bluuebunny/crossref_metadata_2025_split huggingface dataset:
P1-07-05: HER2 Status Resolution in FISH and IHC “Double Equivocal” Breast Carcinomas by Quantitative Real-Time PCR.
Authors: Portier BP , Wang Z , Downs-Kelly E , Budd GT , Lanigan C , Tubbs RR 
Published: June 2012

Abstract
Background: Clinical testing for HER2 amplification/over-expression is performed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) as outlined by the ASCO/CAP guidelines. Although these guidelines standardize testing and reporting, in a subset of patients, HER2 is equivocal by both IHC and FISH (“Double Equivocal”). These double equivocal patients represent a clinically problematic sub-group that currently lack standardized management guidelines. In this study, we utilize Quantitative Real-Time PCR (Q-RT-PCR) to resolve HER2 status in invasive breast cancer cases that could not be resolved via IHC and FISH testing.
Material and Methods: FISH for HER2 was performed on 2259 invasive breast carcinomas from 1/2008 to 12/2010. In accordance with ASCO/CAP, all equivocal HER2 FISH cases were reflex tested by IHC. In double equivocal cases, RNA extraction was performed following macro-dissection using High Pure RNA Paraffin Kit (Roche Applied Biosciences, Indianapolis, IN). Q-RT-PCR was carried out using TaqMan® RNA-to-CT™ 1-Step Kit with primers and probes for HER2, B2M, and GAPDH (Applied Biosystems, Foster City, CA). Q-RT-PCR results were expressed as the relative quantification of HER2 vs. two control genes, all normalized against calibrator RNA from the MCF7 cell line. Cut off for Q-RT-PCR HER2 overexpression was set using ROC curve analysis (MedCalc, Belgium).
Results: In our cohort of 2259 patients, 124 (5.5%) had an equivocal HER2 result by primary FISH testing. Reflex HER2 testing by IHC was unable to resolve the HER2 status in 35 (1.5%) patients. Detection of HER2 overexpression by Q-RT-PCR was validated using 50 FISH confirmed amplified and 50 non-amplified cases. Q-RT-PCR performed on these 2 control populations generated two non-overlapping populations and ROC curve analysis using a cut off value of 7.0 showed 100% sensitivity and specificity in detection of HER2 overexpression. Application of Q-RT-PCR in the double equivocal sub-group resulted in resolution of HER2 status in all cases, 8 HER2 positive (test value ranging from 7.12 - 15.37) and 14 HER2 negative (test value ranging from 1.05 - 6.92).
Conclusion: Application of Q-RT-PCR for HER2 represents a viable approach to resolve HER2 status in cases that fail classification by both FISH and IHC. Q-RT-PCR combines the precision and high sensitivity of real-time PCR with the morphological specificity of histological evaluation and ultimately allows definitive HER2 classification at the time of initial diagnosis. This knowledge of HER2 status at the time of diagnosis allows for comprehensive neoadjuvant treatment although, additional studies correlating response to anti-HER2 therapy and HER2 status by Q-RT-PCR are warranted.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-05.
P1-07-11: Consistency and Control in Clinical Assay Technology over Time: The Oncotype DX Recurrence Score and Assessment of Single Gene Expression Levels.
Authors: Baehner FL , Butler SM , Anderson JM , Ballard J , Tan V , Shak S 
Published: June 2012

Abstract
Background: ASCO® and CAP have recently highlighted the importance of consistency and control in clinical assay technology. To date the Oncotype DX® Recurrence Score® (RS) has been ordered to assist in individualized treatment decision making in over 200,000 estrogen receptor positive, early stage breast cancer patients. The assay quantifies gene expression using RT-PCR from fixed paraffin embedded tissue (FPET) and employs a large number of controls and calibrators to enhance precision and reproducibility. Over 6 years of data on the assay presents an opportunity to explore consistency over time in the RS and quantitative single gene levels (ER, PR, HER2).
Methods: All tumors successfully analyzed in the Genomic Health Laboratory from 1/1/05-3/31/11 were included. Descriptive statistics for the RS, the average reference gene expression level, and expression levels for quantitative single genes were obtained for each calendar year. This was done for the entire data set as well as for subgroups defined by histological tumor type. The associations by year between HER2 and GRB7, ER and HER2, and ER and PR expression levels were explored including scatterplots and summary statistics.
Results: There were a total of 207,691 breast cancer cases, and the number in each calendar year increased over time as shown in the Table. In general the median age increased slightly over time, as did the proportion of patients in the low RS Risk Group. There was no systematic change over time in the average reference gene expression level, or in the expression levels for the individual genes ER, PR or HER2 during the period from 2008 to 2011 when individual gene testing was provided as part of the Oncotype DX assay report. The relationships between HER2 and GRB7, ER and HER2, and ER and PR remained consistent over time.
Conclusions: Active monitoring of the Oncotype DX assay as mandated by ASCO/CAP shows a high degree of consistency in results for both the multigene Recurrence Score and the quantitative single gene results. These results and the approaches used for monitoring consistency are relevant to other institutions in their efforts to maintain and improve assay quality control.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-11.
P1-07-14: Quantum Dot-Labelled Antibodies To Assess HER2 Expression in Breast Cancer.
Authors: Zona S , Blackburn E , Hojjatoleslami AS , Brown IR , Gullick WJ 
Published: June 2012

