BackgroundMany methodologies have been used in research to identify the “intrinsic” subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E) and Basal-like. The PAM50 gene set is often used for gene expression-based subtyping; however, surrogate subtyping using panels of immunohistochemical (IHC) markers are still widely used clinically. Discrepancies between these methods may lead to different treatment decisions.MethodsWe used the PAM50 RT-qPCR assay to expression profile 814 tumors from the GEICAM/9906 phase III clinical trial that enrolled women with locally advanced primary invasive breast cancer. All samples were scored at a single site by IHC for estrogen receptor (ER), progesterone receptor (PR), and Her2/neu (HER2) protein expression. Equivocal HER2 cases were confirmed by chromogenic in situ hybridization (CISH). Single gene scores by IHC/CISH were compared with RT-qPCR continuous gene expression values and “intrinsic” subtype assignment by the PAM50. High, medium, and low expression for ESR1, PGR, ERBB2, and proliferation were selected using quartile cut-points from the continuous RT-qPCR data across the PAM50 subtype assignments.ResultsESR1, PGR, and ERBB2 gene expression had high agreement with established binary IHC cut-points (area under the curve (AUC) ≥ 0.9). Estrogen receptor positivity by IHC was strongly associated with Luminal (A and B) subtypes (92%), but only 75% of ER negative tumors were classified into the HER2-E and Basal-like subtypes. Luminal A tumors more frequently expressed PR than Luminal B (94% vs 74%) and Luminal A tumors were less likely to have high proliferation (11% vs 77%). Seventy-seven percent (30/39) of ER-/HER2+ tumors by IHC were classified as the HER2-E subtype. Triple negative tumors were mainly comprised of Basal-like (57%) and HER2-E (30%) subtypes. Single gene scoring for ESR1, PGR, and ERBB2 was more prognostic than the corresponding IHC markers as shown in a multivariate analysis.ConclusionsThe standard immunohistochemical panel for breast cancer (ER, PR, and HER2) does not adequately identify the PAM50 gene expression subtypes. Although there is high agreement between biomarker scoring by protein immunohistochemistry and gene expression, the gene expression determinations for ESR1 and ERBB2 status was more prognostic.

These new cases, combined with previously described cases, demonstrate that U-type exchange is the most frequent mechanism for this rearrangement and can be observed on most, or perhaps all, chromosome arms.

Background: A single hotspot mutation at nucleotide 1799 of the BRAF gene has been identified as the most common genetic event in papillary thyroid carcinoma (PTC), with a prevalence of 29-83%. Aims: To use a PCR assay to molecularly characterise the BRAF activating point mutation in a series of PTC and benign thyroid cases and correlate the mutation results with histological findings. Methods: Formalin-fixed paraffin-embedded (FFPE) sections were evaluated for the BRAF V600E mutation using LightCycler PCR with allele-specific fluorescent probe melting curve analysis (LCPCR). Results: 42 (37 PTC; 5 benign) surgical tissue samples were analysed for the BRAF V600E activating point mutation. Using LCPCR and direct DNA sequencing, the BRAF mutation was identified in 23/37 (62.2%) PTC FFPE samples. DNA sequencing results demonstrated confirmation of the mutation. Conclusions: Detection of BRAF-activating mutations in PTC suggests new approaches to management and treatment of this disease that may prove worthwhile. Identification of the BRAF V600E activating mutation in routine FFPE pathology samples by a rapid laboratory method such as LCPCR could have significant value.A lthough thyroid cancer represents only 1% of all human malignancies, it accounts for more than 90% of all endocrine cancers.1 The incidence of thyroid cancer has risen in the United States, from a rate of 3.6 per 100 000 in 1973 to 8.7 per 100 000 in 2002.2 The increase in thyroid cancer incidence can be attributed primarily to an increase in the incidence of papillary thyroid carcinoma (PTC). For the time period 1973 to 2002, the incidence of PTC increased from 2.7 to 7.7 per 100 000, a 2.9-fold increase.2 In a report of 15 700 patients in the United States, overall survival rates, corrected for age and sex, were 98% for PTC, 92% for follicular carcinoma, 80% for medullary carcinoma, and 13% for anaplastic carcinoma.3 Among the most curable of cancers, PTC tends to remain localised in the thyroid gland, but in time it may metastasise to regional lymph nodes and, less commonly, to the lungs. Peak incidence of PTC is in the fifth decade of life and it occurs nearly three times more frequently in women than in men. 4A single hotspot mutation at nucleotide 1799 of the BRAF gene has been identified as the most common genetic event in PTC, with a prevalence of 29-83%. [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] Activating BRAF mutations may be an important event in the development of PTC. This mutation had been formerly termed T1796A, based on the NCBI GenBank nucleotide sequence NM 004333, which missed a codon (three nucleotides) in exon 1 of the BRAF gene. With the correct version of the NCBI GenBank nucleotide sequence NT 007914 available, this BRAF mutation is now designated T1799A. 25This thymine (T) to adenine (A) transversion mutation (TRA) results in the substitution of valine with glutamate in codon 600 (V600E, formerly V599E) and converts BRAF into a dominant transforming protein that causes constitutive activati...

BackgroundDetection of cytologic atypia in nipple aspirate fluid (NAF) has been shown to be a predictor of risk for development of breast carcinoma. Manual collection of NAF for cytologic evaluation varies widely in terms of efficacy, ease of use, and patient acceptance. We investigated a new automated device for the non-invasive collection of NAF in the office setting.MethodsA multi-center prospective observational clinical trial involving asymptomatic women designed to assess fluid production, adequacy, safety and patient acceptance of the HALO NAF Collection System (NeoMatrix, Irvine, CA). Cytologic evaluation of all NAF samples was performed using previously described classification categories.Results500 healthy women were successfully enrolled. Thirty-eight percent (190/500) produced fluid and 187 were available for cytologic analysis. Cytologic classification of fluid producers showed 50% (93/187) Category 0 (insufficient cellular material), 38% (71/187) Category I (benign non-hyperplastic ductal epithelial cells), 10% (18/187) Category II (benign hyperplastic ductal epithelial cells), 3% (5/187) Category III (atypical ductal epithelial cells) and none were Category IV (unequivocal malignancy). Overall, 19% of the subjects produced NAF with adequate cellularity and 1% were found to have cytologic atypia.ConclusionThe HALO system is a simple, safe, rapid, automated method for standardized collection of NAF which is acceptable to patients. Cytologic assessment of HALO-collected NAF showed the ability to detect benign and pre-neoplastic ductal epithelial cells from asymptomatic volunteers.