Challenges in the Commercialization of Array-Based Tests

Since the advent of array-based molecular diagnostics early in the last decade, the tests have faced a number of challenges, including an evolving regulatory environment, costs associated with developing a test and bringing it through a regulatory clearance process, costs associated with the technology itself, both the assay kits and the underlying platforms, hesitance from insurers to reimburse tests, questions about the clinical utility of the new assays, community awareness of the tests’ benefits, and competition from other technology platforms. While there are many obstacles to achieving success, array-based tests used in constitutional cytogenetics have been widely adopted and are now considered the standard of care. Revenues for other tests continue to grow, though not in line with earlier predictions. This chapter examines the challenges associated with bringing an array-based test to market and how they have been overcome.

The use of predictive biomarkers can help to improve therapeutic options for the individual cancer patient. For the treatment of colon cancer patients with anti-EGFR-based drugs, the KRAS mutation status has to be determined to pre-select responders that will benefit from this medication. Amongst others, array-based tests have been established for profiling of the KRAS mutation status. Within this article we describe an on-chip hybridization technique to screen therapeutic relevant KRAS codon 12 mutations. The DNA chip-based platform enables the reliable discrimination of selected mutations by allele-specific hybridization. Here, silver deposits represent robust endpoint signals that allow for a simple naked eye rating. With the here presented assay concept a precise identification of heterozygous and homozygous KRAS mutations, even against a background of up to 95% wild-type DNA, was realizable. The applicability of the test was successfully proven for various cancer cell lines as well as clinical tumour samples. Thus, the chip-based DNA hybridization technique seems to be a promising tool for KRAS mutation analysis to further improve personalized cancer treatment.

A direct heating model to overcome the edge effect in microplates

The introduction of genome-wide arrays in postnatal and prenatal diagnosis raises challenging ethical issues. Here, we explore questions with regard to the ethics of consent. One important issue is whether informed consent for genome-wide array-based testing is in fact feasible, given the wide range of possible outcomes and related options. The proposed alternative of "generic consent" will have to be studied in practice. From an ethical point of view, the question is whether consent would still be sufficiently "informed" in a generic approach. Another issue that has not yet been given much attention is how far parents, or pregnant women and their partners, should be allowed to determine the range of possible outcomes that will or will not be reported back to them. The scope and limits of parents' and prospective parents' right to know or not to know are far from clear. The complex normative issues on the content and weight of these rights can only be answered by taking full account of the rights and interests of all the parties involved: prospective and actual parents, children, and relatives. This paper is the result of a working group meeting preceding the European Society of Human Genetics 2011 Conference, where these issues were addressed.

A simple array-based test structure has been developed to characterize AC variability in deeply scaled MOSFETs. Each test structure consists of 128 devices under test (DUTs) whose relative delays are characterized using a logic gate-based delay detector circuit. The delay measurement technique only requires a single off-chip DC voltage measurement for each DUT. A design-time optimization is performed on each DUT array to ensure that the measured delays of each DUT primarily reflects its AC, or short time-scale, characteristics rather than previously well-studied DC characteristics such as saturation current, threshold voltage, and channel length. The circuit is implemented in an advanced CMOS SOI technology and occupies an area of 400μm × 20μm. Simulations show that the test circuit effectively isolates the possible presence of AC effects from known DC variation sources for the transistors.

The scale of testing required in clinical analysis has of necessity driven analytical methods to a variety of multiplexed formats. A single assay in a test tube has evolved to automated multiple testing in cuvettes in multicuvette carousels, or wells of a microplate with up to 9600 wells (1). Other formats for multiplex testing include 2-dimensional microarrays of spots of reagents on a planar surface and microbeads either in suspension [so-called liquid or 3-dimensional (3D)1 arrays] or held in wells on the end of a fiber optic bundle (2)(3). The microarray testing format has grown in popularity for both protein and nucleic acid analysis, and is now the dominant method for applications such as gene expression and single nucleotide polymorphism analysis. Multiplex testing presents specific analytical and quality control challenges. One factor that complicated early array-based tests in a microplate format was the regional differences in results due to different thermal properties of the outer vs the inner wells of the plate—the so-called edge effect. It was observed that the thermal properties of a well in the interior of a microplate differed significantly from wells at the edge of the array. The consequent temperature differences affected the results of immunoassays performed in microplates, a problem resolved by better control of incubations (4). In most modern-day microarray-based tests, a variety of performance controls are included to monitor analytical performance and safeguard the quality of the analytical data. Such controls include blank areas, positive controls, negative controls, normalization controls, controls for nonspecific binding and to confirm sample addition, cross-reactivity controls, and controls to assess the activity of assay reagents such as the detection conjugate (5). The report in this issue by Klee and colleagues (6) highlights an underlying concern in microarray-based testing that relates to the quality of …

Consumer genomics databases have reached the scale of millions of individuals. Recently, law enforcement authorities have exploited some of these databases to identify suspects via distant familial relatives. Using genomic data of 1.28 million individuals tested with consumer genomics, we investigated the power of this technique. We project that about 60% of the searches for individuals of European descent will result in a third-cousin or closer match, which theoretically allows their identification using demographic identifiers. Moreover, the technique could implicate nearly any U.S. individual of European descent in the near future. We demonstrate that the technique can also identify research participants of a public sequencing project. On the basis of these results, we propose a potential mitigation strategy and policy implications for human subject research.

As process technologies continually advance, process variation has greatly increased and has gradually become one of the most critical factors for IC manufacturing. Furthermore, these increasingly complex processes continue to make greater use of stressors for mobility enhancement, thus requiring large volumes of data for extensive characterization of layout-dependent effects (LDE) for validation of both SPICE models and design for manufacturing. Transistor threshold voltage (Vt) is a commonly used parameter both for characterization during process development and for monitoring of volume manufacturing. To adequately quantify local process variation or LDE, Vt must be measured for a sufficiently large number of device-under-tests (DUTs) to obtain a statistically representative sample population. The number of Vt measurements required to obtain such a statistically significant result, however, requires extremely long testing time, especially for array-based test structure designs including thousands of DUTs. In this paper, we present a very fast threshold voltage measurement methodology using an operational amplifier-based source-measure unit test configuration, which greatly improves testing efficiency and accuracy, and is not sensitive to process variation. The proposed test methodology can improve Vt testing time by a factor of 5-10 relative to the commonly used binary-search algorithm, and by a factor of ~2 relative to an optimized interpolation algorithm, and achieves better accuracy (standard deviation of Vt = 0.15 mV, versus typical accuracy of ~ 0.5 mV for the two algorithms mentioned). Furthermore, the layout and configuration of conventional test structures need not be modified to adapt the proposed methodology. The measured results from the most advanced process technology nodes demonstrate the testing efficiency and accuracy of the proposed test structure in characterizing the large number of DUTs required for quantifying process variation or LDEs.