Abstract
Background: The Human Epidermal Growth Factor Receptor 2 (HER2) is overexpressed in 18–20% of breast cancers. Herceptin is an effective drug for the treatment of breast cancers expressing high levels of HER2. It is well known that there is a correlation between levels of HER2 expression and response to Herceptin. However a proportion of patients selected for Herceptin treatment do not respond to the drug. The accuracy of the assessment of HER2 levels in breast cancer is therefore important to predict patients’ response to Herceptin therapy. The current techniques in clinical use for the assessment of HER2 are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH); however both IHC and FISH have several limitations which may result in patient misclassification. A more accurate technique, which can quantify HER2 levels more precisely, could help to improve clinical diagnosis, prediction of prognosis and allow more accurate select individual patients for particular drug therapies.
Materials and Methods: We employed QDs labelled antibodies, laser scanning confocal microscopy and image segmentation techniques to quantify HER2 expression in cases of formalin fixed paraffin embedded breast cancers. Quantum dots (QDs) are a new class of fluorochromes made of semiconductor nanocrystal which have several useful properties for quantitative image analysis. In order to validate the system we used a breast cancer HER2−IHC control tissue array with negative, low, moderate and strong expressing cases, and a tissue microarray containing 60 samples of formalin fixed paraffin embedded breast cancer sections, previously examined by IHC and scored semiquantitatively (0-3+). We then applied this system to quantify HER2 expression a tissue microarray containing 150 primary breast cancers scored as 3+ by IHC from patients treated with Herceptin.
Results: We first demonstrated that the QD system could reliably detect HER2 expression in IHC 3+ cases. A comparison of immunofluorescent staining with conventional immunohistochemistry showed that QDs give more linear and scalable measurements of receptor levels. We also quantified HER2 within a set of 150 breast cancers scored as 3+ by IHC, and we found that HER2 is expressed at very different levels, ranging over fifty fold between individual (IHC3+) cases. We currently are evaluating the correlation between HER2 receptor levels, measured by QDs, and patient's response to Herceptin.
Conclusion: QDs and image analysis can produce a more precise measurement of HER2 levels of expression than IHC. This should help to improve clinical diagnosis, prognosis, identify specific treatments for individual patients and reduce costs associated with Herceptin treatment. This technology may be applied to study other members of the EGF family in breast cancers or more widely as a quantitative measurement of biomarkers in tumours.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-14.
P1-07-19: Analysis of HER2−Status in Breast Cancer by Mass Spectrometry in Archival, Formalin-Fixed Tissues.
Authors: Sanders M , Sprung R , Ham A , Sanchez V , Manning S , Arteaga C , Liebler D 
Published: June 2012

