The impact of next generation sequencing technologies on haematological research - A review

Next-generation sequencing (NGS) technologies have begun to revolutionize the field of haematological malignancies through the assessment of a patient's genetic makeup with a minimal cost. Significant discoveries have already provided a unique insight into disease initiation, risk stratification and therapeutic intervention. Sequencing analysis will likely form part of the routine diagnostic testing in the future. However, a number of important issues need to be addressed for that to become a reality with regard to result interpretation, laboratory workflow, data storage and ethical issues. In this review we summarize the contribution that NGS has already made to the field of haematological malignancies. Finally, we discuss the challenges that NGS technologies will bring in relation to data storage, ethical and legal issues and laboratory validation. Despite these challenges, we predict that high-throughput DNA sequencing will redefine haematological malignancies based on individualized genomic analysis.

Genomics and the impact of new technologies on the management of colorectal cancer

High-throughput genomic technologies have the potential to have a major impact on preclinical and clinical drug development and the selection and stratification of patients in clinical trials. These technologies, which are at varying stages of commercialization, include array-based comparative genomic hybridization, single-nucleotide polymorphism arrays, and (the most mature example) expression-based arrays. One of the rate-limiting steps in the routine clinical application of expression array-based technology is the need for suitable clinical samples. One of the major challenges moving forward, therefore, relates to the ability to use formalin-fixed, paraffin-embedded--derived tissue in expression profiling-based approaches.

PTEN mRNA detection by chromogenic, RNA in situ technologies: a reliable alternative to PTEN immunohistochemistry

Immunohistochemical staining for phosphatase and tensin homolog (PTEN) does not have either an acceptable standard protocol or concordance of scoring between pathologists. Evaluation of PTEN mRNA with a unique and verified sequence probe may offer a realistic alternative providing a robust and reproducible protocol. In this study, we have evaluated an in situ hybridization (ISH) protocol for PTEN mRNA using RNAScope technology and compared it with a standard protocol for PTEN immunohistochemistry (IHC). PTEN mRNA expression by ISH was consistently more sensitive than PTEN IHC, with 56% of samples on a mixed-tumor tissue microarray (TMA) showing high expression by ISH compared with 42% by IHC. On a prostate TMA, 49% of cases showed high expression by ISH compared with 43% by IHC. Variations in PTEN mRNA expression within malignant epithelium were quantifiable using image analysis on the prostate TMAs. Within tumors, clear overexpression of PTEN mRNA on malignant epithelium compared with benign epithelium was frequently observed and quantified. The use of SpotStudio software in the mixed-tumor TMA allowed for clear demonstration of varying levels of PTEN mRNA between tumor samples by the mRNA methodology. This was evident by the quantifiable differences between distinct oropharyngeal tumors (up to 3-fold increase in average number of spots per cell between 2 cases). mRNA detection of PTEN or other biomarkers, for which optimal or standardized immunohistochemical techniques are not available, represents a means by which heterogeneity of expression within focal regions of tumor can be explored with more confidence.

Molecular Medicine and Molecular Pathology for Hematologists:II. Lets go Techno; Principles of the Molecular Technologies and their Applications in Haematology

Molecular techniques have a key role to play in laboratory and clinical haematology. Restriction enzymes allow nucleic acids to be reduced in size for subsequent analysis. In addition they allow selection of specific DNA or RNA sequences for cloning into bacterial plasmids. These plasmids are naturally occuring DNA molecules which reside in bacterial cells. They can be manipulated to act as vehicles or carriers for biologically and medically important genes, allowing the production of large amounts of cloned material for research purposes or to aid in the production of medically important recombinant molecules such as insulin. As acquired or inherited genetic changes are implicated in a wide range of haematological diseases, it is necessary to have highly specific and sensitive assays to detect these mutations. Most of these techniques rely on nucleic acid hybridisation, benefitting from the ability of DNA or RNA to bind tighly to complimentary bases in the nucleic acid structure. Production of artificial DNA molecules called probes permits nucleic acid hybridiation assays to be performed, using the techniques of southern blotting or dot blot analysis. In addition the base composition of any gene or region of DNA can be determined using DNA sequencing technology. The advent of the polymerase chain reaction (PCR) has revolutionised all aspects of medicine, but has particular relevance in haematology where easy access to biopsy material provides a wealth of material for analysis. PCR permits quick and reliable manipulation of sample material and its ability to be automated makes it an ideal tool for use in the haematology laboratory.

Suitability, efficiency and microbiological safety of novel physical technologies for the processing of ready-to-eat meals, meats and pumpable products

Consumer studies and market reports show an increase in consumption of ready-to-eat (RTE) foods. Although conventional processing technologies can in most cases produce safe products, they can also lead to the degradation of nutritional compounds and negatively affect quality characteristics. Consumers strongly prefer food that is minimally processed with the maximum amount of health-promoting substances. Novel processing technologies as pre- or post-treatment decontamination methods or as substitutes of conventional technologies have the potential to produce foods that are safe, rich in nutrient content and with superior organoleptic properties. Combining novel with conventional processes can eliminate potential drawbacks of novel technologies. This review examines available scientific information and critically evaluates the suitability and efficiency of various novel thermal and nonthermal technologies in terms of microbial safety, quality as well as nutrient content on the production of RTE meals, meats and pumpable products.

Technologies of Knowledge and Governance on the Front Lines of Emergency Services.

