bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract PD02-03: Added value of HER-2 amplification testing by multiplex ligation-dependent probe amplification (MLPA)
Authors: van Slooten H-J , Kuijpers CC , Moelans CB , Horstman A , Al-Janabi S , Hinrichs JW , van Diest PJ , Jiwa M 
Published: August 2014

Abstract
Introduction Accurate determination of HER-2 status is critical for selection of breast cancer (BC) patients for trastuzumab treatment. According to the most commonly used testing protocol, patients with 3+ immunohistochemistry (IHC) are considered for trastuzumab. In addition, 2+ IHC cases are tested for gene amplification and, when amplified, these patients are considered for trastuzumab treatment as well. Because in our experience IHC results have been proven to be sensitive to pre-analytical variation and inter- and intra-observer variation, we apply amplification testing not solely to 2+, but also to 1+ and 3+ cases. At Symbiant Pathology Expert Centre, a validation study (n = 99) comparing MLPA with chromogenic in situ hybridization (CISH) showed 100% concordance. Starting from April 2011, MLPA has been used as the method for HER-2 amplification testing, because in our hands this technique is more time- and cost-effective than CISH for analyzing large sample numbers. CISH was performed when MLPA was inconclusive, IHC score was heterogeneous or when invasive carcinoma could not be physically separated from DCIS. Here we report the results of a comparison between HER-2 amplification tests and IHC in a cohort of 928 BC patients.
Methods Pathology reports of 928 BC patients from 4 pathology laboratories were retrospectively reviewed. 728 patients were diagnosed between April 2011 and February 2012 in one of three laboratories of Symbiant Pathology Expert Centre. The other 200 patients were diagnosed in University Medical Centre Utrecht between January 2010 and December 2011. 18 patients had multiple tumors that were included as separate cases. In total, 949 tumors were reviewed.
Results With IHC, major differences are observed between the 4 pathology laboratories concerning the percentage of cases scored as 0–1+ and 2+ (Table 1). A considerable number of 3+ cases (6.4%) failed to show gene amplification by MLPA and/or CISH. A smaller percentage of 0–1+ cases (1.8%) did show gene amplification (Table 2). 90 equivocal cases were double tested by CISH and MLPA. In 52/90 of these cases (58%) at least one test was inconclusive. The other 38 (42%) cases showed 100% concordance between MLPA and CISH.

Conclusion MLPA is an accurate and cost-effective method for the determination of HER-2 status. We recommend the use of a gene amplification test to confirm HER-2 status in all IHC scores, not just the 2+ cases. However, it is still unclear whether the small subgroups of patients showing only HER-2 protein overexpression or only HER-2 gene amplification would benefit from trastuzumab. Follow-up data are therefore needed to determine the clinical value of HER-2 status assessed by each technique in order to improve the current standard of care for HER-2 testing.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD02-03.
Abstract PD02-06: Concordance between immunohistochemistry and FISH(fluorescence in sity hybridization) & SISH(silver in situ hybridization) for assessment of the HER2
Authors: Lee M-R , Cho S-H , Kim D-C , Lee K-C , Lee J-H , Kwon H-C , Lee H-W , Lee S-e 
Published: August 2014