Abstract
HER2 (ERBB2) is overexpressed in about 25% of breast cancers and predicts clinical benefit from trastuzumab, as well as response to anthracycline-based chemotherapy. Fluorescence in situ hybridization (FISH) to detect HER2 gene copy number and immunohistochemistry (IHC) to detect HER2 protein levels are approved by the FDA to identify HER2−positive (H2) tumors. However, the 2007 ASCO/CAP report concluded that approximately 20% of HER2 testing may be inaccurate. Further, the available data did not clearly demonstrate clear superiority of either IHC or FISH as a predictor of benefit from anti-HER2 therapy. Discordance between these methods is as high as 5%. Thus, novel complementary quantitative methods for interrogating HER2 expression in tumors are needed.
Targeted protein analysis by multiple reaction monitoring mass spectrometry (MRM-MS) offers a powerful approach to configure assays for specific proteins without using antibodies. Our studies using this platform have demonstrated applicability to formalin-fixed, paraffin-embedded (FFPE) specimens. In the current studies, we used this approach to measure signals from two tryptic peptides specific to HER2, one each from the extracellular and intracellular domains, selected from among 28 candidates based on their signal intensity and sharpness of their chromatographic profiles. Preliminary studies with a HER2−overexpressing BT474 xenograft in mice demonstrated quantitation and detected previously reported HER2 ectodomain shedding. Subsequent analysis of FFPE tissue from five H2 and five triple-negative (TN) tumors yielded measurement of at least 1 femptomole of receptor for H2 tumors and less than 0.2 femptomole of receptor for TN tumors per microgram of digest analyzed. If we assume 200 picograms of protein per cell, the results suggest 110,00 to 468,000 receptors per cell in the H2 tumors and only 2,000 to 14,000 receptors per cell in the TN tumors. Despite significant biological variability in receptor levels measured among the specimens of each type, a clear separation of the H2 and TN tumors was achieved based on the peptide quantitation. This preliminary study demonstrates the potential of MRM-MS in FFPE tissue to provide an alternate approach to IHC-based protein analysis. MRM-MS offers the potential for more, accurate and robust HER2 quantification in clinical breast cancer tissues. The next phase of this work will encompass a larger sample set, including tumors with equivocal and negative FISH and/or IHC test results. Correlation with response to anti-Her2 therapy will be performed in samples with available follow-up data.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-19.
P1-08-07: Survival in US Women Following an Indication of Metastatic Breast Cancer Diagnosis and Chemotherapy Initiation: A SEER-Medicare Analysis.
Authors: Rugo H , Taylor D , Sanon M , Clements K , Balu S , Faria C , Teitelbaum A 
Published: June 2012

Abstract
Objective: Use SEER-Medicare data to identify US women with metastatic breast cancer (MBC) treated (tx) with chemotherapy (CTX) and evaluate survival.
Methods: Key inclusion criteria were women diagnosed (dx) with breast cancer (BC) in 2001–2005 with 1) Medicare enrollment 12 mo prior to dx through follow-up (2008) or death; 2) an indication of tx with CTX at any time after initial BC diagnosis (any stage). Dx of MBC between 2001–2006. MBC dx date was defined as the initial BC dx date if the patient had “distant” disease at entry into SEER or the date of first appearance of secondary malignancy in claims data (ICD9 codes 197.0−198.1, 198.3−198.7, 198.82−198.89) during follow up, at least 2 mo after initial dx. CTX date was defined as the date of first receipt of a CTX agent commonly used to treat BC after the MBC date. Data on oral medications (e.g., most hormone therapies, capecitabine) were not available. Kaplan-Meier survival analyses were performed to describe survival after MBC dx (patients were censored at end of follow-up). Survival was assessed both from the date of MBC and receipt of first intravenous (IV) chemo. Subgroup analyses were performed based on age, type of MBC dx and estrogen receptor (ER) status.
Results: Patient demographics and survival are shown in the table.

Conclusions: Despite recent advances in treatment options, median survival following a dx of MBC is less than two years, and is approximately 16 months after start of IV CTX. Survival is shorter for patients who develop MBC after an initial breast cancer dx compared to those with MBC at diagnosis, and for those with ERnegative tumors. In order to improve clinical outcomes, it is critical to pursue a better understanding of tumor biology and appropriate use of new agents.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-08-07.
P1-08-09: Increased Mortality in Swedish Women Diagnosed with Breast Cancer during and Shortly after Pregnancy.
Authors: Johansson ALV , Andersson TM-L , Cnattingius S , Hsieh C-C , Lambe M 
Published: June 2012

