A genetic typing method for albino mutation in the Mongolian gerbil by PCR‐RFLP analysis
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1. We established a PCR-RFLP analysis targeting R77H mutation in the Tyr gene as a more effective genotyping to identify carrier (C/c) with the albino allele and the agouti phenotypes. 2. Our breeding system, which targets the R77H site, is a useful cue for detecting C/c carriers with the agouti-phenotype and helps us to obtain albinos by mating agouti-phenotype carriers.Keywords:
Genetic Analysis
Objective:A comparison study of polymerase chain reaction (PCR) and serological typing method was used to detect HLA B27.Methods:78 samples from patients suspected with ankylosing spondylitis (AS) were genotyped by PCR and some of them were assayed by serological typing.Results:24/36 samples with HLA B27 gene were compared with serological typing ,the results of 5 samples serological typing were dubious or contradictory with PCR genotyping.21/42 samples without HLA B27 gene were compared with serological typing,the results of 3 samples serological typing were dubious.Conclusion:The method of B27 genotyping by PCR is more rapid,inexpensive and exact than phenotyping by serology.
HLA-B27
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Some individuals are at risk of anti-D alloimmunization if they inherit D antigens that are qualitatively and/or quantitatively different than wild-type D. We hypothesized that patients who showed serologically inconsistent, weak, or historically discordant D typing results by microplate direct agglutination (MDA) on NEO or Echo (Immucor, Norcross, GA) might be at risk of carrying RHD allelic variants. The present study was designed to evaluate patients with RHD allelic variants if they presented with weakly reactive D typing results on the NEO or Echo. Patients were selected for RHD genotyping if their specimens showed weak reactivity with either series 4 or series 5 anti-D typing reagent, if the strength of reactivity was ≤1+ on the NEO or Echo, or if historical or current D typing results were discordant with current results. Patients selected for RHD genotyping were also tested by saline tube testing using the same anti-D series 4 and 5 reagents. Genotyping was performed by the Immucor genotyping laboratory in Warren, NJ. Of 80 patients whose samples met study inclusion, 52 (65.0%) were found to have RHD allelic variants. Sixteen patients (20.0%) expressed possible Ceppellini effect reactivity. Most importantly, 51.25 percent of the patients who presented with weakly reactive D typing results by MDA testing on the NEO (≤1+) or Echo (≤1+) had RHD allelic variants that were associated with the potential for anti-D alloimmunization. Laboratories that use MDA testing on the Neo or Echo for D typing should consider that female patients of childbearing age might be at risk of anti-D alloimmunization if they are classified as D+ based on weakly reactive D typing results.Some individuals are at risk of anti-D alloimmunization if they inherit D antigens that are qualitatively and/or quantitatively different than wild-type D. We hypothesized that patients who showed serologically inconsistent, weak, or historically discordant D typing results by microplate direct agglutination (MDA) on NEO or Echo (Immucor, Norcross, GA) might be at risk of carrying RHD allelic variants. The present study was designed to evaluate patients with RHD allelic variants if they presented with weakly reactive D typing results on the NEO or Echo. Patients were selected for RHD genotyping if their specimens showed weak reactivity with either series 4 or series 5 anti-D typing reagent, if the strength of reactivity was ≤1+ on the NEO or Echo, or if historical or current D typing results were discordant with current results. Patients selected for RHD genotyping were also tested by saline tube testing using the same anti-D series 4 and 5 reagents. Genotyping was performed by the Immucor genotyping laboratory in Warren, NJ. Of 80 patients whose samples met study inclusion, 52 (65.0%) were found to have RHD allelic variants. Sixteen patients (20.0%) expressed possible Ceppellini effect reactivity. Most importantly, 51.25 percent of the patients who presented with weakly reactive D typing results by MDA testing on the NEO (≤1+) or Echo (≤1+) had RHD allelic variants that were associated with the potential for anti-D alloimmunization. Laboratories that use MDA testing on the Neo or Echo for D typing should consider that female patients of childbearing age might be at risk of anti-D alloimmunization if they are classified as D+ based on weakly reactive D typing results.
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Objective To study the method for human leukocyte antigen (HLA) typing. Methods HLA
genotyping was performed by using PCRSSP and PCRSSCP in 20 pairs of bone marrow
transplantation donorrecipients who underwent serologic typing. DNA from 20 pairs of samples
were extracted by a fast salting out method. Results The serological and genotyping results
were identical in 18 cases, serological typing was failure in 2 cases who could be typed easily
by genotyping methods. Between the two genotyping methods, there were 19 cases of identical
results and 1 case of different results. After the patient received the graft, he got grade graft
versus host disease (GVHD). Conclusion The combined application of PCRSSP and PCRSSCP
was an ideal typing method and might be helpful to accurately tpye HLA.
