Nucleic acid sample preparation techniques for bead-based suspension arrays

Multiplexing in biological assays allows the simultaneous detection of multiple analytes in a single reaction, which reduces time, labor, and cost as compared to single reaction-based detection methods. Microsphere- or bead-based suspension array technologies, such as the Luminex® xMAP® system, offer high-throughput detection of nucleic acids through a variety of different assay chemistries. Common with most nucleic acid chemistries, for bead-based or other microarray technologies, is the need for efficient extraction and purification of the nucleic acids from the specimen of interest. Often, the optimal method will be dictated by the requirements of the up-front enzymatic chemistry, such as PCR, primer extension, branched DNA (bDNA), etc. For bead-based microarray platforms, the user must also be cognizant of proteins and other contaminants present in reactions that require heat denaturation, as that can lead to bead aggregation or agglutination, preventing the reading of assay results. This review describes and highlights some of the nucleic acid extraction and purification methods that have been used successfully for bead-based nucleic acid analysis, for both prokaryotic and eucaryotic nucleic acids, from a variety of sample types.

Fast and Efficient Measurement of Clinical and Biological Samples Using Immunoassay-Based Multiplexing Systems

Immunoassay is one of the most commonly used biomedical techniques to detect the expression of an antibody or an antigen in a test sample. Enzyme-linked immunosorbent assay (ELISA) has been used for a variety of applications including diagnostic tools and quality controls. However, one of the main limitations of ELISA is its lack of multiplexing ability, so ELISA may not be an efficient diagnostic tool when a measurement of multiple determinants is needed for samples with limited quantity such as blood or biological samples from newborns or babies. Although similar to ELISA in assay measurement, multiplex platforms such as bead-based Luminex and multi-array-based MSD (Meso Scale Discovery) are widely used to measure multiple biomarkers from a single analysis. Luminex is a xMAP-based technology that combines several different technologies to provide an efficient and accurate measurement of multiple analytes from a single sample. The multiplexing can be achieved because up to 100 distinct Luminex color-coded microsphere bead sets can be coated with a reagent specific to a particular bioassay, allowing the capture and detection of specific analytes from a sample. Using Multi-array and electrochemiluminescence technologies, the MSD platform provides the multiplex capability with similar consistence as observed in ELISA. Various biological samples that can be analyzed by both Luminex and MSD systems include serum, plasma, tissue and cell lysate, saliva, sputum, and bronchoalveolar Lavage (BAL). The most common Luminex and MSD-based assays are to detect a combined set of cytokines to provide a measurement of cytokine expression profiling for a diagnostic purpose.

BACs-on-Beads™ (BoBs™) assay for the genetic evaluation of prenatal samples and products of conception

BACs-on-Beads™ (BoBs™) is a new emerging technology, a modification of comparative genomic hybridization that can be used to detect DNA copy number gains and losses. Here, we describe the application of two different types of BoBs™ assays: (1) Prenatal BoBs (CE-IVD) to detect the most frequent syndromes associated with chromosome microdeletions, as well as the trisomy 13, 18 and 21, and (2) KaryoLite BoBs (RUO) which can detect aneuploidy in all chromosomes by quantifying proximal and terminal regions of each chromosomal arm. The interpretation of the results by BoBsoft™ software is also described. Although BoBs™ may not have the breadth and scope to replace chromosomal microarrays (array comparative genomic hybridization and single nucleotide polymorphism array) in the prenatal setting, particularly when a fetal anomaly has been detected, it is a well suited alternative for FISH or QF-PCR because BoBs™ is comparable, if not superior in terms of cost, turnaround time (TAT) and throughput and accuracy. BoBs™ also has the ability to detect significant fetal mosaicism (≥30% with Prenatal BoBs and ≥50% with KaryoLite BoBs). However, perhaps the greatest strength of this new technology is the fact that unlike FISH or QF-PCR, it has the ability to detect common microdeletion syndromes or additional aneuploidies, both of which may be easily missed despite excellent prenatal sonography. Thus, when BoBs™ is applied in the correct clinical setting and run and analyzed in appropriate laboratories this technique can improve and augment best practices with a personalization of prenatal care.

A multiplex technology platform for the rapid analysis of clinically actionable genetic alterations and validation for BRAF p.V600E detection in 1549 cytologic and histologic specimens

CONTEXT

Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information.

OBJECTIVE

To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens.

DESIGN

Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates.

RESULTS

Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%-100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%-99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%-99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451-48 078).

CONCLUSIONS

The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.

