Quantification of Epstein-Barr virus load in peripheral blood of human immunodeficiency virus-infected patients using real-time PCR

Epstein-Barr virus (EBV) reactivation is more likely to occur in immunocompromised patients with subsequent higher susceptibility to EBV-associated lymphoproliferations. In contrast to transplant recipients, limited data are available concerning the EBV load in HIV-infected patients, with or without AIDS-related non-Hodgkin's lymphomas. We developed a TaqMan real-time PCR assay, allowing both the EBV genome and a cellular gene to be quantified in order to obtain a reliable normalized measurement of the EBV load in peripheral blood mononuclear cells (PBMCs). With a wide 6-log(10) quantification range and inter-assay variations of less than 24%, this quantitative PCR was sufficiently accurate and reproducible for routine follow-up. The EBV load was determined in PBMCs from 113 HIV-infected patients, 11 patients with primary HIV infection and 24 HIV-seronegative healthy controls. The rates of EBV detection were similar in the three groups. However, EBV loads were higher in the HIV-infected group (P < 0.00001) except for the patients with primary HIV infection. Unexpectedly, EBV loads were not correlated with the clinical stages of HIV infection or HIV replication, and did not depend on the degree of immunodepression, as judged by CD4+ counts. This study contributes towards the definition of the baseline EBV load during HIV infection and stresses the broad inter-individual variability of the EBV load in HIV-infected patients. Real-time PCR provides a useful tool that can be used in further longitudinal studies to assess the relevance of the EBV load to identify HIV-infected patients with a high risk of EBV-associated lymphoproliferations.     

Variation in microdeletions of the cyclic AMP‐responsive element‐binding protein gene at chromosome band 16p13.3 in the Rubinstein‐Taybi syndrome

Most reported microdeletions of the CREB‐binding protein (CBP) gene in the Rubinstein‐Taybi syndrome (RTS) were detected by fluorescence in situ hybridization (FISH) with a single cosmid probe specific to the 3′ region of the gene. In order to test the hypothesis that the rate of microdeletion‐positive cases would be greater if the entire gene was evaluated, we performed FISH on 66 patients with an established diagnosis of RTS, using a panel of five cosmids that span the CBP gene. Five of 66 patients had deletions by FISH (9%), consistent with those rates reported in various series that ranged between 3–25%. Among our cases, different deletions were observed; one was deleted for the 5′ but not the 3′ region of the CBP gene (case 055). Other deletions included a total CBP deletion extending from the 5′ through the 3′ region (case 017), a deletion of all but the 5′ region (cases 006 and 060), and an interstitial deletion in the 3′ region (case 028). Fine breakpoint mapping with additional cosmid and yeast artificial chromosome (YAC) constructs was performed on these patients. The findings of a partial 5′ deletion and of interstitial deletions of the CBP gene add to the known spectrum of mutations of this gene in RTS and demonstrate the need for evaluation of the entire CBP gene region for deletions rather than only the 3′ region in RTS patients. These results further suggest that the true rate of microdeletion across the CBP gene detectable by FISH has yet to be established firmly. No phenotypic differences between partial deletion, complete deletion, and nondeletion patients were observed, supporting a haploinsufficiency model for RSTS. Am. J. Med. Genet. 90:29–34, 2000. © 2000 Wiley‐Liss, Inc.     

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.     

实时荧光定量PCR在周围髓鞘蛋白22基因重复或缺失检测中的应用

目的 应用实时荧光定量PCR在腓骨肌萎缩症和遗传性压力易感性神经病患者中检测周围髓鞘蛋白22基因（peripheral myelin protein 22，PMP22）重复或缺失。方法 采用实时荧光定量PCR检测113个腓骨肌萎缩症家系先证者、4个遗传性压力易感性神经病家系先证者和50名正常人PMP22基因重复或缺失突变。结果 113个腓骨肌萎缩症家系中发现有36个存在PMP22基因重复，4个遗传性压力易感性神经病先证者均存在PMP22基因缺失，50名正常人未发现异常。结论 我国PMP22基因重复突变的致病频率为31．9％（36／113），PMP22基因缺失突变是遗传性压力易感性神经病常见的致病原因。     