Tissue typing
Histocompatibility Testing
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Abstract Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low‐cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes Hpy CH4V and Nla III. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR‐positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non‐specific amplifications with PCR. In conclusion, this PCR‐RFLP method using restriction enzymes Hpy CH4V and Nla III is simple, non‐labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples. J. Med. Virol. 85:1229–1234, 2013 . © 2013 Wiley Periodicals, Inc.
Papillomaviridae
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BackgroundGenotyping of Neisseria gonorrhoeae (NG) is essential for surveillance to monitor NG transmission and dissemination of resistant strains. Current genotyping methods rely on bacterial culture which frequently fails.AimOur aim was to develop a culture-free genotyping method that is compatible with the widely used N. gonorrhoeae multi-antigen sequence typing (NG-MAST) database, which facilitates genotyping of NG detected at separate anatomical sites in individual patients.MethodsSpecific primers for both PCR targets porB and tbpB were designed and technically validated by assessing the analytical sensitivity, cross-reactivity with 32 non-gonoccocal Neisseria species, and concordance with NG-MAST. Clinical application was assessed on 205 paired samples from concurrent NG infections at different anatomical sites of 98 patients (81 men who have sex with men and 17 women) visiting our sexually transmitted infections clinic.ResultsTyping could be consistently performed on samples with a PCR quantification cycle (Cq) value <35. Furthermore, the method showed no cross-reactivity and was concordant with NG-MAST. Culture-free NG-MAST improved the typing rate from 62% (59/95) for cultured samples to 94% (89/95) compared with culture-dependent NG-MAST. Paired samples of 80 of 98 patients were genotyped, revealing distinct NG strains in separate anatomical sites in 25% (20/80) of the patients.ConclusionsThis NG-specific genotyping method can improve NG surveillance as it facilitates genotyping of non-culturable and extra-genital samples. Furthermore, 25% of patients were infected with multiple NG strains, which is missed in current culture-dependent surveillance. Including non-culturable and concurrent NG infections in surveillance informs actions on dissemination of multidrug-resistant NG strains.
Neisseria gonorrhoeae
Concordance
Neisseria
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The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.
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Objective To evaluate the effects of serological typing and PCR-SSP genotyping which were used for Rh blood typing and genetic basis of the Rh D- index case and her family members. Methods Rh D,C, c, E, e antigens were detected by serological typing. The characteristic sequence fragments of RHD and RHCE were amplified by PCR-SSP with a commercial reagent. Results Rh phenotypes of the proband' s family members were normal. The genotypes of PCR were consistent with their serological phenotypes. The full specific RHD bands of the proband were found. No specific RHCE bands were detected. The full specific bands of RHD and RHCE of her family members were normal. Conclusion Serological typing and PCR-SSP genotyping were complementary to RhD- diagnosis. Combination of the two technologies can help to analyze the genetic background of RhD-.
Key words:
RhD-; Serological typing; PCR-SSP; Genotyping; Genetic background
Proband
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ABSTRACT The combination of preventive vaccination and diagnostic typing of viral isolates from patients with clinical poliomyelitis constitutes our main protective shield against polioviruses. The restriction fragment length polymorphism (RFLP) adaptation of the reverse transcriptase (RT)-PCR methodology has advanced diagnostic genotyping of polioviruses, although further improvements are definitely needed. We report here on an improved RFLP procedure for the genotyping of polioviruses. A highly conserved segment within the 5′ noncoding region of polioviruses was selected for RT-PCR amplification by the UC 53 -UG 52 primer pair with the hope that it would be most resistant to the inescapable genetic alteration-drift experienced by the other segments of the viral genome. Complete inter- and intratypic genotyping of polioviruses by the present RFLP method was accomplished with a minimum set of four restriction endonucleases ( Hae III, Dde I, Nco I, and Ava I). To compensate for potential genetic drift within the recognition sites of Hae III, Dde I, or Nco I in atypical clinical samples, the RFLP patterns generated with Hpa II and Sty I as replacements were analyzed. The specificity of the method was also successfully assessed by RFLP analysis of 55 reference nonpoliovirus enterovirus controls. The concerted implementation of these conditional protocols for diagnostic inter- and intratypic genotyping of polioviruses was evaluated with 21 clinical samples with absolute success.
Restriction site
Restriction fragment
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Primer (cosmetics)
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In principle, restriction fragment length polymorphism (RFLP) typing can be applied to strains of all mycobacterial species for which suitable probes have been identified. International consensus has been achieved regarding the methodology of IS6110 RFLP typing of Mycobacterium tuberculosis complex isolates (1) and IS1245 RFLP typing of Mycobacterium avium strains (2). This chapter describes the technical details of these standardized methods regarding the isolation of DNA, restriction enzymes, electrophoresis conditions, internal- and external-size markers, Southern blotting, and several probes used for hybridization. Furthermore, RFLP typing of isolates of some other mycobacterial species is described.
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