Abstract
Goals: Accurate assessment of the human epidermal growth factor receptor 2 (HER2) of invasive breast cancer with Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) & Silver in situ hybridization(SISH) is very important to decide treatment of targeted therapy with the humanized monoclonal antibody trastuzumab and the dual tyrosine kinase inhibitor lapatinib. The accuracy of these three testing methods can be adversely affected by various factors. We performed a retrospective analysis of the concordance of IHC and FISH & SISH analysis for HER2/neu at Donga-A Medical Center and reviewed possible causes of disparity between these two methods.
Methods: We performed retrospective review of a total of 416 invasive ductal carcinomas evaluated for HER2/neu at the Department of Surgery in Dong-A Medical Center between 2005 and 2011. We reviewed this data retrospectively and evaluated the concordance between IHC and FISH & SISH.
Results: Comparison of the routinely assessed immunohistochemical HER2 status and FISH & SISH revealed that ten invasive carcinomas diagnosed immunohistochemically as highly overexpressed (score 3+) did not show amplification of the HER2 gene by FISH n that these are false positives (SISH: false positive: 7 cases). Eight invasive carcinomas diagnosed immunohistochemically as Negatively expressed (score 0) showed amplification of the HER2 gene by SISH on that these are false negative. Fourteen tumor, which scored as 2+ by IHC, was proven to be amplified on initial testing with FISH (SISH: 6 cases). Concordance between IHC and FISH analysis was good (171/181= 94.5%) (false positive: 5.5%) (SISH: 228/235=97.0%, false positive 3.4%, false negative 2.9%) and within the published range.
Conclusion: IHC as first-line testing for HER2 may result in false positive and false negative results. The novel ASCO/CAP criteria for the immunohistochemical evaluation of the HER2 status may prevent some false positive results. The discordant cases between IHC and FISH & SISH represent a well-recognized subset of genetic heterogeneity in HER2/neu, which is known to contribute to positive IHC and negative FISH & SISH tests. The most powerful method for studying HER2 status is ISH. However, in heterogeneous carcinomas even FISH may not succeed in a correct evaluation of HER2.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD02-06.
Abstract PD04-03: Is breast conservation therapy an option for young women with operable breast cancer? Local recurrence rates in young women following surgery: a single centre experience.
Authors: Lewis CR , Smith R , Matthews A , Choo E , Lee C 
Published: August 2014

Abstract
Background: Breast cancer (BC) is less common in young women (defined here as ≤ 40 years age), but is associated with more aggressive biological features, higher risk of local recurrence (LR) and poorer overall survival. This study examines and compares the incidence of LR following breast conservation therapy (BCT) versus mastectomy in women with operable BC treated at our centre.
Methods: The POWCC breast cancer database was retrospectively reviewed for the period January 1995 to December 2008. 2250 eligible women with BC undergoing primary breast surgery were identified. LR rate was compared between young women and older women (age &gt; 40 years), and according to type of surgery. Data were analysed using a competing risk Cox model to account for distant recurrence and death as competing events for local recurrence.
Results: Median follow-up was 70 months. Of 2250 women, 246 (11%) were young women, and the mastectomy rate was 49.2%. In older women (89%), mastectomy rate was 41.7%. LR occurred in 17 (6.9%) and 57 (2.8%) in young and older women respectively (p = 0.001). Amongst the young women, 12 (9.6%) and 5 (4.1%) patients recurred locally in BCT and mastectomy respectively (p = 0.09). Amongst the older women, 43 (3.7%) and 14 (1.7%) patients recurred locally in BCT and mastectomy respectively (p = 0.008). In univariate Cox analysis, significant risk factors for LR were BCT (p = 0.003), positive surgical margins (p = 0.03), age ≤ 40 years (p = 0.001), premenopausal status (p = 0.003) and no adjuvant systemic therapy (0.02). Age remains a significant predictor of LR in multivariate Cox analysis (Table). There was no significant interaction between age and type of surgery on LR (p = 0.72).
Discussion: Our results demonstrate that young women who undergo BCT have the highest risk of early LR. Adjuvant systemic therapy is protective of early LR. This study is hypothesis-generating and a definitive prospective clinical trial is required to better determine the optimal type of breast surgery in young women.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD04-03.
Abstract PD04-05: Molecular predictors for type of recurrence following conservative treatment for DCIS
Authors: Sakr RA , Andrade VP , Chandarlapaty S , Giovanni C , Giri D , Heguy A , De Brot M , Olvera N , Muhsen S , Koslow S , Van Zee KJ , Morrow M , Rosen N , King TA 
Published: August 2014

