Quantitative assessment of the BCR-ABL transcript using the Cepheid Xpert BCR-ABL Monitor assay.

CONTEXT: Chronic myelogenous leukemia (CML) and the assessment of the BCR-ABL transcript has become a new paradigm. Novel tyrosine kinase inhibitors as mainstream therapeutic options for the CML patient warrant routine quantification of the BCR-ABL transcript. The Xpert BCR-ABL Monitor assay is a nested reverse transcriptase polymerase chain reaction that greatly reduces technical time by using a single cartridge to isolate RNA and run a quantitative reverse transcriptase polymerase chain reaction. OBJECTIVE: To evaluate the Xpert BCR-ABL Monitor assay for quantitative assessment of the BCR-ABL transcript in CML patients. DESIGN: A standard curve of K-562 cells diluted in normal peripheral blood was used to test the sensitivity, linearity, and percent coefficient of variation of the assay. Specimen stability was tested by running standard curves immediately and after 24 hours or 96 hours of storage at 4 degrees C. Specimens from normal controls, patients known to have CML, or patients suspected of having CML were also tested. RESULTS: The sensitivity of the assay was sufficient to detect 1 K-562 cell in 10(5) normal cells. The R2 of the standard curve was 0.98 and the percent coefficient of variation for each data point was 15% to 24%. Eleven of 14 patients with known CML on imatinib treatment tested positive for the BCR-ABL transcript, whereas 10 normal controls tested negative. CONCLUSIONS: The Xpert BCR-ABL Monitor assay is a rapid, sensitive method for monitoring the presence of the BCR-ABL transcript in CML patients. The single-use cartridge minimizes hands-on technical time, minimizes the potential for contamination, and allows quantitative BCR-ABL testing to be performed in a random access fashion.

Detection of the C282Y and H63D polymorphisms associated with hereditary hemochromatosis using the ABI 7500 fast real time PCR platform.

Classic hereditary hemochromatosis is an autosomal recessive disorder characterized by iron overload and sequence variants in the HFE gene. The HFE gene is located at 6p21.3 and contains 2 common single nucleotide polymorphisms (SNPs) C282Y and H63D, which are routinely tested for in the molecular diagnostics laboratory. In this study, we used DNA samples from 59 patients in which clinicians wanted to confirm or rule-out hereditary hemochromatosis that had been previously tested for the HFE SNPs using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay and the ABI 7700 real time PCR assay with a MGB Eclipse ASR Probe system. The new assay used TAQman SNP Genotyping Assays, which were performed on the ABI 7500 FAST real time PCR platform. Allelic discrimination was determined during a postamplification plate read. Of the 59 samples genotyped, 7 were homozygous for C282Y, 6 were heterozygous for C282Y, 9 were homozygous for H63D, 10 were heterozygous for H63D, 6 were compound heterozygotes, and 20 were wild type. With the exception of one sample that was indeterminate by the TAQman SNP Genotyping Assay, all others showed 100% concordance between the 3 assays. The one indeterminate sample was heterozygous for C282Y by the PCR-RFLP and ABI 7700 real time PCR assays, but there was an insufficient quantity of DNA to perform the TAQman SNP Genotyping Assay. Our study suggests that the ABI 7500 FAST TAQman SNP Genotyping Assay is comparable with the PCR-RFLP and ABI 7700 real time PCR methods in detecting and characterizing these 2 HFE SNPs. Improved software and thermocycling capabilities have resulted in a very robust TAQman assay with the advantage of a much improved turn-around-time and throughput.

Increased brain activation during working memory in cognitively intact adults with the APOE epsilon4 allele.

