Clinical utility of microarrays: current status, existing challenges and future outlook

Cytochrome P450 enzymes: a review on drug metabolizing enzyme inhibition studies in drug discovery and development

Assessment of drug candidate's potential to inhibit cytochrome P450 (CYP) enzymes remains crucial in pharmaceutical drug discovery and development. Both direct and time-dependent inhibition of drug metabolizing CYP enzymes by the concomitant administered drug is the leading cause of drug-drug interactions (DDIs), resulting in the increased toxicity of the victim drug. In this context, pharmaceutical companies have grown increasingly diligent in limiting CYP inhibition liabilities of drug candidates in the early stages and examining risk assessments throughout the drug development process. This review discusses different strategies and decision-making processes for assessing the drug-drug interaction risks by enzyme inhibition and lays particular emphasis on in vitro study designs and interpretation of CYP inhibition data in a stage-appropriate context.

Strategies to Improve the Clinical Outcomes for Direct-to-Consumer Pharmacogenomic Tests

Direct-to-consumer genetic tests (DTC-GT) have become a bridge between marketing and traditional healthcare services. After earning FDA endorsement for such facilities, several fast-developing companies started to compete in the related area. Pharmacogenomic (PGx) tests have been introduced as potentially one of the main medical services of such companies. Most of the individuals will be interested in finding out about the phenotypic consequences of their genetic variants and molecular risk factors against diverse medicines they take or will take later. Direct-to-consumer pharmacogenomic tests (DTC-PT) is still in its young age, however it is expected to expand rapidly through the industry in the future. The result of PGx tests could be considered as the main road toward the implementation of personalized and precision medicine in the clinic. This narrative critical review study provides a descriptive overview on DTC-GT, then focuses on DTC-PT, and also introduces and suggests the potential approaches for improving the clinical related outcomes of such tests on healthcare systems.

Micro-scale technologies propel biology and medicine

Historically, technology has been central to new discoveries in biology and progress in medicine. Among various technologies, microtechnologies, in particular, have had a prominent role in the revolution experienced by the life sciences in the last few decades, which will surely continue in the years to come. In this Perspective, we illustrate how microtechnologies, with a focus on microfluidics, have evolved in trends/waves to tackle the boundary of knowledge in the life sciences. We provide illustrative examples of technology-enabled biological breakthroughs and their current and future use in clinics. Finally, we take a closer look at the translational process to understand why the incorporation of new micro-scale technologies in medicine has been comparatively slow so far.

Challenges and Future Trends for Microarray Analysis

The current situation in microarray data analysis and prospects for the future are briefly discussed in this chapter, in which the competition between microarray technologies and high-throughput technologies is considered under a data analysis view. The up-to-date limitations of DNA microarrays are important to forecast challenges and future trends in microarray data analysis; these include data analysis techniques associated with an increasing sample sizes, new feature selection methods, deep learning techniques, covariate significance testing as well as false discovery rate methods, among other procedures for a better interpretability of the results.

A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study

A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.

Cost-effectiveness of using a gene expression profiling test to aid in identifying the primary tumour in patients with cancer of unknown primary

We aimed to investigate the cost-effectiveness of a 2000-gene-expression profiling (GEP) test to help identify the primary tumor site when clinicopathological diagnostic evaluation was inconclusive in patients with cancer of unknown primary (CUP). We built a decision-analytic-model to project the lifetime clinical and economic consequences of different clinical management strategies for CUP. The model was parameterized using follow-up data from the Manitoba Cancer Registry, cost data from Manitoba Health administrative databases and secondary sources. The 2000-GEP-based strategy compared to current clinical practice resulted in an incremental cost-effectiveness ratio (ICER) of $44,151 per quality-adjusted life years (QALY) gained. The total annual-budget impact was $36.2 million per year. A value-of-information analysis revealed that the expected value of perfect information about the test's clinical impact was $4.2 million per year. The 2000-GEP test should be considered for adoption in CUP. Field evaluations of the test are associated with a large societal benefit.

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization

The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets.

Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections

The p53 tumor suppressor gene (TP53) is reported to be mutated in nearly half of all tumors and plays a central role in genome integrity. Detection of mutations in p53 can be accomplished by many assays, including the AmpliChip p53 Research Test. The AmpliChip p53 Research Test has been successfully used to determine p53 status in hematologic malignancies and fresh frozen solid tissues but there are few reports of using the assay with formalin fixed, paraffin-embedded (FFPE) tissue. The objective of this study was to describe analytical performance characterization of the AmpliChip p53 Research Test to detect p53 mutations in genomic DNA isolated from archival FFPE human ovarian tumor tissues. Method correlation with sequencing showed 96% mutation-wise agreement and 99% chip-wise agreement. We furthermore observed 100% agreement (113/113) of the most prevalent TP53 mutations. Workflow reproducibility was 96.8% across 8 samples, with 2 operators, 2 reagent lots and 2 instruments. Section-to-section reproducibility was 100% for each sample across a 60 μm region of the FFPE block from ovarian tumors. These data indicate that the AmpliChip p53 Research Test is an accurate and reproducible method for detecting mutations in TP53 from archival FFPE human ovarian specimens.

Current landscape of direct-to-consumer genetic testing and its role in ophthalmology: a review

The sequencing of the human genome has seen the emergence of the direct-to-consumer (DTC) genetic-testing market, which allows individuals to obtain information about their genetic profile and its many health and lifestyle implications. Genetics play an important role in the development of many eye diseases, however, little information is available describing the influence of the DTC industry in ophthalmology. In this review, we examined DTC companies providing genetic test products for eye disease. Of all eye conditions, the majority of DTC companies provided susceptibility testing or risk assessment for age-related macular degeneration (AMD). For the 15 companies noted to offer products, we found considerable variation in the cost, scope and clarity of informational content of DTC genetic testing for ophthalmic conditions. The clinical utility of these tests remains in question, and the American Academy of Ophthalmology recommendations against routine testing for many conditions probably still apply.

Mobilizing clinical decision support to facilitate knowledge translation: a case study in China

BACKGROUND

A wide gulf remains between knowledge and clinical practice. Clinical decision support has been demonstrated to be an effective knowledge tool that healthcare organizations can employ to deliver the "right knowledge to the right people in the right form at the right time". How to adopt various clinical decision support (CDS) systems efficiently to facilitate evidence-based practice is one challenge faced by knowledge translation research.

METHOD

A computer-aided knowledge translation method that mobilizes evidence-based decision supports is proposed. The foundation of the method is a knowledge representation model that is able to cover, coordinate and synergize various types of medical knowledge to achieve centralized and effective knowledge management. Next, web-based knowledge-authoring and natural language processing based knowledge acquisition tools are designed to accelerate the transformation of the latest clinical evidence into computerized knowledge content. Finally, a batch of fundamental services, such as data acquisition and inference engine, are designed to actuate the acquired knowledge content. These services can be used as building blocks for various evidence-based decision support applications.

RESULTS

Based on the above method, a computer-aided knowledge translation platform was constructed as a CDS infrastructure. Based on this platform, typical CDS applications were developed. A case study of drug use check demonstrates that the CDS intervention delivered by the platform has produced observable behavior changes (89.7% of alerted medical orders were revised by physicians).

DISCUSSION

Computer-aided knowledge translation via a CDS infrastructure can be effective in facilitating knowledge translation in clinical settings.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Recent advances in the molecular characterization of circulating tumor cells

Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch® system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a "real-time liquid biopsy" that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing.

The prevalence of chromosomal deletions relating to developmental delay and/or intellectual disability in human euploid blastocysts