Abstract
Background: The identification of molecular predictors of type of recurrence (non-invasive vs invasive) after local therapy for ductal carcinoma in situ (DCIS) remains a challenge. We hypothesized that gene expression profiling using a panel of 32 breast cancer-related genes could identify a signature predictive of type of recurrence.
Methods: From a prospectively maintained database of 1873 pts treated with conservative surgery +/− radiation for DCIS (1991–2006), we identified 190 (10%) patients who recurred. Original DCIS archival blocks were available for 108 (57%) of these cases. Freshly cut sections were obtained for microdissection of pure DCIS lesions, RNA was extraction and mRNA transcript quantification was performed with the Nanostring™ nCounter® system. Data were normalized using the nCounter® digital analyzer software for analysis.
Results: Among the 108 studied cases, 66 (61%) recurred as DCIS and 42 (39%) recurred as invasive cancer. Median time to recurrence was 40 months (range 7–156 mo) and did not differ by type of recurrence. Similarly, patient age, grade of DCIS, ER status, use of radiation or tamoxifen therapy did not differ. Unsupervised hierarchical clustering using all 32 genes demonstrated two predominant groups, one enriched for recurrent-as-invasive (RI) tumors, and the other enriched for recurrent-as-DCIS (RD) tumors. Refined analysis by selection of 14 genes with significant differential expression between the RI and the RD tumors identified four main groups. The first cluster was dominated by ERBB2 over-expression and is equally composed of RI and RD tumors. The second cluster was composed almost exclusively of RI tumors and showed high level of COX2 and CCND1 and low level of CDKN2A (p16). The clusters 3 and 4 were enriched for RD tumors, with the fourth cluster completely devoid of RI cases. This RD-only group showed the lowest level of CCND1, but highest level of AKT3, EGFR, CDKN2A, and MKI67, thus displaying molecular traits typical of basal-like tumors.
Conclusion: In this cohort of patients who recurred following conservative treatment for DCIS, HER2 expression was not predictive, however gene expression analysis demonstrated that high COX2 and CCND1 and low CDKN2a (p16) levels were strongly associated with invasive recurrences (RI), whereas increased AKT3 and MKI67 were associated with non-invasive recurrences (RD). Although the optimal combination of predictive markers requires validation, these data suggest that molecular alterations associated with RI differ from those associated with RD and warrant further investigation.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD04-05.
Abstract PD04-08: Cell cycle algorithm correlates with grade of DCIS and p53 status, allows elimination of ‘intermediate grade’ disease and gives clinically meanignful information.
Authors: Sainsbury R , Loddo M , Proctor I , Stoeber K , Williams G , Thorat M , Cuzick J 
Published: August 2014

Abstract
We have previously shown that multi-parameter analysis of the DNA replication initiation machinery (Mcm2-7, geminin) and mitotic proteins (Plk1, Aurora A, H3S10ph), expressed during various phases of the cell division cycle, provides a method to accurately assess the proliferative state of dynamic tumour cell populations. We have shown that this novel form of cell cycle biomarker analysis allows separation of breast cancers into three discrete cell cycle phenotypes of major prognostic significance including (i) an out-of-cycle state, (ii) a G1-delayed/arrested state and (iii) an actively cycling state. Importantly, we identified groups of patients with apparently good grade cancers on routine clinicopathological criteria but who nevertheless exhibited the poor prognostic actively cycling phenotype (iii) and might therefore benefit from adjuvant chemotherapy. Additionally, we identified patients with typically poor prognosis tumours but which were actually cycling slowly (phenotype i or ii) and therefore likely not to have benefited from chemotherapy. Notably, when this cell cycle algorithm was used in a multi-variate analysis, the effect of Ki-67 disappeared.
We have now applied the algorithm to 72 cases of DCIS (all of which were re-graded by one pathologist for consistency) and also to a TMA of 136 cases with known outcome from the UK DICS trial. There was excellent correlation between tumour grade and p53 status. The high grade DCIS was positively associated with a high cell cycle score (actively cycling phenotype iii; 28 out of 34 tumours) and low grade DCIS was associated with a low score (namely phenotypes i and ii; 13 out of 19). Interestingly, 7 of the 10 intermediate grade DCIS could be classified as phenotype, i or iii suggesting that the algorithm may be useful in stratifying this group of patients.
A clinical correlation between phenotype III and recurrence and/or progression to invasive disease was evident. Further analysis of this from data derived from the TMAs generated from the UK DCIS trial will be presented. If the early findings are confirmed we may be able to solve the dilemma of which cases of DCIS need treatment and which we currently overtreat.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD04-08.
Abstract PD10-04: Predictive genomic markers to chemotherapy and adjuvant trastuzumab via whole genome expression DASL profiling in the N9831 adjuvant study
Authors: Perez EA , Eckel-Passow JE , Ballman KV , Anderson SK , Thompson EA , Asmann YW , Jen J , Dueck AC , Lingle WL , Sledge GW , Winer EP , Gralow J , Jenkins RB , Reinholz MM 
Published: August 2014

