Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial.

Gene expression data obtained in large studies hold great promises for discovering disease signatures or subtypes through data analysis. It is also prone to technical variation, whose removal is essential to avoid spurious discoveries. Because this variation is not always known and can be confounded with biological signals, its removal is a challenging task. Here we provide a step-wise procedure and comprehensive analysis of the MINDACT microarray dataset. The MINDACT trial enrolled 6693 breast cancer patients and prospectively validated the gene expression signature MammaPrint for outcome prediction. The study also yielded a full-transcriptome microarray for each tumor. We show for the first time in such a large dataset how technical variation can be removed while retaining expected biological signals. Because of its unprecedented size, we hope the resulting adjusted dataset will be an invaluable tool to discover or test gene expression signatures and to advance our understanding of breast cancer.

Performance Characteristics of the BluePrint® Breast Cancer Diagnostic Test.

The analytical performance of a multi-gene diagnostic signature depends on many parameters, including precision, repeatability, reproducibility and intra-tumor heterogeneity. Here we study the analytical performance of the BluePrint 80-gene breast cancer molecular subtyping test through determination of these performance characteristics. BluePrint measures the expression of 80 genes that assess functional pathways which determine the intrinsic breast cancer molecular subtypes (i.e. Luminal-type, HER2-type, Basal-type). Knowing a tumor's dominant functional pathway can help allocate effective treatment to appropriate patients. Here we show that BluePrint is a highly precise and highly reproducible test with correlations above 98% based on the generated index and subtype concordance above 99%. Therefore, BluePrint can be used as a robust and reliable tool to identify breast cancer molecular subtypes.

MammaPrint and BluePrint Molecular Diagnostics Using Targeted RNA Next-Generation Sequencing Technology.

Next-generation DNA sequencing is rapidly becoming an indispensable tool for genome-directed cancer diagnostics, but next-generation RNA sequencing (RNA-seq) is currently not standardly used in clinical diagnostics for expression assessment. However, multigene RNA diagnostic assays are used increasingly in the routine diagnosis of early-stage breast cancer. Two of the most widely used tests are currently available only as a central laboratory service, which limits their clinical use. We evaluated the use of RNA-seq as a decentralized method to perform such tests. The MammaPrint and BluePrint RNA-seq tests were found to be equivalent to the clinically validated microarray tests. The RNA-seq tests were highly reproducible when performed in different locations and were stable over time. The MammaPrint RNA-seq test was clinically validated. Our data demonstrate that RNA-seq can be used as a decentralized platform, yielding results substantially equivalent to results derived from the predicate diagnostic device.

A breast cancer gene signature for indolent disease.

PURPOSE: Early-stage hormone-receptor positive breast cancer is treated with endocrine therapy and the recommended duration of these treatments has increased over time. While endocrine therapy is considered less of a burden to patients compared to chemotherapy, long-term adherence may be low due to potential adverse side effects as well as compliance fatigue. It is of high clinical utility to identify subgroups of breast cancer patients who may have excellent long-term survival without or with limited duration of endocrine therapy to aid in personalizing endocrine treatment. METHODS: We describe a new ultralow risk threshold for the 70-gene signature (MammaPrint) that identifies a group of breast cancer patients with excellent 20 year, long-term survival prognosis. Tumors of these patients are referred to as "indolent breast cancer." We used patient series on which we previously established and assessed the 70-gene signature high-low risk threshold. RESULTS: In an independent validation cohort, we show that patients with indolent breast cancer had 100% breast cancer-specific survival at 15 years of follow-up. CONCLUSIONS: Our data indicate that patients with indolent disease may be candidates for limited treatment with adjuvant endocrine therapy based on their very low risk of distant recurrences or death of breast cancer.

Equivalence of MammaPrint array types in clinical trials and diagnostics.

MammaPrint is an FDA-cleared microarray-based test that uses expression levels of the 70 MammaPrint genes to assess distant recurrence risk in early-stage breast cancer. The prospective RASTER study proved that MammaPrint Low Risk patients can safely forgo chemotherapy, which is further subject of the prospective randomized MINDACT trial. While MammaPrint diagnostic results are obtained from mini-arrays, clinical trials may be performed on whole-genome arrays. Here we demonstrate the equivalence and reproducibility of the MammaPrint test. MammaPrint indices were collected for breast cancer samples: (i) on both customized certified array types (n = 1,897 sample pairs), (ii) with matched fresh and FFPE tissues (n = 552 sample pairs), iii) for control samples replicated over a period of 10 years (n = 11,333), and iv) repeated measurements (n = 280). The array type indicated a near perfect Pearson correlation of 0.99 (95 % CI: 0.989-0.991). Paired fresh and FFPE samples showed an excellent Pearson correlation of 0.93 (95 % CI 0.92-0.94), in spite of the variability introduced by intratumoral tissue heterogeneity. Control samples showed high consistency over 10 year's time (overall reproducibility of 97.4 %). Precision and repeatability are overall 98.2 and 98.3 %, respectively. Results confirm that the combination of the near perfect correlation between array types, excellent equivalence between tissue types, and a very high stability, precision, and repeatability demonstrate that results from clinical trials (such as MINDACT and I-SPY 2) are equivalent to current MammaPrint FFPE and fresh diagnostics, and can be used interchangeably.

