A molecular approach (multiplex polymerase chain reaction) for diagnosis of rhinosporidiosis

A New multiplex PCR have been developed in our laboratory using primer sets, aiming amplification of both D.N.A target fragments obtained in 18S RNA of commonly encountered fungi in human being and in Rhinosporidium seeberi using F1-fw/F2-rev (500 bp target) and Rhino-fw/ Rhino-rev (.177 bp target). This multiplex PCR has been found to be able to delect R. seeberi from clinical samples and differentiate it from other fungi. Furthermore, by this multiplex PCR, R. seeberi, phylogenitically appears to belong to a member of so called DRIPs clade of fish parasite not a cyanobacterium as claimed previously, by some workers.     

Polish population study on Y chromosome haplotypes defined by 18 STR loci

Polymorphism of 18 STR loci specific to the human Y chromosome (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS426, DYS437, DYS438, DYS439, DYS460, GATA H4.1, DYS385 a/b, and YCAII a/b) was evaluated by means of a multiplex (octadecaplex) PCR reaction and capillary electrophoresis in a Polish population sample of 208 unrelated males. A total of 192 different haplotypes and 183 unique haplotypes were identified. The observed haplotype diversity was 0.998, while discrimination capacity was 92.3%. DYS389 was shown to be the most valuable in discrimination of similar haplotypes, whereas DYS388, DYS393, DYS426, and DYS438 did not affect the discrimination power of the multiplex.Electronic Supplementary Material Supplementary material is available for this article at .     

Application of multiplex ligation-dependent probe analysis to define a small deletion encompassing PMP22 exons 4 and 5 in hereditary neuropathy with liability to pressure palsies

Hereditary neuropathy with liability to pressure palsies arises as a result of defects at the chromosome 17p11.2-12 locus and in 84% of cases a 1.5 Mb deletion containing the PMP22 gene is detected by analysis that utilises polymorphic (CA)_n repeat markers which flank this gene. We report the clinical and electrophysiological findings observed in a kindred with three members affected by HNPP due to a deletion containing exons 4 and 5 of the PMP22 gene. This small deletion cannot be detected using standard analysis with polymorphic (CA)_n repeat markers and a definitive diagnosis was made by multiplex ligation-dependent probe analysis of PMP22 exons 1A-5. MLPA can be readily utilised as a routine diagnostic laboratory test to detect the common HNPP 1.5 Mb deletion, as well as the reciprocal 1.5 Mb insertion observed in CMT1A, but has the advantage over other diagnostic techniques of being able to define single exon deletions.     

多重PCR法检测Y染色体微缺失

目的探讨多重PCR法检测Y染色体微缺失对男性不育患者的病因学诊断价值。方法采用多重PCR法检测男性不育患者和正常男性Y染色体AZF座位的缺失情况。结果106例患者中Y染色体微缺失28例,缺失率26.4%,30例正常男性Y基因均未发现缺失。结论Y染色体微缺失是不明原因性无精子症或严重少精子症的病因之一,多重PCR检测技术具有快速、高效、灵敏度高等特点。     

Multiplex PCR assay for identification of three major pathogenic Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus

A multiplex PCR assay was developed based on atpA-sequence diversification for molecular identification of 3 major pathogenic Vibrio species: Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. It specifically identified them from among 133 strains of various Vibrio species and other genera, and was applicable for testing seawater, suggesting its usefulness.     

多重聚合酶链反应检测革兰阴性杆菌中质粒介导ampC基因

目的运用多重聚合酶链反应（PCR）检测革兰阴性杆菌的质粒ampC基因,了解该基因在我院的流行情况。方法采用头孢西丁初筛试验筛选出符合头孢菌素酶（AmpC）表型筛选条件的大肠埃希菌、肺炎克雷伯菌共50株,通过热裂解法进行DNA抽提,采用6组ampC特异引物进行PCR扩增,琼脂糖凝胶电泳区分PCR产物,进一步DNA测序确定其基因型。结果50株试验菌中有8株为阳性,分别为肺炎克雷伯菌5株,大肠埃希菌3株,基因型为CIT型1株,DHA型4株,EBC型3株。结论我院质粒介导ampC基因型主要为DHA型、EBC型和CIT型。多重PCR是特异性高、简便检测质粒ampC基因型的分子生物学方法。     

