Measurement of Telomere Length for Longitudinal Analysis: Implications of Assay Precision.

Researchers increasingly wish to test hypotheses concerning the impact of environmental or disease exposures on telomere length (TL), and they use longitudinal study designs to do so. In population studies, TL is usually measured with a quantitative polymerase chain reaction (qPCR)-based method. This method has been validated by calculating its correlation with a gold standard method such as Southern blotting (SB) in cross-sectional data sets. However, in a cross-section, the range of true variation in TL is large, and measurement error is introduced only once. In a longitudinal study, the target variation of interest is small, and measurement error is introduced at both baseline and follow-up. In this paper, we present results from a small data set (n = 20) in which leukocyte TL was measured twice 6.6 years apart by means of both qPCR and SB. The cross-sectional correlations between qPCR and SB were high at both baseline (r = 0.90) and follow-up (r = 0.85), yet their correlation for TL change was poor (r = 0.48). Moreover, the qPCR data but not the SB data showed strong signatures of measurement error. Through simulation, we show that the statistical power gain from performing a longitudinal analysis is much greater for SB than for qPCR. We discuss implications for optimal study design and analysis.

Telomere biology in neuroblastoma: telomere binding proteins and alternative strengthening of telomeres.

PURPOSE: Neuroblastoma (NBL) shows remarkable biologic heterogeneity, resulting in favorable or unfavorable prognoses. Previously, we reported that most unfavorable NBLs express high telomerase activity to maintain telomere length. Recently, telomere binding proteins (TBPs) and alternative lengthening of telomeres (ALTs) have been identified as key factors of telomere maintenance. METHODS: To evaluate the correlation between telomerase activity, telomere length, and the expression levels of TBPs in NBL, we analyzed and quantified these factors in 121 untreated NBLs. RESULTS: Shortened and elongated telomeres were detected in 21 (17.3%) and 11 cases (9.0%), respectively, and there was a significant correlation between telomere length and the length of the 3'-overhang. The tumors with shortened or elongated telomeres showed significant lower expression of TBPs, except for RAP1. Although telomerase activity did not correlate with telomere length, 16 of 22 cases with high telomerase activity and 5 of 9 cases (ALT tumors) that showed long telomeres without high telomerase activity resulted in death. High-dose chemotherapy did not have much effect on these deceased ALT cases, but their survival periods were more than 2 years and relatively long compared with the deceased cases with nonelongated telomeres, suggesting that chemoresistance in ALT tumors may be related to slow growth rates. CONCLUSIONS: High telomerase activity is a poor prognostic factor in NBL. In the cases without high telomerase activity, those with elongated telomere also showed poor outcomes because of chemoresistance. Therefore, ALT and TBPs may be biomarkers for chemosensitivity in NBL. Thus, a better understanding of telomere biology may help define the characteristics of individual NBLs.

Detection of clonal IGH gene rearrangements: summary of molecular oncology surveys of the College of American Pathologists.

CONTEXT: The diagnosis of B-cell lymphoid malignancy can frequently be substantiated by detecting clonal immunoglobulin heavy chain (IGH) gene rearrangements, which is typically done by polymerase chain reaction (PCR) amplification and/or Southern blot analysis. OBJECTIVE: To characterize current laboratory practice for the assessment of IGH rearrangements and to identify opportunities for improvement. DESIGN: The data from the Molecular Oncology Proficiency Survey distributed to participating laboratories by the Molecular Pathology Committee of the College of American Pathologists from 1998 through 2003 were analyzed. RESULTS: Thirty-nine proficiency survey specimens (29 positive and 10 negative for clonal IGH rearrangements) were distributed. For Southern blot analysis, 944 results were reported, with a successful response rate of 95%. For PCR detection, 2349 results were reported, with a successful response rate of 72%. A higher rate of successful responses by PCR was achieved using framework 3 primers in combination with other frameworks (82%) compared with framework 3 primers only (76%) and when fresh/frozen (72%) compared with paraffin-embedded (65%) tissues were analyzed. CONCLUSIONS: The performance of the participating laboratories was very good, by both Southern blot and PCR analysis. As expected, Southern blot analysis consistently detects a higher proportion of IGH rearrangements than PCR analysis. Further improvement and standardization of the IGH PCR assay is important if it is to replace Southern blot analysis as the standard method. Participation in this survey is a valuable tool for assessing laboratory performance and it directs our attention to areas where we may improve laboratory practice.

Comparison of a microtiter plate system to Southern blot for detection of human herpesvirus 8 DNA amplified from blood and saliva.