Using institutional ethnography, a sociology and critical method of inquiry used primarily in North America, this presentation discusses new forms and technologies of knowledge and governance – “forms of language, technologies of representation and communication, and text-based, objectified modes of knowledge through which local particularities are interpreted or rendered actionable in abstract, translocal terms” (McCoy, 2008: 701) on the front line of emergency medical services. I focus specifically on technologies central to health reforms that attempt to reshape how health care is delivered, experienced, and made accountable (Anantharaman, 2004; Ball, 2005; Alberta Health Services, 2008). In additional to exemplifying how institutional ethnography can be used to answer Rankin and Campbell’s (2006) call for additional research into “the social organization of information in health care and attention to the (often unintended) ways ‘such textual products may accomplish…ruling purposes but otherwise fail people and, moreover, obscure that failure’ (p. 182)” (cited in McCoy, 2008: 709), this presentation will introduce the audience to a critical approach to social inquiry that explores how knowledge is socially organized.

Techno-Economic and Life Cycle Assessment on Lignocellulosic Biomass Thermochemical Conversion Technologies: A Review

Bioenergy derived from biomass provides a promising energy alternative and can reduce the greenhouse gas (GHG) emissions generated from fossil fuels. Biomass-based thermochemical conversion technologies have been acknowledged as apt options to convert bioresources into bioenergy; this bioenergy includes electricity, heat, and fuels/chemicals in solid, liquid, and gaseous phases. In this review, the techno-economic and life cycle assessment of these technologies (combustion, gasification, pyrolysis, liquefaction, carbonization, and co-firing) are summarized. Specific indicators (production costs in a techno-economic analysis, functional units and environmental impacts in a life cycle analysis) for different technologies were compared. Finally, gaps in research and future trends in biomass thermochemical conversion were identified. This review could be used to guide future research related to economic and environmental benefits of bioenergy.

Binaural Reproduction of Finite Difference Simulations Using Spherical Array Processing

Due to its efficiency and simplicity, the finite-difference time-domain method is becoming a popular choice for solving wideband, transient problems in various fields of acoustics. So far, the issue of extracting a binaural response from finite difference simulations has only been discussed in the context of embedding a listener geometry in the grid. In this paper, we propose and study a method for binaural response rendering based on a spatial decomposition of the sound field. The finite difference grid is locally sampled using a volumetric array of receivers, from which a plane wave density function is computed and integrated with free-field head related transfer functions, in the spherical harmonics domain. The volumetric array is studied in terms of numerical robustness and spatial aliasing. Analytic formulas that predict the performance of the array are developed, facilitating spatial resolution analysis and numerical binaural response analysis for a number of finite difference schemes. Particular emphasis is placed on the effects of numerical dispersion on array processing and on the resulting binaural responses. Our method is compared to a binaural simulation based on the image method. Results indicate good spatial and temporal agreement between the two methods.

Prognostic and predictive markers in colorectal cancer - The role of new genomic technologies

Colorectal cancer (CRC) is one of the most frequently occurring malignancies worldwide, and the second leading cause of cancer related death in the Western World. Although early stage disease is curable by surgical resection alone, one half of patients with CRC will present with metastatic disease at some stage in the course of their disease. The most active drug in the treatment of CRC is 5-fluorouracil (5-FU) which is used in both the adjuvant and advanced settings. The use of adjuvant therapy is of proven benefit in Stage III CRC, however, its role in Stage II disease is less clear. There is therefore a need to identify those patients with early stage disease who will develop recurrent disease, and who would therefore benefit most from adjuvant treatment. In the advanced setting, the use of irinotecan and oxaliplatin in combination with 5-FU has proven beneficial, with yet further improvements in survival reported with the addition of new targeted agents such as bevacizamab. Despite this, a significant number of patients with advanced disease do not derive any benefit from the chemotherapy they receive, highlighting a need for the development of molecular or genomic markers predictive of response to these chemotherapeutic agents. This review will evaluate the recent advances in pharmacogenomics in CRC, in particular the development of predictive markers of response to chemotherapy. The successful identification of these markers of response will herald an era of personalised treatment, reducing treatment-related toxicity and improving outcome of patients with CRC. -cr 2007 Bentham Science Publishers Ltd.

Use of emerging technologies to assess differences in outdoor physical activity in St. Louis, Missouri.

Introduction: Abundant evidence shows that regular physical activity (PA) is an effective strategy for preventing obesity in people of diverse socioeconomic status (SES) and racial groups. The proportion of PA performed in parks and how this differs by proximate neighborhood SES has not been thoroughly investigated. The present project analyzes online public web data feeds to assess differences in outdoor PA by neighborhood SES in St. Louis, MO, USA.
Methods: First, running and walking routes submitted by users of the website MapMyRun.com were downloaded. The website enables participants to plan, map, record, and share their exercise routes and outdoor activities like runs, walks, and hikes in an online database. Next, the routes were visually illustrated using geographic information systems. Thereafter, using park data and 2010 Missouri census poverty data, the odds of running and walking routes traversing a low-SES neighborhood, and traversing a park in a low-SES neighborhood were examined in comparison to the odds of routes traversing higher-SES neighborhoods and higher-SES parks.
Results: Results show that a majority of running and walking routes occur in or at least traverse through a park. However, this finding does not hold when comparing low-SES neighborhoods to higher-SES neighborhoods in St. Louis. The odds of running in a park in a low-SES neighborhood were 54% lower than running in a park in a higher-SES neighborhood (OR = 0.46, CI = 0.17-1.23). The odds of walking in a park in a low-SES neighborhood were 17% lower than walking in a park in a higher-SES neighborhood (OR = 0.83, CI = 0.26-2.61).
Conclusion: The novel methods of this study include the use of inexpensive, unobtrusive, and publicly available web data feeds to examine PA in parks and differences by neighborhood SES. Emerging technologies like MapMyRun.com present significant advantages to enhance tracking of user-defined PA across large geographic and temporal settings.