Assessment of ERBB2/HER2 Status in HER2-Equivocal Breast Cancers by FISH and 2013/2014 ASCO-CAP Guidelines.

Importance: The 2013/2014 American Society of Clinical Oncology and College of American Pathologists (ASCO-CAP) guidelines for HER2 testing by fluorescence in situ hybridization (FISH) designated an "equivocal" category (average HER2 copies per tumor cell ≥4-6 with HER2/CEP17 ratio <2.0) to be resolved as negative or positive by assessments with alternative control probes. Approximately 4% to 12% of all invasive breast cancers are characterized as HER2-equivocal based on FISH. Objective: To evaluate the following hypotheses: (1) genetic loci used as alternative controls are heterozygously deleted in a substantial proportion of breast cancers; (2) use of these loci for assessment of HER2 by FISH leads to false-positive assessments; and (3) these HER2 false-positive breast cancer patients have outcomes that do not differ from clinical outcomes for patients with HER2-negative breast cancer. Design, Setting, and Participants: We retrospectively assessed the use of chromosome 17 p-arm and q-arm alternative control genomic sites (TP53, D17S122, SMS, RARA, TOP2A), as recommended by the 2013/2014 ASCO-CAP guidelines for HER2 testing, in patients whose data were available through Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and whose tissues were available through the Breast Cancer International Research Group clinical trials. We used data from an international cohort database of invasive breast cancers (1980 participants) and international clinical trial of adjuvant chemotherapy in invasive, node-positive breast cancer patients. Main Outcomes and Measures: The primary objectives were to (1) assess frequency of heterozygous deletions in chromosome 17 genomic sites used as FISH internal controls for evaluation of HER2 status among HER2-equivocal cancers; (2) characterize impact of using deleted sites for determination of HER2-to-internal-control-gene ratios; (3) assess HER2 protein expression in each subgroup; and (4) compare clinical outcomes for each subgroup. Results: Of the 1980 patients in METABRIC,1915 patients were fully evaluated. In addition, 100 HER2-equivocal breast cancers by FISH and 100 comparator FISH-negative breast cancers from the BCIRG-005 trial were analyzed. Heterozygous deletions, particularly in specific p-arm sites, were common in both HER2-amplified and HER2-not-amplified breast cancers. Use of alternative control probes from these regions to assess HER2 by FISH in HER2-equivocal as well as HER2-not-amplified breast cancers resulted in high rates of false-positive ratios (HER2-to-alternative control ratio ≥2.0) owing to heterozygous deletions of control p-arm genomic sites used in ratio denominators. Misclassification of HER2 status was observed not only in breast cancers with ASCO-CAP equivocal status but also in breast cancers with an average of fewer than 4.0 HER2 copies per tumor cell when using alternative control probes. Conclusions and Relevance: The indiscriminate use of alternative control probes to calculate HER2 FISH ratios in HER2-equivocal breast cancers may lead to false-positive interpretations of HER2 status resulting from unrecognized heterozygous deletions in 1 or more of these alternative control genomic sites and incorrect HER2 ratio determinations.

Picomolar sensitive and SNP-selective "Off-On" hairpin genosensor based on structure-tunable redox indicator signals.

A robust and sensitive electrochemical assay for chrononocoulometric detection of nucleic acids at a single nucleotide polymorphism (SNP) level has been developed. The assay exploits hybridization-induced conformational switching of gold-tethered TP53-specific 33-mer and truncated 20-mer hairpin DNA probes and methylene blue (MB) as an intercalating redox indicator. We show that by fine tuning of MB-DNA intercations the enhanced binding of MB to hybrids formed with a cancer-biomarker sequence can be achieved, and that results in robust "off-on" sensing of hybridization, while the stem-loop probe design allows minimized, independent of the DNA length background signals. Both DNA probes were sensitive to the presence of SNP in the targeted DNA sequence already at 10 pM. DNA levels, and the robust "off-on" discrimination of 10 pM perfectly-matched DNA from 50 nM SNP-containing DNA was achieved by time-adjusted chronocoulometry. This label-free hairpin DNA strategy allows systematic design of DNA assays for fast, robust and inexpensive genetic analysis in excessive mixtures of structurally-related DNA sequences and was used for specific analysis of prostate-cancer-realted cellular microRNA in total RNA samples isolated from LNCaP and BPH1 cells.