The recent discovery of human herpesvirus 8 (HHV-8) as the etiologic agent of Kaposi's sarcoma (KS) has led to the interest in the development of PCR for this virus that is accurate, rapid, and convenient. We developed a sensitive PCR assay for HHV-8 with microtiter plate detection of amplimers. DNA was purified from white blood cells and saliva from HIV-infected men with and without Kaposi's sarcoma and one-step PCR was undertaken with primer sets specific for the N-terminal region of the glycoprotein B gene and open reading frame (orf) 26 of HHV-8. PCR was performed on 40 clinical specimens, followed by Southern blot and microtiter plate detection of amplimers. Results from the two methods of detection were nearly identical. Sensitivity for both methods based on serial dilution of a known standard was five to ten copies of HHV-8 per 400 ng of cellular DNA. In conclusion, microtiter plate detection of HHV-8 PCR amplimers is as sensitive and specific as Southern blot with much faster turnaround time at comparable cost, and utilizes common laboratory equipment.

Validation and development of quantitative flow cytometry-based fluorescence in situ hybridization for intercenter comparison of telomere length measurement.

BACKGROUND: Telomeres are highly conserved repeats at the ends of chromosomes that maintain chromosome stability and reflect the replicative potential of cells. Telomere length can be determined by Southern blot hybridization or quantitative fluorescence in situ hybridization (Q-FISH). Recently, two flow cytometry-based (Flow) FISH protocols have been published. METHODS: We compared the telomere length measured by Southern blotting and Flow FISH using standard beads to calibrate and quantify the fluorescence intensity. RESULTS: The telomeric fluorescence of cord blood and peripheral blood mononuclear cells was similar to that reported by other studies. There was a linear relationship between the telomeric fluorescence determined by Flow FISH and the telomere fragment size determined by Southern blotting (r = 0.89; P < 0.001). CONCLUSION: It is important to set up a center-specific curve and select appropriate cell lines for reference. This Q-Flow FISH protocol will facilitate the measurement of telomere length and allow more meaningful comparison of data (in standard fluorescence units or fragment size) between institutes.

A sensitive and specific PCR/Southern blot assay for detection of bovine herpesvirus 4 in calves infected experimentally.

A PCR/Southern blot assay for detection of bovine herpesvirus 4 (BHV-4) in the background of bovine cellular DNA was developed. A BHV-4 specific sequence within the gene coding for the glycoprotein B (gB) was selected for primer sequences to guarantee the specificity of the assay. With a detection limit of six molecules BHV-4 DNA in the background of 1 microg of cellular DNA (equals about 150,000 bovine cells) this PCR/Southern blot assay represents a highly sensitive method for detection of BHV-4 DNA. At low concentrations of BHV-4 genomes, this assay also allows to estimate the copy number of BHV-4: a distinction between fewer than 6, 6-59 and more than 60 BHV-4 genomes/100 microl DNA suspension was possible. Tissue and blood samples of two calves, infected experimentally with BHV-4 were examined for the prevalence of BHV-4 DNA 130 days post infection. Ten days before taking samples, one of the calves was immuno-suppressed with dexamethasone. In both calves, BHV-4 DNA was detected in the leucocyte fraction of the blood, and beyond that in lower quantities in the spleen and the kidney of the immuno-suppressed calf. It is assumed that a latent BHV-4 infection was activated after application of dexamethasone and that the leucocyte fraction of the blood represents one site of latency of BHV-4 in cattle.

Natural defenses against Candida colonization breakdown in the oral cavities of the elderly.

Candida colonization of the oral cavity increases in the elderly. A major predisposing condition is denture use, which also increases in the elderly. To test whether the increase in colonization is age-related in a fashion independent of denture use, we analyzed the frequency (incidence) of carriage, the intensity of carriage, the multiplicity of species, and the genetic relatedness of strains in the oral cavities of 93 test subjects separated into the three age groups: 60 to 69 yr, 70 to 79 yr, and > or = 80 yr. Each age group was further subdivided into subjects with and without dentures, and into males and females. The results demonstrate that the frequency of carriage, the intensity of carriage, and multispecies carriage all increase as a function of age and differ according to gender, in both cases independent of denture use, suggesting that the natural suppression of yeast carriage in the oral cavity breaks down in the elderly. In addition, it is demonstrated that Candida glabrata colonizes the oral cavities of elderly individuals without dentures only after 80 yr of age, suggesting that there are age-related compromising conditions other than denture use in this most elderly age group.

Detection and typing of human papillomavirus DNA in benign and malignant tumours of laryngeal epithelium.

The role of human papillomaviruses (HPV) in laryngeal squamous cell carcinoma has not yet been established. Thirty-three cases of laryngeal squamous cell carcinoma were analysed for the presence of HPV DNA and compared with 25 cases of normal larynx and 29 cases of laryngeal squamous papilloma in their positivity index. The presence of HPV DNA was analysed by using L1 consensus primers and also by primers specific for the E7 gene of HPV types 16 and 18. Four normal laryngeal samples (16%) were positive for HPV DNA against the 24 samples (82%) (p < 0.001) found for laryngeal papilloma and 16 (48.5%) (p < 0.05) found for laryngeal squamous cell carcinoma. HPV 16 was the type most frequently found in laryngeal carcinoma samples. Our results support an etiologic role for this type of HPV in the pathogenesis of laryngeal carcinoma.