Abstract
Background: Adding adjuvant trastuzumab to chemotherapy for patients (pts) with resected HER2+ breast cancer (BC) improves disease free and overall survival (Perez EA, et al. J Clin Oncol 2011). Understanding which pts are most likely to benefit from these therapies is a goal of our team.
Methods: Baseline 1639 annotated tumor specimens from pts enrolled in the phase III N9831 adjuvant trastuzumab trial (NCT00005970) were processed via the &gt;29,000 gene probe DASL technology (Illumina) to identify genomic predictors of pt outcome to Arm A chemotherapy or Arm C chemotherapy plus concurrent trastuzumab. Samples were spotted in 96 well plates, with appropriate replicates. Extensive quality control and internal validation were performed. The association of each gene with recurrence-free survival (RFS) was determined for each treatment arm separately using CoxPH models adjusted for clinical and tumor risk factors. A p &lt; 0.0001 was used to define significance. A geneset analysis (using 408 Kegg/BioCarta genesets) was performed to determine pathways associated with RFS.
Results: PRPF4B, EWSR1, BMI1, CNNM1, FOXO4, CLIP2, MCCC1, CHRM2 were found to be significantly associated with RFS for Arm A and AAK1, DAZAP2, TP53INP1, MACF1 and ADHFE1 were associated with RFS for Arm C. The most significant pathway associated with RFS in Arm A was the KEGG hypertrophic cardiomyopathy pathway and for Arm C, the BioCarta pertussis toxin-insensitive CCR5 signaling in macrophage pathway.
Conclusions: We have identified 8 genes associated with RFS for pts treated with adjuvant chemotherapy, and 5 genes associated with RFS for pts treated with concurrent trastuzumab and chemotherapy in pts with HER2 early stage BC. In addition, geneset analysis identified BioCarta and Kegg pathways associated with RFS for each arm. Validation in an independent cohort is expected to be completed by the end of 2012.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD10-04.
Abstract PL-2: Estrogen Receptor Cistrome: Implications for Breast Cancer
Authors: Carroll JS 
Published: August 2014

Abstract
Estrogen Receptor (ER) is the defining feature of luminal breast cancers, where is functions as a transcription factor. The traditional view of ER getting recruited to promoters of target genes is too simplistic. The recent discovery of ER-DNA interaction regions from ER+ breast cancer cell lines has revealed that ER rarely associates with promoter regions of target genes and instead associates with enhancer elements significant distances from the target genes. The genomic mapping of ER binding events also revealed the enrichment of DNA motifs for Forkhead factors. The Forkhead protein FOXA1 (HNF3α) was subsequently shown to bind to ∼half of the ER binding events in the genome and was required for ER to maintain interaction with DNA. We have extended on these findings to map ER binding events in primary breast cancers and distant metastases. We find context dependent ER cis-regulatory elements (cistromes) that give insight into underlying transcriptional networks. These differential ER binding profiles correlate with clinical response in ER+ breast cancers. We experimentally explore the binding dynamics between drug sensitive and resistant contexts and identify properties that govern ER binding differences. These data suggest that ER-DNA interactions are dynamic and can be modulated by changes in FOXA1. We are currently exploring mechanisms that mediate FOXA1-DNA interactions, in order to better understand ER transcriptional activity in breast cancer biology.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PL-2.
Abstract S4-3: The EndoPredict score identifies late distant metastases in ER+/HER2− breast cancer patients
Authors: Dubsky P , Brase JC , Fisch K , Jakesz R , Singer CF , Greil R , Dietze O , Weber KE , Petry C , Kronenwett R , Rudas M , Knauer M , Gnant M , Filipits M 
Published: August 2014