Estudo comparativo entre um sistema de sonda genética e métodos clássicos na identificação das micobactérias / Gene probes versus classical methods in the identification of mycobacteria

OBJETIVO: O aparecimento da co-infecção tuberculose/HIV e o aumento de casos de doenças provocadas por micobactérias não-tuberculosas (MNT) exigem repostas laboratoriais rápidas tanto no isolamento como na identificação das micobactérias. O objetivo deste trabalho foi avaliar a identificação das micobactérias através de sonda genética em comparação com os métodos bioquímicos clássicos. MÉTODOS: Entre 2002 e 2004, foram analisadas 178 culturas de micobactérias, confirmadas como bacilos álcool-ácido resistentes e obtidas de isolados clínicos de pacientes sintomáticos respiratórios ou com suspeita clínica de tuberculose pulmonar e/ou micobacterioses, atendidos nas Unidades de Saúde da Baixada Santista. RESULTADOS: A sonda genética identificou 137 amostras (77%) como complexo Mycobacterium tuberculosis e 41 (23%) como MNT. A discordância observada de 3% entre os métodos ocorreu apenas no ano de implantação (2002). Ao comparar os métodos, a sensibilidade, especificidade, valor preditivo positivo e valor preditivo negativo da sonda genética foram 98%, 93%, 98% e 93%, respectivamente. CONCLUSÕES: Apesar do custo elevado, a identificação de micobactérias pela técnica molecular é mais rápida: máximo de 3 h vs. 28-30 dias para os métodos clássicos. A utilização de sondas genéticas é uma técnica molecular validada, simples e disponível no mercado, com elevada especificidade, sensibilidade e rapidez, o que justifica sua implantação e uso rotineiro em laboratórios de referência, facilitando o diagnóstico e permitindo uma intervenção clínica ágil.

OBJECTIVE: The emergence of tuberculosis/HIV co-infection and the increase in the number of cases of infection with nontuberculous mycobacteria (NTM) require rapid laboratory test results in the isolation and identification of mycobacteria. The objective of this study was to evaluate the identification of mycobacteria by means of gene probes in comparison with that obtained using classical biochemical methods. METHODS: Between 2002 and 2004, 178 mycobacterial cultures, all testing positive for acid-fast bacilli, were analyzed. Samples were obtained from clinical specimens of patients with respiratory symptoms or with clinical suspicion of pulmonary tuberculosis/mycobacteriosis who were treated in the greater metropolitan area of Santos. RESULTS: The gene probe identified 137 samples (77%) as Mycobacterium tuberculosis complex and 41 (23%) as NTM. Discordant results between the methods (3%) were obtained only in the year of implementation (2002). When comparing the methods, the sensitivity, specificity, positive predictive value and negative predictive value of the gene probe method were 98%, 93%, 98% and 93%, respectively. CONCLUSIONS: Despite the cost, the identification of mycobacteria using the molecular technique is faster: maximum 3 h vs. 28-30 days for classical methods. The use of gene probes is a validated molecular technique. It is fast, easy to use and readily available on the market. It has high specificity and sensitivity, which justifies its implementation and routine use in referral laboratories, since it facilitates the diagnosis providing agile clinical interventions.

Gene expression signature associated with BRAF mutations in human primary cutaneous melanomas.