Chromosomal anomalies in human embryos produced by in vitro fertilization are very common, which include numerical (aneuploidy) and structural (deletion, duplication or others) anomalies. Our previous study indicated that chromosomal deletion(s) is the most common structural anomaly accounting for approximately 8% of euploid blastocysts. It is still unknown if these deletions in human euploid blastocysts have clinical significance. In this study, we analyzed 15 previously diagnosed euploid blastocysts that had chromosomal deletion(s) using Agilent oligonucleotide DNA microarray platform and localized the gene location in each deletion. Then, we used OMIM gene map and phenotype database to investigate if these deletions are related with some important genes that cause genetic diseases, especially developmental delay or intellectual disability. As results, we found that the detectable chromosomal deletion size with Agilent microarray is above 2.38 Mb, while the deletions observed in human blastocysts are between 11.6 to 103 Mb. With OMIM gene map and phenotype database information, we found that deletions can result in loss of 81-464 genes. Out of these genes, 34–149 genes are related with known genetic problems. Furthermore, we found that 5 out of 15 samples lost genes in the deleted region, which were related to developmental delay and/or intellectual disability. In conclusion, our data indicates that all human euploid blastocysts with chromosomal deletion(s) are abnormal and transfer of these embryos may cause birth defects and/or developmental and intellectual disabilities. Therefore, the embryos with chromosomal deletion revealed by DNA microarray should not be transferred to the patients, or further gene map and/or phenotype seeking is necessary before making a final decision.

Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction

Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.

Identification of chromosomal errors in human preimplantation embryos with oligonucleotide DNA microarray

A previous study comparing the performance of different platforms for DNA microarray found that the oligonucleotide (oligo) microarray platform containing 385K isothermal probes had the best performance when evaluating dosage sensitivity, precision, specificity, sensitivity and copy number variations border definition. Although oligo microarray platform has been used in some research fields and clinics, it has not been used for aneuploidy screening in human embryos. The present study was designed to use this new microarray platform for preimplantation genetic screening in the human. A total of 383 blastocysts from 72 infertility patients with either advanced maternal age or with previous miscarriage were analyzed after biopsy and microarray. Euploid blastocysts were transferred to patients and clinical pregnancy and implantation rates were measured. Chromosomes in some aneuploid blastocysts were further analyzed by fluorescence in-situ hybridization (FISH) to evaluate accuracy of the results. We found that most (58.1%) of the blastocysts had chromosomal abnormalities that included single or multiple gains and/or losses of chromosome(s), partial chromosome deletions and/or duplications in both euploid and aneuploid embryos. Transfer of normal euploid blastocysts in 34 cycles resulted in 58.8% clinical pregnancy and 54.4% implantation rates. Examination of abnormal blastocysts by FISH showed that all embryos had matching results comparing microarray and FISH analysis. The present study indicates that oligo microarray conducted with a higher resolution and a greater number of probes is able to detect not only aneuploidy, but also minor chromosomal abnormalities, such as partial chromosome deletion and/or duplication in human embryos. Preimplantation genetic screening of the aneuploidy by DNA microarray is an advanced technology used to select embryos for transfer and improved embryo implantation can be obtained after transfer of the screened normal embryos.

Overview of micro- and nano-technology tools for stem cell applications: micropatterned and microelectronic devices

In the past few decades the scientific community has been recognizing the paramount role of the cell microenvironment in determining cell behavior. In parallel, the study of human stem cells for their potential therapeutic applications has been progressing constantly. The use of advanced technologies, enabling one to mimic the in vivo stem cell microenviroment and to study stem cell physiology and physio-pathology, in settings that better predict human cell biology, is becoming the object of much research effort. In this review we will detail the most relevant and recent advances in the field of biosensors and micro- and nano-technologies in general, highlighting advantages and disadvantages. Particular attention will be devoted to those applications employing stem cells as a sensing element.

Thermostable DNA immobilization and temperature effects on surface hybridization

Monolayer films of nucleic acids on solid supports are encountered in a range of diagnostic and bioanalytical applications. These applications often rely on elevated temperatures to improve performance; moreover, studies at elevated temperatures can provide fundamental information on layer organization and functionality. To support such applications, this study compares thermostability of oligonucleotide monolayers immobilized to gold by first coating the gold with a nanometer-thick film (an "anchor layer") of a polymercaptosiloxane, to which DNA oligonucleotides are subsequently tethered through maleimide-thiol conjugation, with thermostability of monolayers formed via widely used attachment through a terminal thiol moiety on the DNA. The temperature range covered is from 25 to 90 °C. After confirming stability of immobilization and, more importantly, retention of hybridization activity even under the harshest conditions investigated, these thermostable films are used to demonstrate measurements of (1) reversible surface melting transitions and (2) temperature dependence of competitive hybridization, when fully matched and mismatched sequences compete for binding to immobilized DNA oligonucleotides. The competitive hybridization experiments reveal a pronounced impact of temperature on rates of approach to equilibrium, with kinetic freezing into nonequilibrium states close to room temperature and rapid approach to equilibrium at elevated temperatures. Modeling of competitive surface hybridization equilibria using thermodynamic parameters derived from surface melting transitions of the individual sequences is also discussed.