Rapid identification of female carriers of DMD/BMD by quantitative real-time PCR

Recently developed PCR systems offer online-monitoring of amplification and allow simple and reliable DNA quantification. We have used the LightCycler system to develop a simple and rapid method for direct identification of female carriers of deletions and duplications in the dystrophin gene. The challenge resides in the ability to identify the presence of a deleted or duplicated allele over the background contributed by the normal allele. Quantification is based on the determination of the ratio between potentially deleted/duplicated dystrophin exons and non-deleted/-duplicated reference exons using the unspecific dsDNA-dye SYBRgreen I. In a retrospective study, we evaluated our method in female relatives of DMD/BMD patients with known carrier status by comparative analysis of deleted or duplicated versus non-deleted/-duplicated exons. Carrier status was accurately attributed in 100% of cases, the mean ratios being 0.52+/-0.12 for deletion carriers (expected value: 0.5) and 1.56+/-0.18 for duplication carriers (expected value: 1.5) vs. 1.022+/-0.17 for non-carriers (expected value: 1.0). The method proved to be simple, rapid, reliable, and cost-effective. It may be used for direct determination of deletions/duplications in potential DMD/BMD carriers and may easily be adapted for other genetic conditions involving deletions and duplications.     

Detection of human cytomegalovirus DNA in perilymph of patients with sensorineural hearing loss using real-time PCR

Although cytomegalovirus (CMV) has been detected in the inner ear fluid of patients who succumbed to the complications of symptomatic congenital CMV infection, it has not been detected in the inner ear fluid of living patients. In this study, real-time polymerase chain reaction (PCR) was used to measure CMV DNA in clinical samples (including perilymph) collected from five patients with deafness. In case 1, diagnosed as a symptomatic congenital CMV infection, 3 copies/microl of CMV DNA were detected in perilymph, although no viral DNA was detected in peripheral blood mononuclear cells (PBMCs) or urine samples. In case 4, a suspected asymptomatic congenital CMV infection, 36 copies/microg of CMV DNA were detected in PBMCs, but neither perilymph nor urine contained viral DNA. Likewise, in case 5, a case of deafness of unknown origin, 48 copies/microg of CMV DNA were detected in the PBMCs, but none in the perilymph or urine. CMV DNA was not detected in the samples obtained from the remaining two cases with deafness of unknown etiology. To our knowledge, this is the first report to detect CMV DNA in an inner ear sample obtained from a living human subject.     

多重实时定量PCR快速诊断唐氏及爱德华综合征

目的 建立多重实时定量聚合酶链反应(real-time quantitative polymerase chain reaction,RTqPCR)技术,快速分子诊断唐氏及爱德华综合征.方法 应用PCR方法同时扩增位于21号染色体上的淀粉样前蛋白基因(amyloid precursor protein gene,APP)和18号染色体上的胸苷酸合成酶基因(thymidylate synthetase gene,TYMS),以相对定量指标△CT值区分唐氏、爱德华综合征及正常人.用此方法检测4组样本:36名正常人外周血(A组)、15名正常核型的羊水细胞(B组)、21例唐氏综合征(C组)和6例爱德华综合征(D组).结果 A～D 4组样本△CT均值分别为-0.48±0.15、-0.49±0.12、-1.26±0.17和0.25±0.12.B组与A组间差异无统计学意义(P＞0.05);C组与A组、D组与A组间差异有统计学意义(P＜0.01),且无交叉重叠.结论 多重实时荧光定量PCR技术同时快速诊断唐氏及爱德华综合征是可行的.     

应用实时荧光定量PCR快速分子诊断唐氏综合征

目的探讨一种快速、准确诊断唐氏综合征的方法。方法采用实时荧光定量PCR技术，对25例唐氏患者、50名正常人外周血标本，扩增21号及1号、19号染色体上的多态位点，定量分析比较正常组及唐氏患者组的4对△Ct值。结果唐氏患者组△Ct值明显低于正常组，两组比较差异有统计学意义（P〈0．001）。初步建立了临床应用的参考值范围，可以有效区分出唐氏样本和正常样本。结论应用实时荧光定量PCR技术可快速、准确诊断唐氏综合征，为唐氏综合征的快速产前诊断开辟了新的途径。     

Detection of hemizygosity in Hermansky-Pudlak syndrome by quantitative real-time PCR

Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder characterized by oculocutaneous albinism, a bleeding diathesis and, in some patients, pulmonary fibrosis or granulomatous colitis. HPS is associated with biosynthesis defects of melanosomes, platelet-dense bodies, and lysosomes. There are seven genetic HPS subtypes; HPS-1 is the most common. We used a real-time quantitative PCR (qPCR) approach to investigate six HPS-1 patients, previously assigned as having homozygous mutations in the HPS1 gene. HPS1 gene copy numbers, calculated by use of a comparative Ct method, revealed that one patient was in fact hemizygous for her c.1189delC (S396delC) HPS1 mutation. The causative deletion/insertion was 13,966 bp in size, with defined breakpoints, and involved an adjacent gene (C10orf33). A mechanism of formation is proposed for the deletion/insertion, and both multiplex and qPCR indicated that the deletion/insertion was present in the patient, her brother, and her father. qPCR amplification is valuable for detecting deletions too small to be identified by fluorescence in situ hybridization. This demonstration of hemizygosity, performed using genomic DNA, can eliminate concerns about non-paternity and can verify the diagnosis of an autosomal recessive disorder when a DNA alteration appears to be homozygous by standard PCR and sequencing methods, and its pathogenicity is in doubt.     

Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay

A sensitive and specific real-time RT-PCR assay to detect rotavirus in stool samples was optimized and validated using a wide range of rotavirus genotypes. The target of the original TaqMan(R) assay is an 87 bp fragment of the highly conserved non-structural protein 3 (NSP3) gene. Here we modified the original assay by introducing degeneracy into the forward primer to account for sequence variation between rotavirus genotypes, added four nucleotides at the 3' end of the reverse primer to reduce its stability, and modified the probe label. Amplification and detection conditions were optimized using purified dsRNA from two cultivated strains. The limit of detection of the modified assay was calculated to be approximately 44 genome copies per reaction. To validate the reactivity of the assay, 103 archived RNAs that had been extracted from stools and genotyped during routine U.S. surveillance were tested. Samples were selected to represent both rare and common genotypes that have been detected in U.S. children. Nine genotypes known to be circulating in the United States were detected by the real-time assay demonstrating broad reactivity. In addition, other enteric viruses were not detected demonstrating that the assay is specific for rotavirus and does not cross-react with other viruses potentially present in stool samples. This real-time assay is an important addition to the arsenal of molecular tools available to quickly identify rotavirus in stool samples during routine surveillance.     

A novel real-time PCR system for simultaneous detection of human viruses in clinical samples from patients with uncertain diagnoses

A novel simultaneous detection system for human viruses was developed using a real-time polymerase chain reaction (PCR) system to identify causes of infection in clinical samples from patients with uncertain diagnoses. This system, designated as the "multivirus real-time PCR," has the potential to detect 163 human viruses (47 DNA viruses and 116 RNA viruses) in a 96-well plate simultaneously. The specificity and sensitivity of each probe-primer set were confirmed with cells or tissues infected with specific viruses. The multivirus real-time PCR system showed profiles of virus infection in 20 autopsies of acquired immunodeficiency syndrome patients, and detected frequently TT virus, cytomegalovirus, human herpesvirus 6, and Epstein-Barr virus in various organs; however, RNA viruses were detected rarely except for human immunodeficiency virus-1. Pathology samples from 40 patients with uncertain diagnoses were examined, including cases of encephalitis, hepatitis, and myocarditis. Herpes simplex virus 1, human herpesvirus 6, and parechovirus 3 were identified as causes of diseases in four cases of encephalitis, while no viruses were identified in other cases as causing disease. This multivirus real-time PCR system can be useful for detecting virus in specimens from patients with uncertain diagnoses.     

慢性粒细胞白血病患者中C/EBPζ基因转录本的定量研究

目的研究慢性粒细胞白血病（chronic myeloid leukemia，CML）患者中CCAAT／增强子结合蛋白ξ（CCAAT／enhancer binding protein，C／EBPξ）的表达及其意义。方法建立实时定量聚合酶链反应对76例不同阶段CML患者和16名正常对照的骨髓单个核细胞中C／EBPξ转录本含量进行检测。结果与正常对照（中位12．20）相比，慢性期、加速期和急变期CML患者中C/EBPξ转录本明显降低，中位含量分别为2，5、3．31和2，22（P〈0，01、〈0，05，〈0，01），8例治疗后达到细胞遗传学缓解者则恢复至正常水平（中位15．43，P〉0．05），而干扰素治疗无效的4例患者中表达水平则进一步下降（中位1．56，P〈0．01）。结论CML患者中C／EBPξ基因表达下降，可能与其发病相关。     

Performance of Bordetella pertussis IS481 real-time PCR in a vaccine trial setting