With the aim to correlate BRAF mutation status with gene expression in human primary cutaneous melanomas, and thus to get more insight on the consequences of BRAF mutation on cell biology, we analyzed all expression data obtained in melanomas from which DNA was extracted from the same tissue slides that were used for the expression study. A cohort of 69 frozen primary melanoma whose oligonucleotide micro-array expression data were available, were genotyped for BRAF and NRAS genes. The expression data from these melanomas were re-analyzed according to BRAF mutational status. A set of 250 probes representing 209 genes that were significantly (raw P< or =0.001) associated with BRAF mutation status was identified and 17 of these were previously shown to be implicated in cutaneous melanoma progression or pigmentation pathway-associated genes driven by the microphthalmia transcription factor (MITF). The list of 34 top probes contained no more than 1% of false discoveries with a probability of 0.95. Among the genes that differentiated most strongly between BRAF mutated and non-mutated melanomas, there were those involved in melanoma immune response such as MAGE-D2, CD63, and HSP70. These findings support the immunogenicity of BRAF(V600E), eliciting patients T-cell responses in various in vitro assays. The genes whose expression is associated with BRAF mutations are not simply restricted to the MAPK/ERK signaling but also converge to enhanced immune responsiveness, cell motility and melanosomes processing involved in the adaptative UV response.

Polycythemia vera is not initiated by JAK2V617F mutation.

OBJECTIVE: The somatic JAK2(V617F) mutation is seen in most polycythemia vera (PV) patients; however, it is not clear if JAK2(V617F) is the PV-initiating mutation. METHODS: In order to examine this issue, we developed a novel real-time quantitative allele-specific PCR, in which allelic discrimination is enhanced by the synergistic effect of a mismatch in the -1 position, and a locked nucleic acid (LNA) nucleoside at the -2 position. RESULTS: Determination of allelic frequencies was reproducible (SD = 1.5%) and sensitive--0.1% mutant allele detected in 40 ng of DNA. The JAK2(V617F) frequency in clonal granulocytes from 3 PV females was less than 50% (27.5 +/- 11) and in 7 females greater than 50% (75 +/- 10.5). We also found that wild-type JAK2 BFU-E colonies from PV patients can grow without erythropoietin. The identification of the primary genetic lesion resulting in PV is essential for the development of novel therapeutic strategies. CONCLUSION: Our studies correlating the frequency of JAK2(V617F) mutant allele and clonality, as well as the presence of homozygous wild-type JAK2 erythropoietin-independent erythroid colonies, provide compelling evidence that the JAK2(V617F) is not the PV-initiating mutation. This supports a model wherein the JAK2(V617F) mutation arises as a secondary genetic event. Furthermore, our results indicate that an undefined molecular lesion, preceding JAK2(V617F), is responsible for clonal hematopoiesis in PV. We conclude that development of therapeutic strategies that target the JAK2(V617F) clonal cells may not be sufficient for eradication of PV.

Entamoeba histolytica: inflammatory process during amoebic liver abscess formation involves cyclooxygenase-2 expression in macrophages and trophozoites.

It has been demonstrated that expression of cyclooxygenase-2 (COX-2) isoform is induced by Entamoeba histolytica in macrophages and polymorphonuclear cells during amoebic liver abscess (ALA) formation in hamsters. Trophozoites present in the lesion were also positive for COX-2 signal. However, no cross reactivity of the anti-COX-2 antibody with protein extract of cultivated trophozoites was found. To clarify if trophozoites are involved in PGE(2) production during ALA development, COX-2 expression was detected by in situ hybridization and RT-PCR in liver tissue from intrahepatically infected hamsters. COX-2 mRNA was in polymorphonuclear cells since 4h postinfection, and subsequently, local macrophages expressed COX-2 mRNA in a similar way. Additionally, a positive signal for COX-2 mRNA expression was detected in E. histolytica trophozoites, suggesting that, in vivo, parasite COX expression may be an important mechanism to promote inflammation.

Combining gene expression data from different generations of oligonucleotide arrays.

BACKGROUND: One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. RESULTS: We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. CONCLUSIONS: Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively.

Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.

Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms.

Quantitative assessment of minimal residual disease in childhood lymphoid malignancies using an allele-specific oligonucleotide real-time quantitative polymerase chain reaction.