Two cases of chromosome 4q35-linked early onset facioscapulohumeral muscular dystrophy with mental retardation and epilepsy.

Two cases of early onset facioscapulohumeral muscular dystrophy (FSHD) with mental retardation and epilepsy are reported. They were sporadic, unrelated, severely affected females. In both cases, Southern blot analysis of the EcoRI-digested genomic DNA, using probes p13E-11 and pFR-1, detected the shortest 10 kb EcoRI fragments reported to date. Patient 1 showed infantile spasms at the age of 4 months and localization-related epilepsy at the age of 2.5 years. Muscular atrophy in the face, shoulder girdle and upper arms was observed from the age of 4 years. In Patient 2, lack of facial expression was noticed since the age of 1 year, and at 4 years she was noted to have a loss of bilateral upward gaze. She developed localization-related epilepsy at the age of 9 years. From the age of 10 years, weakness of the lower limbs progressed and she became wheelchair-bound at the age of 14 years and 8 months. She had moderate sensorineural hearing loss, a loss of bilateral upward gaze and tongue atrophy. Their IQs were 33 and 45, respectively. The two patients suggest that mental retardation and epilepsy may be part of the clinical spectrum of FSHD, especially in very early onset patients with large deletions.

The use of digoxigenin-labelled probes to detect DNA sequences specific for plant pathogenic bacteria.

Southern blot hybridization is a valuable method in the assessment of the pathogenicity of bacterial strains or isolates. It is also a powerful tool for the demonstration of the presence of foreign DNA sequences in the genome of genetically-engineered plant cells. In this respect, cold, digoxigenin-labelled DNA probes can be used in place of classical radioactive probes, whether hybridizations are performed on bacterial genomic or plasmidic DNA, or on plant genomic DNA. The versatility of this cold labelling makes it suitable for the detection of unique bacterial genomic or plasmid sequences, even though these are located on large plasmids. The sensitivity of this cold probe technique also permits the detection of subpicogram quantities of DNA in plant genomic preparations. Their long term storage stability allows them to be frequently re-used over long periods of time, making this technique quite cost efficient.

Detección del papilomavirus humano en ADN de tejido normal y lesiones premalignas del cérvix por hibridación molecular / Identification of human papilloma virus in DNA of normal tissue and precursor lesions of uterine cervix by molecular hybridization

Se analizaron 64 muestras de ADN obtenido de tejido histológicamente normal del cérvix y de lesiones tempranas del cáncer cervical por hibridación dot-blot, para detectar la presencia de papilomavirus humano(PVH). Utilizando ADN de controles adecuados y sondas específicas, detectamos la infección por PVH en 39 por ciento(25 de 64) de los casos; mientras que 61 por ciento (39 de 64) resultó negativo a PVH. Se detectó PVH del grupo de ®bajo riesgo¼ (tipo 6/11) en un 80 por ciento (20 de 25) de las muestras de ADN; mientras que un 8 por ciento (2 de 25) fue positivo a PVH del grupo de ®alto riesgo¼ (tipo 16/18). Además, encontramos 12 por ciento (3 de 25) de las muestras positivas a ambos grupos de virus

Detection of rearrangements of the BCL2 major breakpoint region in follicular lymphomas. Correlation of polymerase chain reaction results with Southern blot analysis.

The translocation t(14;18)(q32;q21) occurs in 70% of follicular lymphomas and places the BCL2 proto-oncogene, normally located at 18q21, under the control of the immunoglobulin heavy chain (IgH) gene at 14q32. Its detection by the polymerase chain reaction (PCR), made possible by the close clustering of most of the BCL2 breakpoints in the major breakpoint region (MBR) of the gene, has numerous clinical applications. Since the PCR covers shorter lengths of DNA than Southern blotting, PCR-based tests may be more susceptible to microheterogeneity in breakpoint location. There have been no published studies of the impact of breakpoint microheterogeneity on the detection rate of this translocation by PCR. We studied 30 follicular lymphomas with the t(14;18), in which a BCL2 MBR rearrangement had previously been demonstrated and mapped by conventional Southern blotting, by PCR with the commonly used IgH and BCL2 MBR primers. Twenty-five cases (83%) had a junction fragment demonstrable by PCR. All three cases in which the MBR rearrangement mapped outside of the 4.3-kb HindIII fragment containing the MBR, as determined by Southern blotting, were negative by PCR. In addition, two cases with rearrangements within the HindIII fragment were also negative. All negative results were repeated at least once and were confirmed to be true negatives by actin PCR. Our results suggest that negative PCR results in this setting are attributable to small variations in BCL2 MBR breakpoint location and cannot be interpreted without the corresponding conventional Southern blotting data. With this caveat in mind, PCR analysis for the t(14;18) remains an extremely useful technique, especially in the follow-up and monitoring for minimal residual disease in previously characterized cases of follicular lymphoma.