of Epicoccum nigrum has been studied using several phenotypic approaches. In addition, the abilities of phenotypic and genotypic techniques for the differentiation of a set of isolates are compared. METHODS AND RESULTS: The methodology used include the study of isozymes (acetyl esterase and alkaline phosphatase), HPLC profile of metabolites and antibiotic activities against a panel of bacteria, yeasts and filamentous fungi, and cytotoxicity against three mammalian cell lines. Two procedures for assessing the relationships within a collection of isolates, using a combination of the techniques, were evaluated, comparing the advantages and disadvantages of each method. CONCLUSIONS: The results showed that each individual technique allows differentiation of the isolates studied to some degree and that the information provided by each technique could be considered as complementary. Genotypic techniques were more powerful than the phenotypic ones to discriminate among the strains. SIGNIFICANCE AND IMPACT OF THE STUDY: This work evaluates the predictive value of several phenotypic techniques on a collection of fungal isolates, and compares the results obtained with genotypic techniques performed on the same strains.
Acetylesterase↗
Molecular polymorphism of Kaposi's sarcoma-associated herpesvirus (Human herpesvirus 8) latent nuclear antigen: evidence for a large repertoire of viral genotypes and dual infection with different viral genotypes.
Molecular polymorphism was found in Kaposi's sarcoma-associated herpesvirus (KSHV) latent nuclear antigen (LNA), mapped to the internal repeat domain of the encoding orf73 gene, and used to develop a novel genotyping technique, KSHV LNA genotyping (KVNAtyping). KVNAtype was stable during latent and lytic viral replication in cell culture and in humans. Diverse KVNAtypes were identified in 43 specimens: 6 KSHV cell lines and 6 Kaposi's sarcoma (KS) and 4 primary effusion lymphoma (PEL) tumor samples from the United States, 15 KS tumor samples from Italy, and 12 KS tumor samples from Zambia. A single KVNAtype was detected in each of 41 specimens, and 2 KVNAtypes were detected in each of 2 KS specimens. Multifocal KS from 3 patients showed the same single KVNAtype at all sites in each patient. These results demonstrate a large repertoire of KSHV genotypes and suggest that the development of most KSs and PELs is associated with a single viral genotype.
Antigens, Viral↗
Molecular genotyping of human cryptosporidiosis in Northern Ireland: epidemiological aspects and review.
BACKGROUND: Cryptosporidium parvum is the most common of the protozoal pathogens associated with gastrointestinal disease in Northern Ireland. Genotyping techniques are valuable in helping to elucidate sources and modes of transmission of this parasite. There have been no reports on the prevalence of genotypes in Northern Ireland, mainly due to a lack of discriminatory genotyping techniques, which recently have become available. AIM: To investigate the genotype of C. parvum oocysts isolated from human faeces in sporadic cases of cryptosporidiosis in Northern Ireland. METHODS: Thirty-nine isolates of C. parvum, representing 79.6% of the total 1998 laboratory reports for the Eastern Health and Social Services Board, were investigated. Following DNA extraction from oocysts the thrombospondin-related adhesive protein 2 (TRAP-C2) locus was amplified by polymerase chain reaction (PCR) and subsequently sequenced. RESULTS: The majority of isolates (87.2%) were classified as bovine genotype II with the remainder (12.8%) being the human genotype I. CONCLUSIONS: There is a high prevalence of the bovine genotype II parasite in sporadic cases around the greater Belfast area. Epidemiologically, this suggests that the most frequent mode of transmission may be from animals to humans, but does not suggest a high proportion of human to human spread.
Adolescent↗
Establishment of the amplified fragment length polymorphism (AFLP) technique for genotyping of pollen beetle (Meligethes aeneus)--a noxious insect pest on oilseed rape (Brassica napus).
In order to conduct studies concerning genetic variability of pollen beetles (Meligethes aeneus), a genotyping protocol was established. No genome information is available for pollen beetles so the amplified fragment length polymorphism (AFLP) technique was chosen since it does not depend on any prior sequence information of the samples and also is a sensitive and robust technique. However, several modifications were needed in order to adapt the method for analysis of pollen beetles. Basic modifications included (i) alterations of DNA purification, (ii) use of two six-cutter restriction enzymes, (iii) and modified PCR conditions. This protocol resulted in a favourable number of fragments of an appropriate size range for standard gel analysis by a DNA sequencer applicable to a single insect and even body parts enabling different assays to be conducted on a single specimen. Pollen beetles from different areas of Sweden were analysed to verify the reproducibility and efficacy of the protocol as well as for phenetic analysis. The high reproducibility of the modified AFLP protocol allows it to be used as a reliable tool for genotype analysis of pollen beetles.
Animals↗