Abstract
Background: The incidence of pregnancy-associated breast cancer (PABC), i.e. breast cancer diagnosed during pregnancy or within two years after delivery, is increasing in Sweden. Results from epidemiological studies suggest that women with PABC have worse prognosis than women of same age and no recent birth. We studied the mortality in women with PABC, compared to women with a diagnosis of breast cancer not close to pregnancy, and in relation to when the PABC diagnosis occurred (during pregnancy, different postpartum periods). We also studied whether mortality varied over time since diagnosis.
Materials and Methods: We used data from the Swedish National Cancer Register to identify all women diagnosed with breast cancer between ages 15–44 years during 1963–2002 (n=15,729). The study cohort was linked to the Multi-Generation Register to obtain information on childbirths and when they occurred. We estimated mortality rates among women with and without PABC, and subdivided by time of detection among PABC patients (PABC during pregnancy, or during months 1–3, 4–6, 7–12, 13–18, 19–24 after delivery). Hazard ratios (HR) with 95% confidence intervals (CI) were estimated using the novel method of flexible parametric survival models. These models use splines to model the baseline hazard rate, and are able to pick up more subtle time-dependent effects than the more commonly used piecewise splitting of the timescale (for example in Poisson regression).
Results: Women with PABC had higher mortality than women diagnosed at the same age and calendar period and with no recent birth. In women with PABC (n=1,110), 46% died during follow-up, compared to 34% of the non-PABC patients (n=14,611). The mortality in both groups peaked at around two years after diagnosis, with the highest peak occurring in women diagnosed 4–6 months after delivery (HR=3.8, 95% CI 2.4−5.9). Also, among women diagnosed during pregnancy the mortality was higher compared to women diagnosed further away from delivery. An increased mortality among women with PABC remained up to 10 years after diagnosis.
Discussion: Women with PABC had a poorer prognosis compared to women with breast cancer and no recent birth. The worse prognosis may be due to diagnostic delays or tumour promoting hormonal boosts or changes in the tumour micro-environment post-partum. Taken together, our findings indicate that women with PABC represent a high-risk group of young breast cancer patients that may require special management. Also, by applying novel statistical methods we were able to detect time dependent effects in that the elevated mortality associated with PABC varied by timing of diagnosis and time since diagnosis.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-08-09.
P1-08-21: Demographic and Clinical Characteristics of Metastatic Breast Cancer Patients and Biomarker-Based Prevalence in the UK, Germany, France, Spain and Italy (EU-5).
Authors: Ganguli A , DeKoven M , Bonthapally V , Lee WC , Ray S 
Published: June 2012

Abstract
Background: Much peer-reviewed literature focuses on metastatic breast cancer (mBC) treatment regimens. However, research around mBC patients’ demographic/clinical characteristics across Europe is limited. This study compared such mBC characteristics as well as biomarker-based prevalence across the EU-5.
Methods: IMS LifeLink™ Oncology Analyzer (OA) database, based upon practicing oncologist surveys, was used to identify mBC patients aged ≥18 between 01/2005-06/2010. The study investigated the distribution of mBC population based on age, biomarker, co-morbidities and stage at diagnosis. This study also estimated the proportion of patients, and sites of metastasis, by lines of drug therapies (LOT).
Results: A total of 186,640 mBC patients were identified — Germany (30.2%), France (22.4%), UK (21.2%), Italy (17.7%) and Spain (8.4%). The majority of patients were aged 61–70yrs (24%-32%), except in Spain (22.3% aged 71–80yrs). Proportion of mBC patients with ≥1 co-morbid condition were highest in Germany (36.3%), followed by Spain (32.8%), UK (31.5%), Italy (27.6%) and France (20.1%), with diabetes (12.9−23.9%) and cardiac dysfunction (5.2−21.7%) being most prevalent. The distribution of mBC patients by biomarker status was 53.9% HER-/HR+, 17.8% HER+/HR+, 11.1% HER+/HR- and 17.2% triple negative, and was similar amongst the EU5 countries. The top three metastatic sites were bone (54.4%), lung (36.0%) and liver (32.7%), with proportion of bone metastasis increasing from 1st LOT (38.1%) to 4th LOT (69.6%). Almost 50% of the mBC patients were diagnosed at Stage IV, 14% at Stage III, 26% at Stage II and 6% at Stage I. Of all mBC patients, 93% received 1st LOT, 31% received 2nd LOT, 27% received 3rd LOT and 6.8% received 4thLOT.
Conclusion: In the EU-5, mBC patients were primarily elderly and HER-/HR+. The burden of bone metastasis was higher in later LOTs. Following the 1st LOT, fewer patients moved to subsequent treatments. Additional research on EU-5 clinical practice patterns is warranted.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-08-21.
P1-08-22: Treatment Patterns and Clinical Outcomes in Elderly Patients with HER2−Positive Metastatic Breast Cancer from the registHER Observational Study.
Authors: Kaufman PA , Brufsky AM , Mayer M , Rugo HS , Tripathy D , Ulcickas Yood M , Feng S , Wang LI , Brammer MG , Yardley DA 
Published: June 2012