Digital transplantation pathology: combining whole slide imaging, multiplex staining and automated image analysis

Conventional histopathology is the gold standard for allograft monitoring, but its value proposition is increasingly questioned. "-Omics" analysis of tissues, peripheral blood and fluids and targeted serologic studies provide mechanistic insights into allograft injury not currently provided by conventional histology. Microscopic biopsy analysis, however, provides valuable and unique information: (a) spatial-temporal relationships; (b) rare events/cells; (c) complex structural context; and (d) integration into a "systems" model. Nevertheless, except for immunostaining, no transformative advancements have "modernized" routine microscopy in over 100 years. Pathologists now team with hardware and software engineers to exploit remarkable developments in digital imaging, nanoparticle multiplex staining, and computational image analysis software to bridge the traditional histology-global "-omic" analyses gap. Included are side-by-side comparisons, objective biopsy finding quantification, multiplexing, automated image analysis, and electronic data and resource sharing. Current utilization for teaching, quality assurance, conferencing, consultations, research and clinical trials is evolving toward implementation for low-volume, high-complexity clinical services like transplantation pathology. Cost, complexities of implementation, fluid/evolving standards, and unsettled medical/legal and regulatory issues remain as challenges. Regardless, challenges will be overcome and these technologies will enable transplant pathologists to increase information extraction from tissue specimens and contribute to cross-platform biomarker discovery for improved outcomes.

Evaluation of a microarray-based genotyping assay for the rapid detection of cytochrome P450 2C19 *2 and *3 polymorphisms from whole blood using nanoparticle probes

Numerous drugs such as clopidogrel have been developed to reduce coagulation or inhibit platelet function. The hepatic cytochrome P450 (CYP) pathway is involved in the conversion of clopidogrel to its active metabolite. A recent black-box warning was included in the clopidogrel package insert indicating a significant clinical link between specific CYP2C19 genetic variants and poor metabolism of clopidogrel. Of these variants, *2 and *3 are the most common and are associated with complete loss of enzyme activity. In patients who are carriers of a CYP2C19 *2 or *3 allele, the conversion of clopidogrel to its active metabolite may be reduced, which can lead to ischemic events and negative consequence for the patient. We examined the ability of the Verigene CLO assay (Nanosphere, Northbrook, IL) to identify CYP2C19 *2 and *3 polymorphisms in 1,286 unique whole blood samples. The Verigene CLO assay accurately identified homozygous and heterozygous *2 and *3 phenotypes with a specificity of 100% and a final call rate of 99.7%. The assay is fully automated and can produce a result in approximately 3.5 hours.

Provision of personalized genomic diagnostic technologies for breast and colorectal cancer: an analysis of patient needs, expectations and priorities

AIM

Several novel pharmacogenomic diagnostic tests are commercially available for breast and colorectal cancer, and are increasingly being used in clinical practice for improving treatment decisions. However, there is little evidence evaluating the value of these new genomic technologies from the perspective of patients. As part of an ongoing effort to understand the continuum of the process of adoption of genomic diagnostics, our aim in this study was to examine the value of genomic diagnostics to breast and colorectal cancer patients, and their willingness to adopt and use genomic diagnostics.

PATIENTS & METHODS

We conducted six focus groups of breast and colorectal cancer patients from the oncology clinics at The Methodist Hospital, Houston, TX, USA. An adapted Q-sort instrument was also administered to focus group participants.