OBJECTIVE: Altered patterns of brain activity during cognitive tasks have been demonstrated using functional magnetic resonance imaging (fMRI) in mild cognitive impairment and Alzheimer's disease. However, there have been few studies of adults at genetic risk for Alzheimer's disease prior to the onset of symptoms. The purpose of this study was to determine whether brain activation patterns associated with working memory differ as a function of apolipoprotein E (APOE) genotype in cognitively intact adults. METHOD: Participants were cognitively intact, healthy adults who completed genotyping, comprehensive neuropsychological testing, and structural and functional neuroimaging. Twenty-two participants had the APOE epsilon3/epsilon3 genotype, and 13 participants had the APOE epsilon3/epsilon4 genotype. The study employed an auditory verbal N-back task to probe working memory-related brain activity. RESULTS: The epsilon3/epsilon3 and epsilon3/epsilon4 groups did not differ in demographic characteristics, cognitive ability, mood, or in-scanner task performance. The epsilon3/epsilon4 group showed greater activity during working memory in the medial frontal and parietal regions bilaterally and in the right dorsolateral prefrontal cortex. There were no regions in which the epsilon3/epsilon3 group showed greater activation than the epsilon3/epsilon4 group. CONCLUSIONS: These results indicate that differences in brain activity are evident in cognitively intact individuals who are at risk for late-onset Alzheimer's disease by virtue of their APOE allele status. As neuroprotective interventions become available, early detection will increase in importance. The combination of genetic and functional neuroimaging strategies may prove useful for monitoring individuals at risk for Alzheimer's disease before the onset of cognitive symptoms.

BRCA1 and BRCA2 mutation screening using SmartCycler II high-resolution melt curve analysis.

CONTEXT: Real-time polymerase chain reaction technologies have replaced many of the more labor-intense methods in the molecular diagnostics laboratory. Similarly, melt curve analysis can provide a rapid means of mutation screening. OBJECTIVE: To determine if real-time polymerase chain reaction and melt curve analysis using the SmartCycler II could be used as a screening tool for 3 common mutations in BRCA1 and BRCA2. DESIGN: Real-time polymerase chain reaction amplification with SYBR Green I detection was performed on DNA from cell lines known to carry the 185delAG or 5382insC mutation in BRCA1 or the 6174delT mutation in BRCA2. The melting temperatures and the melt curves were analyzed for differences between wild-type DNA and cell lines that were heterozygous for each mutation. RESULTS: Significant differences were present in the melt curves for each of the mutations compared with those of the wild-type sequences. The melt curve for the 185delAG mutation showed a separate peak at a lower temperature, which represented the melting temperature of the heteroduplex. For the 6174delT mutation, the melt curve had a shoulder at a lower temperature, while the melt curve for the 5382insC mutation was shifted to the left and was broader than that for the wild-type sequences. CONCLUSIONS: High-resolution melt curve analysis is a quick, reliable method for identifying mutations due to small deletions or insertions. As a proof of principle, we used this assay to identify the 3 most common BRCA1 and BRCA2 mutations in the Ashkenazi Jewish population.

Multiple endocrine neoplasia 2A due to a unique C609S RET mutation presents with pheochromocytoma and reduced penetrance of medullary thyroid carcinoma.

OBJECTIVE: We have identified a large kindred with multiple endocrine neoplasia 2A (MEN 2A) due to a mutation at RET codon 609 that results in a cysteine to serine substitution, a mutation previously identified in only one case in the literature. We characterized the clinical phenotype of the kindred and the biochemical mechanism of this new mutation. PATIENTS AND DESIGN: The index case, a 42-year-old woman, presented with pheochromocytoma. We screened 29 family members for the presence of the mutation. Of the 15 mutation-positive family members, 11 agreed to undergo further evaluation by physical examination, calcium and pentagastrin-stimulated calcitonin levels, measurement of urinary metanephrines, adrenal imaging and serum calcium levels. Biochemical characterization of the mutation was by transient transfection of human neuroblastoma cells and Western blot analysis. RESULTS: This kindred demonstrated an inheritance pattern consistent with autosomal dominant pheochromocytoma. Strikingly, no clinically evident case of medullary thyroid cancer (MTC) was observed among mutation-positive family members. Thyroidectomy in six cases revealed C-cell hyperplasia in all and microscopic MTC in two cases. Transfection experiments using human neuroblastoma cells showed that the mutant RET, unlike the wild-type receptor, is constitutively phosphorylated in the absence of ligand, and thus resembles other previously characterized MEN 2A mutations. CONCLUSIONS: The identification of a new mutation causing a MEN 2A phenotype that features pheochromocytoma and the surprising absence of clinically apparent MTC has significant implications for carriers of this mutation and provides further insights into the genotype-phenotype correlation in MEN 2A.