Abstract
Background: ER+/HER2− negative (ER+) breast cancers have a proclivity for late recurrence. A first step to an improved adjuvant treatment of late metastasis is to identify women at risk and understand the underlying biology. Several prognostic multigene tests have been developed for ER+ breast cancer patients. Some of these tests have been validated to predict early recurrence events. However, few gene expression assays have been shown to predict late metastases.
Here, we assess whether the prognostic EndoPredict (EP) score, which incorporates both the expression levels of proliferative - and ESR1-related genes, can be used to identify late relapse events in ER+ breast cancer patients.
Methods: Patients included in this study participated in the ABCSG-6 (tamoxifen-only arm) or ABCSG-8 phase III adjuvant trial and received either tamoxifen for 5 years or tamoxifen for 2 years followed by anastrozole for 3 years. All 1702 ER+/HER2− breast cancer patients were retrospectively assigned into risk categories based on the EP and on common clinical parameters. The primary endpoint was distant metastasis. Ongoing collection of follow-up events allowed estimation of metastasis rates using the Kaplan–Meier method in an early and late time cohort: 0–5 years/early recurrence and 5–10 years/late recurrence.
Results: 49% of all patients were classified as low-risk according to the EP score. Kaplan Meier analysis demonstrated that the EP low-risk group had a significantly improved clinical outcome in the first (0–5 years; p &lt; 0.0001) and second time interval (5–10 years; p = 0.002). Nodal metastasis was also significantly associated with the clinical outcome in both time intervals, with node-positive tumors showing a considerably higher rate of late recurrence events. In contrast, Ki67 levels and grading were not significantly associated with late metastasis. Multivariate analysis showed that EP was an independent prognostic parameter after adjustment for age, grade, lymph node status, tumor size and Ki67 in both the first and second time interval. The EPclin – a combination of the EP and the clinical risk factors nodal status and tumor size – showed the best performance in predicting late relapse events. Exploratory analyses of proliferative - versus ESR-1 related genes as contributors to early and late distant metastases show differential effects.
Conclusions: The EndoPredict test identified a subgroup of patients that have a low likelihood of developing late metastases. The eight genes contained in the test provide complimentary prognostic information to clinico-pathologic parameters. Both the expression of proliferative - and ESR1-related genes contributes to the underlying biology of late distant metastases.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S4-3.
Abstract S5-3: PHARE Trial results of subset analysis comparing 6 to 12 months of trastuzumab in adjuvant early breast cancer
Authors: Pivot X , Romieu G , Bonnefoi H , Pierga J-Y , Kerbrat P , Guastalla J-P , Lortholary A , Espié M , Fumoleau P , Khayat D , Pauporte I , Kramar A 
Published: August 2014

Abstract
Background: Since 2005, One year trastuzumab (T) treatment has been providing survival beneﬁt to patients with early breast cancer and HER2 overexpression. However, the optimal duration of T has been debatable due to concerns for cardiac toxicity and results from the FinHer trial which showed that 9 weeks of T provided a similar magnitude of benefit than the 1-year treatment. The French National Cancer Institute (INCa) initiated an academic randomised non-inferiority trial aiming to compare a shorter T exposure of 6 months versus the standard 12 months. This trial, named PHARE for ‘Protocol for Herceptin® as Adjuvant therapy with Reduced Exposure’ [NCT00381901] was approved byan independent ethics committee with regularly planned IDMC meetings.
Patients and methods: Patients with HER2 + early breast cancer who received at least 4 cycles of (neo)-adjuvant chemotherapy were eligible. Randomization 1:1 using a minimisation algorithm was stratified on concomitant or sequential T administration with chemotherapy, oestrogen receptors (ER) status and center. The primary objective was to compare disease free survival (DFS). Overall survival (OS) and cardiac toxicity were investigated as secondary aims. An absolute loss of 2% in DFS in the experimental arm was defined as the non-inferiority margin (1.15 in relative terms) and required 3400 patients with alpha=0.05 and 80% power.
Results: Between 5/2006 and 7/2010, 3382 patients were randomized to 6 or 12 months of T following the IDMC recommendation for accrual interruption and extended follow-up. Disease and treatment characteristics were well balanced between the 2 arms: median age 55 years (range 21–86), median tumour size 20 mm (0–270), node involvement 45%, SBR grade III 56%, ER positive 58%, radiotherapy 88%; concomitant T administration 58%, anthracyclin and taxane containing chemotherapy 73%. The data-base was locked on July 30th, 2012. The 95% HR confidence interval was ranged between 1.09–1.66 for DFS between the 2 arms and it included the pre-specified non-inferiority margins of 1.15. Thus the results were inconclusive regarding the non-inferiority (p = 0.14). A subset analysis based on stratification factors will be presented at SABCS.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S5-3.