A real-time PCR method targeting the Bordetella pertussis IS481 gene fragment was evaluated in a vaccine trial setting in which real-time PCR results could be validated against culture and serology results. Two commonly used DNA extraction methods, Amplicor Respiratory Preparation kit and the QIAamp DNA Mini Kit, were compared. An approximately 50-fold higher sensitivity was achieved using the Amplicor kit. 89 of 276 aspirates analysed with the IS481 real-time PCR were positive. Interestingly, six of these were culture negative and came from serology-negative patients. Defining true positive cases either as culture-positive or as PCR-positive cases that had been confirmed with a serology-positive result or verified with a newly constructed recA PCR, the sensitivity and specificity of the IS481 real-time PCR were 89% and 98%, respectively. This study confirms the specificity and high diagnostic sensitivity of IS481-based PCR methods for diagnosis of B. pertussis.     

Analysis of children with Chlamydophila (Chlamydia) pneumoniae and Mycoplasma pneumoniae respiratoryinfections by real-time PCR assay and serological tests

We examined 73 children with respiratory infections for Chlamydophila (Chlamydia) pneumoniae and Mycoplasma pneumoniae using real-time PCR assay and serological tests. C. pneumoniae and M. pneumoniae infections were found in 11 (15.1%) and 6 (8.2%) cases, respectively. The sensitivities and specificities of real-time PCR versus definite diagnosis of acute infection were 63.6% and 100% for C. pneumoniae, and 100% and 100% for M. pneumoniae, respectively. C. pneumoniae PCR-negative results appeared to be due to poor growth of the organism. The sensitivity and specificity of ImmunoCard tests were 33.3% and 82.1%, respectively, indicating that the efficacy of rapid diagnosis was disputable. The present results suggest that real-time PCR is suitable for rapid diagnosis as a first screening test to determine first-line antibacterial agents to be used against these infectious diseases.     

Monitoring of human cytomegalovirus glycoprotein B genotypes using real-time quantitative PCR in immunocompromised Chinese patients

Based on sequence variation in the N-terminus of glycoprotein B (gB), human cytomegalovirus (HCMV) can be classified into four gBn genotypes, and these genotypes are associated with different clinical outcomes. The distribution of gBn genotypes and the level of gBn DNA load were examined in immunocompromised Chinese patients using real-time quantitative PCR. In addition, the PCR and pp65 antigenemia results were compared. In 1480 specimens, 81.4% were antigen-positive, 12.6% were PCR-positive. The gB genotype distribution was as follows among PCR-positive samples: gBn1, 63.1%; gBn2, 13.4%; gBn3, 8.6%; gBn4, not detected; mixed genotypes, 14.9% (gBn1 and gBn3, 14.4%; gBn2 and gBn3, 0.5%). The gBn3 and gBn1 genotypes had the highest and lowest copy numbers, respectively (p < 0.05). The quantity of gBn DNA found in PCR-positive, pp65-negative samples was significantly lower than that found in PCR-positive, pp65-positive samples (p < 0.05). The PCR and antigenemia results did not differ among bone marrow transplant patients, solid organ transplant patients, and immunocompromised patients without transplantation (p > 0.05). HCMV gBn genotyping using real-time quantitative PCR was established successfully, and the distribution of gBn genotypes in immunocompromised Chinese patients was investigated. This method may help to understand better the relationship between gBn genotype and clinical outcome and aid in clinical detection.     

Development and application of a one‐step real‐time RT‐PCR using a minor‐groove‐binding probe for the detection of a novel bunyavirus in clinical specimens

A highly sensitive one‐step real‐time RT‐PCR method using a minor‐groove‐binding (MGB) probe was developed for detection and quantitation of severe febrile with thrombocytopenia syndrome virus (SFTSV). The assay could discriminate SFTSV infection from other related viral diseases in human with a minimum detection limit of 10 viral RNA copies/µl and was 1,000 times more sensitive than the conventional PCR. Strong linear correlations (r² > 0.99) between the C_t values and viral RNA standards over a linear range were obtained. The coefficients of variation of intra‐ and inter‐assay reproducibility were both less than 2%. The RT‐PCR was also shown to be highly specific, as no positive signals were detected for other related viruses. Evaluation of this assay with serum samples from laboratory confirmed cases and healthy donors showed 100% clinical diagnostic sensitivity and over 99% specificity. Clinical application with samples from 287 patients admitted to the hospital with suspected SFTSV infection showed that 15% were infected by SFTSV. This assay was rapid, requiring just over 2 hr, including the nucleic acid extraction step. J. Med. Virol. 85:370–377, 2013. © 2012 Wiley Periodicals, Inc.