Developing a sustainable process to provide quality control materials for genetic testing.

PURPOSE: To provide a summary of the outcomes of two working conferences organized by the Centers for Disease Control and Prevention (CDC), to develop recommendations for practical, sustainable mechanisms to make quality control (QC) materials available to the genetic testing community. METHODS: Participants were selected to include experts in genetic testing and molecular diagnostics from professional organizations, government agencies, industry, laboratories, academic institutions, cell repositories, and proficiency testing (PT)/external Quality Assessment (EQA) programs. Current efforts to develop QC materials for genetic tests were reviewed; key issues and areas of need were identified; and workgroups were formed to address each area of need and to formulate recommendations and next steps. RESULTS: Recommendations were developed toward establishing a sustainable process to improve the availability of appropriate QC materials for genetic testing, with an emphasis on molecular genetic testing as an initial step. CONCLUSIONS: Improving the availability of appropriate QC materials is of critical importance for assuring the quality of genetic testing, enhancing performance evaluation and PT/EQA programs, and facilitating new test development. To meet the needs of the rapidly expanding capacity of genetic testing in clinical and public health settings, a comprehensive, coordinated program should be developed. A Genetic Testing Quality Control Materials Program has therefore been established by CDC in March 2005 to serve these needs.

Real-time polymerase chain reaction and laser capture microdissection for the diagnosis of BK virus infection in renal allografts.

We used real-time polymerase chain reaction (PCR) technology to detect BK virus (BKV) in H and E-stained kidney biopsy sections, using laser capture microdissection. Renal allograft biopsy specimens from 4 patients with the histopathologic diagnosis of BKV-associated nephropathy (BKVAN; group 1) and 3 patients suspected to have BKVAN but without diagnostic histologic features (group 2) were retrieved. Diagnostic inclusion-bearing cells were microdissected by laser capture microscopy from group 1. Renal tubular epithelial cells were microdissected randomly in group 2. DNA was extracted and real-time amplification performed using primers targeting the large "T" and small "t" regions of the BKV and JC virus genomes. Tubular epithelial cells from a case without evidence of BKV infection were used as negative controls in a similar reaction. BKV presence was demonstrated only in epithelial cells containing typical viral inclusions. Group 2 and negative control samples were confirmed as negative for BKVAN. Real-time PCR technology can be used to detect BKV in H and E-stained, paraffin-embedded tissue sections. This technique detected BKV in tubular epithelial cells of renal allografts. To our knowledge, this is the first report of detecting BKV in laser capture microdissected renal biopsy specimens using real-time PCR.

Parameters involved in the conversion of real-time PCR assays from the ABI prism 7700 to the Cepheid SmartCycler II.

OBJECTIVE: We examined several critical parameters that must be optimized when converting between the ABI Prism 7700 real-time PCR platform and the Cepheid SmartCycler II while using the same primer and probe sequences. DESIGN AND METHODS: A lyophilized master mix, MgCl(2) concentration, PCR cycling conditions, and ramp times were evaluated. RESULTS: Optimization of each parameter, including use of the OmniMix HS-lyophilized beads, 6 mM MgCl(2) concentration, changes in PCR cycling parameters, and increased ramp time were necessary to convert this real time PCR assay to a new platform. CONCLUSION: We conclude that careful consideration of several analytical parameters can result in a smooth transition of assays between real time PCR platforms.

Factors affecting the detection rate of human papillomavirus.