An optimized technology platform for the rapid multiplex molecular analysis of genetic alterations associated with leukemia

Molecular methods play a critical role in the accurate diagnosis of leukemia by complementing morphologic, cytochemical, immunophenotypic, and cytogenetic analyses. We developed a multiplex reverse transcription-polymerase chain reaction (RT-PCR) method combined with liquid bead array cytometry for the rapid detection of genetic alterations associated with leukemia. Fusion transcripts corresponding to the most common recurrent chromosomal translocations were reproducibly detected in as low as 0.1-10 ng of total RNA with an analytical sensitivity of 0.01-1%. Multiday, multilot, multioperator, and multi-instrument precision studies, for a total of 678 independent measures in 46 runs, showed a very high reproducibility with 100% agreement among replicates. Using multiplex panels for four to 20 independent targets, we demonstrate the flexibility of the method to codetect rare splicing isoforms, discriminate among multiple variants generated by unique cytogenetic abnormalities, identify distinct chromosomal partners involved with 11q23 or 17q21 rearrangements, and assess cryptic abnormalities not detectable by standard cytogenetics such as the t(12;21), del(1p32), or NPM1 mutations. Overall, three different internal control transcripts and 34 variants resulting from 18 abnormal chromosomal sites were evaluated. These results underscore the value of the multiplex assay system as a sensitive and reliable technology platform for the characterization of relevant genetic alterations in leukemia.

Application of multiple response optimization design to quantum dot-encoded microsphere bioconjugates hybridization assay

The optimization of DNA hybridization for genotyping assays is a complex experimental problem that depends on multiple factors such as assay formats, fluorescent probes, target sequence, experimental conditions, and data analysis. Quantum dot-doped particle bioconjugates have been previously described as fluorescent probes to identify single nucleotide polymorphisms even though this advanced fluorescent material has shown structural instability in aqueous environments. To achieve the optimization of DNA hybridization to quantum dot-doped particle bioconjugates in suspension while maximizing the stability of the probe materials, a nonsequential optimization approach was evaluated. The design of experiment with response surface methodology and multiple optimization response was used to maximize the recovery of fluorescent probe at the end of the assay simultaneously with the optimization of target-probe binding. Hybridization efficiency was evaluated by the attachment of fluorescent oligonucleotides to the fluorescent probe through continuous flow cytometry detection. Optimal conditions were predicted with the model and tested for the identification of single nucleotide polymorphisms. The design of experiment has been shown to significantly improve biochemistry and biotechnology optimization processes. Here we demonstrate the potential of this statistical approach to facilitate the optimization of experimental protocol that involves material science and molecular biology.

Proteomics and the search for biomarkers of female reproductive diseases

Over the past decade, high-throughput proteomics technologies have evolved considerably and have become increasingly more commonly applied to the investigation of female reproductive diseases. Proteomic approaches facilitate the identification of new disease biomarkers by comparing the abundance of hundreds of proteins simultaneously to find those specific to a particular clinical condition. Some of the best studied areas of female reproductive biology applying proteomics include gynaecological cancers, endometriosis and endometrial infertility. This review will discuss the progress that has been made in these areas and will highlight some of the emerging technologies that promise to contribute to better understanding of the female reproductive disease.

Simple fabrication of a smart microarray of polystyrene microbeads for immunoassay

We describe a simple method to fabricate an array of polystyrene microbeads (PS microbeads) conjugated with an elastin-like polypeptide (ELP) on a glass surface using a removable polymer template (RPT). A thin layer of adhesive was spun-cast on glass and cured by UV radiation. Micropatterns of an RPT were then transferred onto the surface by microcontact printing. The adhesion of PS microbeads on the surface depended on the adhesion performance of the adhesive layer, which could be adjusted by irradiation time. An array of PS microbeads conjugated with ELP was used for a smart immunoassay of prostate-specific antigen (PSA), a cancer marker. By controlling the phase transition of ELP molecules, PSA molecules were selectively adhered or released from the bead surface. The selective and reversible binding of PSA molecules on the bead surface was characterized with fluorescence microscopy.