RESULTS

The majority of breast and colorectal cancer patients are interested in using novel genomic diagnostics for deciding about treatment options. Most participants in our study expressed a willingness to pay out-of-pocket for genomic testing (z = 0.736). Reliability and validity of genomic testing were of significant concern (z = 1.32) for the majority of breast and colorectal cancer patients. Participants identified several facilitators and barriers within health systems that might either facilitate or impede the widespread adoption and use of genomic diagnostics in healthcare delivery.

CONCLUSION

This study demonstrates breast and colorectal cancer patients' willingness to adopt and pay for novel genomic diagnostics, as well as identifies several salient factors associated with patient preferences for genomic diagnostics.

Cancer of unknown primary: progress in the search for improved and rapid diagnosis leading toward superior patient outcomes

This paper explores the enigma of cancer of unknown primary (CUP) in relation to rapidly improving molecular diagnostic approaches. It is based on the first global collaboration meeting on improving research and clinical outcomes in CUP organized by the CUP Foundation. We review the difficulties of classifying this widely heterogeneous disease and the available diagnostic and pathological evaluative techniques, focusing on molecular profiling. Retrospective studies in CUP patients are shown to provide indirect validation of the accuracy of several platforms of gene expression profiling assays that may identify CUP subsets that respond favorably to active chemotherapy regimens. This review concludes that the recent major improvements in pathologic and molecular diagnostics, coupled with new improved therapies for several specific advanced solid tumors, need to be harmonized with more evidence from clinical-translational trials. All patients with CUP could thus be appropriately managed without the constant uncertainty that has previously severely hampered patient care and optimal outcomes. The longer-term objective is to understand the biology of highly metastatic disease, leading to the development of future global therapeutic programs. Current clinical studies, such as CUP-ONE, will address some of these issues.

Optical tweezers directed one-bead one-sequence synthesis of oligonucleotides

An optical tweezers directed parallel DNA oligonucleotide synthesis methodology is described in which controlled pore glass (CPG) beads act as solid substrates in a two-stream microfluidic reactor. The reactor contains two parallel sets of physical confinement features that retain beads in the reagent stream for synthetic reaction but allow the beads to be optically trapped and transferred between the reagent and the inert streams for sequence programming. As a demonstration, we synthesized oligonucleotides of target sequence 25-nt, one deletion and one substitution using dimethoxytrityl (DMT) nucleoside phosphoramidite chemistry. In detecting single-nucleotide mismatches, fluorescence in situ hybridization of the bead-conjugated probes showed high specificity and signal-to-noise ratios. These preliminary results suggest further possibilities of creating a novel type of versatile, sensitive and multifunctional reconfigurable one-bead one-compound (OBOC) bead array.

Assessing affymetrix GeneChip microarray quality

BACKGROUND

Microarray technology has become a widely used tool in the biological sciences. Over the past decade, the number of users has grown exponentially, and with the number of applications and secondary data analyses rapidly increasing, we expect this rate to continue. Various initiatives such as the External RNA Control Consortium (ERCC) and the MicroArray Quality Control (MAQC) project have explored ways to provide standards for the technology. For microarrays to become generally accepted as a reliable technology, statistical methods for assessing quality will be an indispensable component; however, there remains a lack of consensus in both defining and measuring microarray quality.

RESULTS

We begin by providing a precise definition of microarray quality and reviewing existing Affymetrix GeneChip quality metrics in light of this definition. We show that the best-performing metrics require multiple arrays to be assessed simultaneously. While such multi-array quality metrics are adequate for bench science, as microarrays begin to be used in clinical settings, single-array quality metrics will be indispensable. To this end, we define a single-array version of one of the best multi-array quality metrics and show that this metric performs as well as the best multi-array metrics. We then use this new quality metric to assess the quality of microarry data available via the Gene Expression Omnibus (GEO) using more than 22,000 Affymetrix HGU133a and HGU133plus2 arrays from 809 studies.

CONCLUSIONS

We find that approximately 10 percent of these publicly available arrays are of poor quality. Moreover, the quality of microarray measurements varies greatly from hybridization to hybridization, study to study, and lab to lab, with some experiments producing unusable data. Many of the concepts described here are applicable to other high-throughput technologies.