Abstract
Background: Data are lacking regarding treatment patterns and outcomes in elderly patients (pts) with HER2−positive (HER2+) metastatic breast cancer (MBC).
Methods: registHER is a large, observational cohort of pts with HER2+ MBC diagnosed within 6 months of enrollment. Pts (N=1,001) were followed until death, disenrollment, or June 2009 (median follow-up 27 months). In these analyses, pts were stratified into three groups based on age at MBC diagnosis: younger (&lt;65 years), older (65-74 years), elderly (≥75 years). For Progression Free Survival (PFS) and Overall Survival (OS) analyses of 1st-line trastuzumab (T) vs. no T, older and elderly pts were combined due to small number of events in elderly. Hierarchical multivariate analyses were adjusted for baseline characteristics and treatments.
Results: ER/PR status was similar across age groups (Table 1). Elderly pts with HER2+ MBC had higher rates of underlying cardiovascular disease (CVD) than younger or older pts. In pts receiving T-based 1st-line treatment, elderly pts were less likely to receive chemotherapy (C), and more likely to receive T alone or combined with hormone therapy (HT). Central nervous system (CNS) events decreased with increasing age. In T-treated pts, incidence of left ventricular dysfunction (grade ≥3) was higher in elderly pts (3/63 [4.8%]) than in younger (21/746 [2.8%]) or older pts (2/134 [1.5%]). Across age groups, unadjusted median PFS (months) was significantly higher for pts treated with T in 1st-line than those who were not (&lt;65 years T: 11.0; &lt;65 years no T: 3.4; ≥65 years T: 11.7; ≥65 years no T: 4.8). In pts &lt;65 years, unadjusted median OS (months) was significantly higher in T-treated pts; in pts ≥65 years, median OS was similar (&lt;65 years T: 40.4, &lt;65 years no T: 25.9; ≥65 years T: 31.2, ≥65 years no T: 28.5). In multivariate analyses, T in 1st-line was associated with significant improvement in PFS across age (Table 2). In OS, significant improvement was observed for pts &lt;65 years; results were suggestive for pts ≥65 years.
Conclusions: Elderly pts (≥75 years) with HER2+ MBC in registHER had higher rates of underlying CVD than younger counterparts and received less aggressive treatment, including less 1st-line T. These population-based, real-world data suggest improved PFS with T as 1st-line therapy across all age groups.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-08-22.
P1-09-09: Fetal Microchimerism and In Situ Breast Cancer.
Authors: Eun JK , Gadi VK 
Published: June 2012

Abstract
Background: Haploidentical fetal cells acquired and maintained by a woman in her blood and tissues long after pregnancy completion, also known as fetal microchimerism, is inversely associated with invasive breast cancer. Furthermore, in healthy women, absence of fetal microchimerism serves as a risk factor for development of future breast cancer (J Clin Oncol 29: 2011 suppl; abstr 1574). Here, we test the hypothesis that failure to maintain fetal microchimerism following pregnancy is also associated with in situ breast cancer.
Methods: Buffy coat specimens were obtained from the Roswell Park Cancer Institute Data Bank and BioRepository from parous patients with in situ breast cancer and parous control volunteers with no prior history of cancer. Using quantitative PCR, DNA extracts from peripheral blood buffy coat specimens were tested by a single female operator blinded to case:control status for the presence (and concentrations) of Y chromosome sequence DYS14, a marker of male fetal microchimerism.
Results: In this interim analysis, 83% (34/41) of healthy control women and 55% (29/53) in situ breast cancer patients tested positively for the presence of DYS14. The unadjusted odds ratio was 0.25 (95%-CI of 0.08−0.72; p=0.008). Median concentrations were also greater in healthy women compared to women with in situ cancer, 0.15 versus 0.02 fetal cell equivalents per 10^5 proband genomes, respectively (p=0.004).
Summary: Preliminary results suggest that the associations of fetal microchimerism and in situ breast cancer are similar in magnitude and direction to that observed for invasive disease. The natural history of in situ breast cancer is for a large portion of patients to develop invasive disease in 8–10 years absent of comprehensive locoregional control; results here point to a failure to maintain or loss of haploidentical fetal cells well before development of invasive disease. Final results from the entire cohort planned (n=200) with adjustment for anthropometric, reproductive, and cancer specific factors will be presented at the meeting.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-09-09.