A high-throughput microtiter plate-based screening method for the detection of full-length recombinant proteins

The Gram-negative bacterium Escherichia coli is an important host for the (heterologous) production of recombinant proteins. The development and optimization of a protocol to overproduce a desired protein in E. coli is often tedious. A novel high-throughput screening method based on the Luminex xMAP bead technology was developed allowing a rapid evaluation of a certain expression strategy. A variant of green fluorescent protein (GFPuv) from Aequorea victoria was used as a reporter to establish the methodology. The N-terminus and the C-terminus of GFPuv were engineered to contain a His(6)- and an HA-tag (YPYDVPDYA), respectively. The double-tagged protein was loaded onto Luminex-microspheres via its His(6)-tag, the presence of the HA-tag was verified using an anti-HA antibody. High-throughput detection of full-length proteins (containing both tags) on the beads was performed using an automated Luminex 100IS analyzer. The results were compared to results obtained by classical Western blot analysis. Comparison of the two methods revealed that the Luminex-based method is faster and more economical in detecting full-length (intact) soluble recombinant protein, allowing one to routinely screen a high number of parameters in gene expression experiments. As proof of concept, different protocols to overproduce double-tagged model eucaryotic proteins (human protein S6 kinase 1 and human tankyrase) in E. coli were monitored using the new approach. Relevant parameters for optimizing gene expression of the corresponding genes were rapidly identified using the novel high-throughput method.

Synergism between particle-based multiplexing and microfluidics technologies may bring diagnostics closer to the patient

In the field of medical diagnostics there is a growing need for inexpensive, accurate, and quick high-throughput assays. On the one hand, recent progress in microfluidics technologies is expected to strongly support the development of miniaturized analytical devices, which will speed up (bio)analytical assays. On the other hand, a higher throughput can be obtained by the simultaneous screening of one sample for multiple targets (multiplexing) by means of encoded particle-based assays. Multiplexing at the macro level is now common in research labs and is expected to become part of clinical diagnostics. This review aims to debate on the “added value” we can expect from (bio)analysis with particles in microfluidic devices. Technologies to (a) decode, (b) analyze, and (c) manipulate the particles are described. Special emphasis is placed on the challenges of integrating currently existing detection platforms for encoded microparticles into microdevices and on promising microtechnologies that could be used to down-scale the detection units in order to obtain compact miniaturized particle-based multiplexing platforms.

Technical standards and guidelines for reproductive screening in the Ashkenazi Jewish population

DISCLAIMER

These Technical Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular standard or guidelines was adopted, and to consider other relevant medical and scientific information that becomes available after that date.

Multifunctional nanorods for biomedical applications

Multifunctional nanorods have shown significant potential in a wide range of biomedical applications. Nanorods can be synthesized by a top down or bottom-up approach. The bottom-up approach commonly utilizes a template deposition methodology. A variety of metal segments can easily be incorporated into the nanorods. This permits high degrees of chemical and dimensional control. High aspect-ratio nanorods have a large surface area for functionalization. By varying the metal segments in the nanorods, spatial control over the binding of functional biomolecules that correspond with the unique surface chemistry of the metal segment can be achieved. Functionalized multicomponent nanorods are utilized in applications ranging from multiplexing, protein sensing, glucose sensing, imaging, biomolecule-associated nanocircuits, gene delivery and vaccinations.

Rapid microsphere assay for identification of cryptosporidium hominis and cryptosporidium parvum in stool and environmental samples

Cryptosporidium hominis and Cryptosporidium parvum are associated with massive disease outbreaks worldwide. Because these two species have different transmission cycles, identification of these parasites to the species level in clinical samples may provide laboratory data of crucial importance in epidemiologic investigations. To date, the most reliable way to differentiate C. hominis and C. parvum is based on DNA sequencing analysis of PCR amplicons. Although this approach is very effective for differentiation of Cryptosporidium species, it is labor-intensive and time-consuming compared with methods that do not require DNA sequencing analysis as an additional step and that have been successfully used for specific identification of a number of pathogens. In this study, we describe a novel Luminex-based assay that can differentiate C. hominis from C. parvum in a rapid and cost-effective manner. The assay was validated by testing a total of 143 DNA samples extracted from clinical specimens, environmental samples, or samples artificially spiked with Cryptosporidium oocysts. As few as 10 oocysts per 300 microl of stools could be detected with this assay. The assay format includes species-specific probes linked to carboxylated Luminex microspheres that hybridize to a Cryptosporidium microsatellite-2 region (ML-2) where C. hominis and C. parvum differ by one nucleotide substitution. The assay proved to be 100% specific when samples that had been characterized by direct fluorescent antibody test (DFA) and DNA sequencing analysis were tested. In addition, the assay was more sensitive than DFA and provided species identification, which is an advantage for epidemiologic studies.