Gene expression profiles in peripheral blood for the diagnosis of autoimmune diseases

Gene expression profiling in clinical genomics has yet to deliver robust and reliable approaches for developing diagnostics and contributing to personalized medicine. Owing to technological developments and the recent accumulation of expression profiles, it is a timely and relevant question whether peripheral blood gene expression profiling can be used routinely in clinical decision making. Here, we review the available gene expression profiling data of peripheral blood in autoimmune and chronic inflammatory diseases and suggest that peripheral blood mononuclear cells are suitable for descriptive and comparative gene expression analyses. A gene-disease interaction network in chronic inflammatory diseases, a general protocol for future studies and a decision tree for researchers are presented to facilitate standardization and adoption of this approach.

Is there a niche for DNA microarrays in molecular diagnostics?

DNA microarrays, 15 years after their appearance, have achieved presence in a number of medical settings. Several tests have been introduced and have obtained regulatory approval, mostly in the fields of bacterial identification, mutation detection and the global assessment of genome alterations, a particularly successful case being the whole-genome assay of copy-number variations. Gene-expression applications have been less successful because of technical issues (e.g., reproducibility, platform-to-platform consistency and statistical issues in data analysis) and difficulties in demonstrating the clinical utility of expression signatures. In their different applications, DNA arrays have faced competition from PCR-based assays for low and intermediate multiplicity. Now they have a new competitor, new-generation sequencing, that can provide a wealth of direct sequence information, or digital gene-expression data, at a constantly decreasing cost. In this article we evaluate the strengths and weaknesses of the DNA microarray approach to diagnostics, and highlight the fields in which it is most likely to achieve a durable presence.

Molecular classification of cancers of unknown primary site

Cancer of unknown primary site is a common metastatic cancer, diagnosed in about 50 000 patients per year in the US. The diagnosis, classification, and management of patients with carcinoma of unknown primary site has been difficult and frustrating. The therapy has usually been empiric for the majority of patients, and their prognosis has been poor. Molecular classification of metastatic cancers with known primary sites has been accurate (76-89%), as reported from several studies. Molecular profiling of initial biopsy specimens has tremendous potential as a test to diagnose the site of tumor origin in patients with unknown primary cancer. Several retrospective studies of molecular profiling assays have provided indirect validation of the accuracy of primary site prediction, based on correlations with clinicopathologic features. One additional study of initial diagnostic biopsies in unknown primary cancer patients, where primary tumor sites were identified months to years later, has provided more direct validation of the accuracy of molecular classification (the primary tumor sites of 15 of 20 patients were correctly predicted). The ability to diagnose and classify unknown primary cancer more precisely would allow for more site-specific or targeted therapy, and likely improve patient outcomes. Several clinical studies are in progress or planned to test this concept.

Nanopediatrics: enabling personalized medicine for children

The topic of the special series of reviews in this issue will be nanobiology and nanomedicine, with a focus on the impact of nanotechnology on children and their health; hence, the title of this collection and this introduction, Nanopediatrics: Enabling Personalized Medicine for Children. We will address what is meant when we discuss these nanodisciplines and why we developed a NanoPediatrics Program at University of California, Los Angeles. We will consider the implications of these nanodisciplines for individuals and society. The nature of research, diagnosis, and screening in nanomedicine and nanopediatrics will be illustrated by selected projects in nanodiagnostics and nanotherapeutics by our group and our collaborators, and the combined use of diagnostics and therapeutics in a single nanodevice referred to as "theranostics." We will conclude this introductory review with a summary of the reasons for developing the discipline of nanopediatrics.

Technical advances in rhinologic basic science research

Chronic rhinosinusitis (CRS) is the single most common self-reported chronic health condition in the United States and is estimated to affect 16% of the adult population annually. Despite the prevalence of this disease, there still exists an incomplete understanding of CRS pathophysiology. In this review, the authors highlight technological advances in rhinology: real-time polymerase chain reaction, epithelial cell culture, flow cytometry, genomics/single-nucleotide polymorphism detection, microarrays, and genetic/nongenetic animal models of sinusitis. The purpose of this review is to describe these methodologies and their contributions toward achieving a better understanding of CRS.