BACKGROUND: Maximizing the accuracy of human papillomavirus (HPV) detection from a single sample is important for clinical and research purposes. The purpose of this study was to determine whether cyclic hormonal variation, recent sexual intercourse, interval between samplings, and the technique used to sample affect the detection of HPV. METHODS: This study was a prospective, longitudinal, randomized controlled trial. Three techniques for self-sampling (2 consecutive synthetic polyester fiber [Dacron] swabs, a single Dacron swab, and a tampon) were repeated at 3 different sampling times during a period of 4 to 6 weeks in addition to 1 clinician-directed sampling of the ectocervix and endocervix at the first sampling time. All self-samplings were taken in a proscribed randomized order. Women (aged 18 to 68 years) attending a colposcopy clinic for abnormal cytology or abnormal cervical appearance participated in the study. The outcome measure was the detection of HPV by polymerase chain reaction amplification. RESULTS: The 103 participants provided 1,189 cervicovaginal samplings. Logistic regression indicated that intercourse within 48 hours of sampling did not result in a greater detection of high-risk or any HPV type (odds ratio [OR] = 1.05, 95% confidence interval [CI], 0.65-1.69; OR = 1.08, 95% CI, 0.73-1.60, respectively). Among those women who have regular menstrual cycles, there was no cyclic effect on HPV detection for high-risk and any HPV types. Time from previous sampling did not affect HPV detection. Among the self-sampling techniques, using a single self-swab and the tampon resulted in the detection of HPV between 10% and 35% less often than using 2 consecutive swabs (P < .025). Self-sampling with 2 swabs was not significantly different from clinician sampling for detecting high-risk HPV types (OR for self-sampling = 0.87 (95% CI, 0.66-1.13)). CONCLUSIONS: HPV detection is not dependent on menstrual cycle timings, the recency of intercourse, or the time between samplings, but it is dependent on the sampling technique.

Tampon samplings with longer cervicovaginal cell exposures are equivalent to two consecutive swabs for the detection of high-risk human papillomavirus.

BACKGROUND: Self-sampling for human papillomavirus (HPV) is useful for triage of ASCUS Papanicolaou (Pap) smears. Tampons with 10-second cervicovaginal cell exposure can detect HPV but appear to be less efficient than two consecutive swabs. GOAL: The purpose of this study was to evaluate increased vaginal tampon exposures for detecting high-risk HPV. STUDY DESIGN: This longitudinal cohort study followed women who self-sampled weekly with tampons for progressively longer periods of time. A tampon was inserted for 10 seconds at the office visit and 1 hour, 4 hours, and overnight for the three subsequent home samples. Two concurrent swabs were used with each tampon sampling for contemporaneous comparisons. The MY09/MY11 PCR primer system with reverse line blot detection strips was used to detect 18 distinct high-risk HPV types. RESULTS: Of the 309 tampons and 618 swabs used at home, 83% were returned. Among normal women, the 10-second tampon detected fewer with normal histology and high-risk HPV than did its swabs ( = 0.0412), but the 1-hour, 4-hour, and overnight tampons had high-risk-HPV detection rates equal to their swabs. In women with CIN, all tampons and swabs equally identified those with high-risk HPV. CONCLUSION: Self-sampling for HPV detection is acceptable, feasible, and technically accurate for both tampons with longer cervicovaginal exposures and swabs. The choice of technique is dependent on the woman, her culture, and her clinician.

Randomized clinical trial of PCR-determined human papillomavirus detection methods: self-sampling versus clinician-directed--biologic concordance and women's preferences.

OBJECTIVE: The purpose of this study was to compare the high-risk human papillomavirus detection rates from self-sampled swabs and tampons with standard clinician-directed speculum sampling and to assess women's acceptance of self-sampling methods. STUDY DESIGN: One hundred three women who required a colposcopy underwent order randomization of the human papillomavirus sampling technique. Kappa and McNemar test statistical results were used to measure the agreement between clinician-directed and self-sampling techniques for high-risk types of human papillomavirus and the acceptance of self-sampling techniques. RESULTS: All self-directed samplings were equivalent to clinician sampling for all cervical intraepithelial neoplasia disease states. High-risk human papillomavirus was detected by self- and clinician-directed methods in 83% of the women with cervical intraepithelial neoplasia, grade 2/3. The 2 sequential swabs trend toward better detection of high-risk types of human papillomavirus than all other techniques for women with normal histologic factors (P =.0736, by McNemar's chi2 test). Ninety-four percent of women would accept self-sampling for their yearly cervical screen. CONCLUSION: Self-sampling is equivalent to clinician sampling for the detection of high-risk human papillomavirus and is acceptable to women as a yearly screen.