We developed an assay using a real-time quantitative polymerase chain reaction (RQ-PCR) for the quantitative assessment of minimal residual disease (MRD) in childhood lymphoid malignancies by using a consensus V-region probe combining a allele-specific oligonucleotide (ASO) reverse primer. Our strategy employs a set consisting of a consensus V-region probe, an ASO reverse primer, and a patient-specific forward primer for clonal antigen-receptor (IgH, immunoglobulin heavy chain; TCR, T-cell receptor) gene rearrangements (IgH-ASO and TCR-ASO RQ-PCR assays). The limit of detection in both assays was 5 copies of the target/10(5) cell equivalents. We tested the assays in 17 childhood malignancies (14 cases of acute lymphoblastic leukemia and 3 of non-Hodgkin's lymphoma). High correlation coefficients of the standard curves (>0.980) and PCR efficiency (>0.95) were achieved with all primer/probe sets. In 2 (12%) of the 17 patients, ASO primers could not be designed because there was no junctional N-sequence. The quantitative data suggest that the copy number of clonal antigen receptors markedly decreased after induction therapy in 15 of 17 patients and that 1 patient relapsed and died of the disease. Consensus probes make it possible to examine a large number of patients with only a limited number of probes. The strategy used for IgH-ASO and TCR-ASO RQ-PCR assays is accurate and reliable in the clinical prospective study of MRD in childhood lymphoid malignancies.

Competitive cytokeratin 19 RT-PCR for quantification of breast cancer cells in blood cell suspensions.

Detection of residual tumor cells in BM and PBPC products has been correlated with worse outcome of breast cancer patients. Still, there is a considerable demand for studies investigating the influence of the actual tumor cell number on prognosis, as quantification routinely has been cumbersome and time consuming and, thus, was evaded. We developed and evaluated a competitive RT-PCR-ELISA assay for cytokeratin 19 (CK19) with standard curve quantification that allows quantification of multiple samples within a working day; mRNA isolation, RT-PCR reaction, and automated ELISA detection were carried out using commercial kits. Results were expressed as OD420nm ratios of CK19 and an internal competitor. Values were then converted into tumor cell numbers using a standard curve of MCF-7 tumor cells. The assay had high specificity because of primers and capture probes with great heterogeneity to both published pseudogenes, which was confirmed by BLAST sequence alignment. We achieved a sensitivity of detecting 1 tumor cell per 10(6) mononuclear cells (MNC). Between-batch precision (n = 8) for quantification was consistent and reasonable, with a coefficient of variation around 25%. Therefore, this assay should be suitable and sufficient for routine quantification of tumor cell numbers in BM or PBPC samples.

ViraPap: can it help to reduce the need for colposcopy?

Two new tests recently became available for identifying cervical human papillomavirus (HPV). This study investigated the usefulness of the ViraPap and ViraType in the clinical setting. Thirty-six subjects considered to be at risk for HPV infection were examined; had specimens obtained for Papanicolaou smear (Pap smear), ViraPap, and ViraType; and were then referred for colposcopy. Results of these examinations were then compared to the findings of colposcopy and/or colposcopic biopsy. The sensitivity and specificity of the ViraPap in predicting an abnormality being found on colposcopic examination were 61.5% and 70%, respectively. Identifying the specific viral type by use of the ViraType did not prove to be clinically helpful in this population.

Implementación de sondas genéticas biotiniladas para la identificación de E. coli diarreogénico en niños con diarrea / Implementation of biotinilates genetic probes for identification of E. coli diarreogenic in children with diarrhea

Escherichia coli constituye el agente etiológico más importante de la diarrea aguda infantil en los países en vías de desarrollo. Para la identificación de las distintas categorías y determinación de su importancia relativa en grandes poblaciones se ha requerido de técnicas sofisticadas y engorrosas. Como una respuesta a la necesidad de contar con una técnica de alta sensibilidad y especificidad, que no requiere de instalaciones costosas, ni un tiempo largo de procesamiento, se han desarrollado las sondas genéticas, como un aporte más del avance en la tecnología del ADN recombinante. De gran importancia fue poder reemplazar el uso de radioisótopos por sistemas de marca más simples y fáciles de manipular, como la biotina. Nuestro interés fue dar a conocer la experiencia de la implementación de esta tecnología en la identificación de las diversas categorías de E. coli diarreogénico en muestras de deposiciones de niños con diarrea y controles sanos, comoparte de un estudio de campo de la diarrea aguda. Demostrándose que es posible desarrollar esta tecnología en Chile y que los resultados obtenidos constituyen un aporte al conocimiento de la epidemiología de E. coli diarreogénico

Evaluation of biotinylated DNA probes for the detection of gene rearrangements in clinical specimens.