自行设计的多重链接探针扩增组合对多发畸形患儿的诊断价值

目的 尝试基于多重链接探针扩增（MLPA）技术设计的探针组合对多发畸形(MCA)患儿的诊断价值。方法 以临床发现≥2个的畸形表型患儿为病例,基于MLPA技术选择13种常见的MCA的关键基因和关键区域自行设计MLPA探针组合（SIGMA公司合成）,以微阵列比较基因组杂交（aCGH）作为金标准,检验该探针组合的诊断准确性,再以MLPA探针组合行MCA临床诊断效果评估,对MLPA探针组合阳性的病例结合临床资料进行分析。结果 ①MLPA探针组合涉及的13种常见MCA,包括：21-三体综合征（KCNJ6、DYRK1A、RCAN1基因）、18-三体综合征（MC2R、DTNA、TCF4基因）、13-三体综合征（EDNRB、CENPJ、ERCC5、FREM2基因）、1p36区域缺失综合征（GABRD、SKI、TP73基因）、 5q35.3区域缺失综合征（Sotos综合征,NSD1基因）、CHARGE综合征（CHD7基因）、7q11.23区域缺失综合征（Williams Beuren综合征,CLIP2、ELN、LIMK1基因）;22q11.21区域缺失、重复综合征（DiGeorge综合征,SNAP29、TBX1、ZNF74基因）、17p11区域缺失综合征（Smith-Magenis综合征,RAI1、MFAP4基因）、5p15.2区域缺失综合征（Cri du Chat综合征, CTNND2、TERT基因）、15q11-13区域缺失综合征（Prader-Willi综合征,OCA2、UBE3A、GABRB3基因）、4p16.3区域缺失综合征（Wolf Hirschhorn综合征,MSX1、WHSC1、LETM1基因）、17q21.31区域缺失综合征（MAP3K14、MAPT基因）。②35例MCA中,aCGH检测阳性11例（31.4%）,共诊断9种;MLPA探针组合检测阳性6例（17.1%）,共诊断4种;MLPA组合探针检测阳性的6例微缺失和重复与11例aCGH检测阳性一致,6例MLPA探针组合检测阳性的变异位点均位于设计的MLPA探针组合中,122例临床MCA中,MLPA探针组合检测阳性21例（17.2%）,诊断6种。③在157例MCA患儿中,应用MLPA探针组合共诊断阳性病例27例,共检出7种（53.8%）,分别为21-三体综合征8例,18-三体综合征1例,5p15区域缺失综合征3例,22q11区域重复综合征1例、缺失综合征9例,5q35区域缺失综合征1例,15q11-q13区域缺失综合征3例,7q11.23区域微缺失综合征1例。结论 自行设计合成的MLPA探针组合对非典型临床表型的MCA病例有较好的诊断价值。     

Can we integrate method-specific age-predictive models?: Analysis method-induced differences in detected DNA methylation status

Forensic research surrounding the use of DNA methylation (DNAm) markers to predict age suggests that accurate prediction of chronological age can be achieved with just several DNAm markers. Several age-prediction models are based on DNAm levels that are detectable by a diverse range of DNAm analysis methods. Among the many DNAm analysis methods, targeted amplicon-based massively parallel sequencing (MPS) and single-base extension (SBE) methods have been widely studied owing to their practicality, including their multiplex capabilities. Since these two DNAm analysis methods share an identical amplification step during their experimental processes, several studies have compared the differences between the methods to construct integrated age-prediction models based on both MPS and SBE data. In this study, we compared the specific differences in DNAm levels between these two commonly exploited analysis methods by analyzing the identical PCR amplicons from the same samples and quantifying the actual bisulfite-converted DNA amount involved in the PCR step. The DNAm levels of five well-studied age-associated markers—CpGs on the ELOVL2, FHL2, KLF14, MIR29B2CHG, and TRIM59 genes—were obtained from blood samples of 250 Koreans using both DNAm analysis methods. The results showed that only ELOVL2 is interchangeable between the MPS and SBE methods, while the rest of the markers showed significant differences in DNAm values. These differences may result in high errors and consequential lowered accuracy in age estimates. Therefore, a DNAm analysis method-specific approach that considers method-induced DNAm differences is recommended to improve the overall accuracy and reliability of age-prediction methods.     

The development and evaluation of a single step multiplex PCR method for simultaneous detection of Brugia malayi and Wuchereria bancrofti

A single step novel multiplex polymerase chain reaction (PCR) has been developed for simultaneous detection of human filarial parasites, Brugia malayi and Wuchereria bancrofti, from blood samples and mosquitoes. The primers used were novel and have been tested with the parasite DNA amplifying 188bp (BM) and 129bp (WB) DNA fragments, specific to B. malayi and W. bancrofti, respectively, in a single reaction. The specificity of the PCR product was confirmed by DNA sequencing and slot blot hybridization assay. The test was found highly sensitive for both B. malayi and W. bancrofti by detecting the parasitaemia up to the level of one microfilaria per reaction. The assay was further evaluated on 98 blood samples and 144 mosquito samples collected from filarial endemic areas. The PCR was found to be more efficient in comparison to microscopy by detecting 8% and 5% more filarial parasites in field-collected blood and mosquito samples, respectively. This novel PCR that offers scope for simultaneous detection of both the parasites may be used as a diagnostic tool for the detection of filariasis in population and can be adopted for rapid surveillance and monitoring of mosquitoes for use in the effective control of filariasis.