Opioids in chronic non-cancer pain.

INTRODUCTION: The use of chronic opioid therapy for chronic non-cancer pain is growing and is now accepted as an effective treatment modality. AREAS COVERED: Although there are guidelines and reviews for chronic opioid therapy for chronic non-cancer pain patients, physicians may still have concerns and be reluctant to prescribe strong opioids for chronic non-cancer pain. Common issues and concerns when prescribing opioid for chronic pain management are reviewed and discussed. The literature search was done using Medline with key words 'chronic non-cancer pain', 'chronic opioid therapy', 'effectiveness', 'opioid tolerance', 'opioid-induced hyperalgesia', 'adverse effect', 'opioid dependency', 'addiction', 'monitoring', 'opioid contract' and various combinations with these key words. Studies from 1990 - 2010 have been included. This article helps readers to update, clarify and understand the common concerns when using opioid for chronic non-cancer pain. Clinical effectiveness and adverse effects with chronic opioid therapy, opioid tolerance and opioid-induced hyperalgesia, opioid dependency and addiction, monitoring during chronic opioid use, and opioid contact are discussed in detailed. EXPERT OPINION: Not much strongly positive data supports the long-term use of opioids for pain relief, and the evidence for an improvement in functional activity is inconclusive. With careful selection of patients, meticulous prescription and monitoring protocol, chronic non-cancer pain patients who are likely to benefit from potent opioids should not be prevented from obtaining this treatment.

Adult epiglottitis: 6 years experience in a university teaching hospital in Hong Kong.

Adult epiglottitis is a relatively rare but potentially lethal disease. It seems to be increasing in incidence in other countries. The objective of this study was to examine the common presentations and clinical course of adult epiglottitis in Hong Kong. Retrospective review of 80 consecutive cases of adult epiglottitis admitted between 2000 and 2005. A rising trend in the incidence of adult epiglottitis was observed. The mean age (SD) was 49 years (15.7) and the male-to-female ratio was 2.5:1. Disease presentation was nonspecific and sore throat was the most common symptom. All patients were admitted to hospital; 47 (59%) patients were admitted to the intensive care unit (ICU) and 31 (39%) had provision of an artificial airway. Mean (SD) length of stay in ICU and hospital was 1.9 (2.2) and 6.3 (2.9) days, respectively. Six patients (7.5%) were complicated by epiglottic abscess formation. No deaths occurred in this series. Patients who required airway intervention had a higher ICU admission rate and a higher bacterial identification rate. Flexible laryngoscopy was more sensitive than lateral neck radiography in diagnosing epiglottitis (100 vs. 81.4%). The laryngoscopic finding of a narrowed airway was strongly related to the requirement for airway intervention (odds ratio=23.7, 95% confidence interval=4.2-132.6, P<0.001). A high index of suspicion is required for making the diagnosis of adult epiglottitis. Proper airway assessment and close monitoring are of the utmost importance in patient management. Flexible laryngoscopy is the key investigation of choice in the emergency department.

Perioperative management and the associated rate of adverse events in dermatological procedures performed by dermatologists in New Zealand.

Dermatological surgery performed in an outpatient setting is common and generally perceived as safe, but the potential for serious adverse events does exist. Furthermore, there is a current lack of guidelines regarding preoperative and intraoperative monitoring of such patients. This is a retrospective study that involved a written questionnaire sent to current practising New Zealand dermatologists. Aspects investigated include their practice relating to preoperative assessments and intraoperative monitoring during standard dermatological procedures, and the resulting rate of adverse events. We found that most respondents performed dermatological procedures in dedicated theatres in outpatient clinics. The majority of survey respondents would screen for and optimize risk factors prior to surgery. Most respondents would not record vital sign measurements either preoperatively or intraoperatively. Antibiotic prophylaxis was generally only prescribed if clinically indicated, and anticoagulation and antiplatelet therapies were in the majority of cases never withheld prior to surgery. Infection (<3.5%) and bleeding (<2%) were the most common postoperative complications, with other serious adverse events being extremely rare. Although dermatological surgery continues to be safely performed in the outpatient setting, attempts should still be made to identify patients who are at higher risk for surgery and extra precautions should be applied to these selected patients.

Using hexamers to predict cis-regulatory motifs in Drosophila.

BACKGROUND: Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered. RESULTS: We present a simple, efficient method (HexDiff) based only on hexamer frequencies of known CRMs and non-CRM sequence to predict novel CRMs in regulatory systems. On a data set of 16 gap and pair-rule genes containing 52 known CRMs, predictions made by HexDiff had a higher correlation with the known CRMs than several existing CRM prediction algorithms: Ahab, Cluster Buster, MSCAN, MCAST, and LWF. After combining the results of the different algorithms, 10 putative CRMs were identified and are strong candidates for future study. The hexamers used by HexDiff to distinguish between CRMs and non-CRM sequence were also analyzed and were shown to be enriched in regulatory elements. CONCLUSION: HexDiff provides an efficient and effective means for finding new CRMs based on known CRMs, rather than known binding sites.