To determine whether a nonisotopic procedure is suitable for analyzing clinical specimens for gene rearrangements, the authors hybridized DNA from 15 specimens of lymphoid tissue with biotinylated DNA probes directed to J beta I + J beta II (T-cell receptor beta chain gene), JH (immunoglobulin gene heavy chain J region), and J kappa (immunoglobulin gene kappa light chain J region). Five cases of benign lymphoid hyperplasia, one case of dermatopathic lymphadenopathy, and one case of small noncleaved follicular center cell lymphoma had germline hybridization patterns when digested with Bam HI, Eco RI, and Hind III restriction endonucleases. Four cases of B-cell lymphoma and three cases of T-cell lymphoma had clearly detectable rearrangements of the genes for immunoglobulin or the T-cell receptor or both. One case of dermatopathic lymphadenopathy had a faint, clonal rearrangement of the T-cell receptor after digestion with Eco RI and Bam III. The authors conclude that biotinylated DNA probes can be useful for analyzing gene rearrangements in clinical specimens.

A comparison of biotin- and 35S-based in situ hybridization methodologies for detection of human papillomavirus DNA.

In situ hybridization is commonly used for the detection of human papillomavirus (HPV) DNA in genital tract lesions. Systems based on biotin complexes are quicker and easier to use than 35S-based systems, although reportedly less sensitive. We compared three in situ hybridization systems for HPV DNA detection: two biotin [PathoGene DNA probe assay [Enzo Diagnostics] and Viratype in situ HPV probes and HPV tissue hybridization kit [Life Technologies Inc. (LTI)] and one 35S based. By using serial sections from 80 female genital tract lesions with the histologic features of an HPV infection, sequences homologous to HPV DNA were detected in 59 cases (74%) with the LTI system and 25 cases (31%) with the Enzo system. The Enzo system uses a streptavidinbiotinylated horseradish peroxidase complex and 2% 3-amino-9-ethylcarbazole as the chromogen. The LTI system uses a streptavidin alkaline phosphatase conjugate in which the chromogen is 5-bromo-4-chloro-3-indolylphosphate in the presence of nitroblue tetrazolium. Replacing the Enzo detection system with the LTI detection system increased the sensitivity of the Enzo kit. The LTI biotin system was equally sensitive when compared against 35S-labeled HPV probes. The sensitivity with the biotin probes, reported to be less than the 35S probes in a previous study (Lab Invest 58:354, 1988), was increased if the current LTI detection system replaced the detection system used in that study. It is concluded that biotin-labeled DNA probes can be equally sensitive to 35S-labeled DNA probes for the detection of sequences homologous to HPV DNA. The enhanced sensitivity for the biotin system is primarily due to improved detection of the probe/target complex.

Construcción de una sonda de DNA para identificar Adenovirus humanos

Fragmentos de restricción del DNA del Adenovirus humano tipo 8, fueron ligados al plásmido pBR322 a nivel del gen de resistencia a la tetraciclina y clonados en la E. coli HB101. El plásmido recombinante obtenido del clón bacteriano No. 117 fué seleccionado como sonda para realizar ensayos de hibridazación, utilizando marcaje radioactivo. Según análisis de restricción e hibridización, éste plásmido contiene un fragmento de DNA viral con una longitud aproximada de 4.65 Kb, que corresponde a la región del genoma localizada entre 55.1 y 68.8 um, la cual codifica para la proteina del hexón y para la proteina 55 Kd, que estáligada al extremo 5' del DNA viral. La sonda clonada fué evaluada mediante la técnica de hibridización "dot blot", empleando DNAs de Adenovirus representantes de los subgéneros A, B, C, D, y E. Los resultados permitieron concluir que la región del genoma Adenoviral localizada entre 55.1 y 68.8 um, contiene secuencias nucleotidicas homólogas en 5 diferentes subgéneros y por lo tanto podría utilizarse como sonda para detectar ácido nucleico a partir de muestras clínicas