Multiplex quantitative competitive polymerase chain reaction based on a multianalyte hybridization assay performed on spectrally encoded microspheres

Quantitative polymerase chain reaction (PCR) may be performed by two general approaches, namely, real-time PCR and quantitative competitive PCR (QC-PCR). QC-PCR makes use of the concept of a DNA competitor, which is the "gold standard" approach to circumvent the problem of the variation of amplification efficiency. However, QC-PCR in its classical form is a low-throughput method since it requires titration of each sample with the competitor followed by electrophoresis. The throughput of QC-PCR has been improved by capillary electrophoresis and microtiter well-based hybridization assays. The present work introduces a multiplex QC-PCR method, which is based on a multianalyte hybridization assay that is performed on spectrally encoded microspheres. The DNA competitors use the same primers and have equal size with their corresponding target DNA sequences but differ in a short (24 bp) centrally located sequence. Following multiplex PCR, biotinylated amplification products from all DNA targets and competitors are heat-denatured and hybridized with oligonucleotide probes, which are attached to addressable sets of fluorescent microspheres. The hybrids react with a streptavidin-phycoerythrin conjugate. The microspheres are then analyzed by flow cytometry employing two lasers. A red laser line is used for classification of the microspheres, and a green line excites phycoerythrin, whose fluorescence is related to the concentration of the analyte DNA. As a model, we have developed a multiplex quantitative competitive PCR assay for four targets. The amplification products from targets and competitors (a total of 8 DNA fragments) are determined simultaneously by the multianalyte hybridization assay. The limits of quantification for the hybridization assay of all amplified DNA fragments are below 13 pM. The multiplex quantitative competitive PCR assay detects approximately 500 copies from each target DNA. To our knowledge, the proposed method is the only approach to quantitative PCR that offers such a high potential for multiplexing.

Classification of spectroscopically encoded resins by Raman mapping and infrared hyperspectral imaging

Barcoded resins (BCRs) were recently introduced as a potential platform for pre-encoded multiplexed synthesis, screening, and biomedical diagnostics. A key step toward the development of this strategy is the ability to rapidly interrogate and classify the BCRs in a high-throughput, noninvasive manner. Here, we describe a one-step strategy based on Raman mapping and Fourier transform infrared imaging to classify and spatially resolve randomly distributed BCRs. To illustrate this methodology, mixtures of up to 25 different BCRs were imaged and classified with 100% confidence. This strategy can be readily extended to a larger pool of resins, provided each BCR features a unique vibrational fingerprint (spectroscopic barcode). We have also established that reliable single-bead Raman spectra can be recorded in 10 ms, thus confirming that Raman mapping, in particular, could be a very fast method to classify the BCRs.

Spectroscopically encoded resins for high throughput imaging time-of-flight secondary ion mass spectrometry

Spectroscopic barcoding was recently introduced as a new pre-encoding strategy wherein the resin beads are not just carriers for solid phase synthesis, but are, in addition, the repository of the synthetic scheme to which they were subjected. To expand the repertoire of spectroscopically barcoded resins (BCRs), here we introduce a new family of halogenated polystyrene-based polymers designed for high-throughput combinatorial analysis using not only infrared and Raman spectroscopy but also imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS). In particular, we have established that (a) the halogen content of these new resins can be used as an encoding element in quantitative imaging ToF-SIMS and (b) the number of styrene monomers used to generate unique vibrational fingerprints can be significantly reduced by using monomers in different molar ratios. The combination of quantitative imaging ToF-SIMS and vibrational spectroscopy is anticipated to dramatically increase the repertoire of possible BCRs from a few hundreds to several thousands.

Development of a whole-virus multiplex flow cytometric assay for antibody screening of a specific pathogen-free primate colony

Our goal was to determine if a multiplex technique using a fluorescent bead-based flow cytometric assay could yield results comparable to traditional enzyme-linked immunosorbent assay (ELISA) in terms of sensitivity, specificity, cross-reactivity, and throughput. We applied both techniques to serologic screening of specific pathogen-free macaques, for type D simian retrovirus, simian T-lymphotropic virus, Cercopithicine herpesvirus 1, and simian immunodeficiency virus, and found a high correlation between the bead-based multiplex assay and ELISA. The multiplex assay demonstrated greater sensitivity with no loss in specificity when compared to the ELISA. A lower false-positive rate with the multiplex assay decreased the number of confirmatory Western blots required. Using the multiplex assay, we were able to screen samples for 4 viruses simultaneously in the time it took to perform a single-virus ELISA, resulting in a faster turnaround time and higher throughput. The multiplexed assay provided greater sensitivity, increased stability, and better performance than ELISA.

Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection

Background

As we enter the post-genome sequencing era and begin to sift through the enormous amount of genetic information now available, the need for technologies that allow rapid, cost-effective, high-throughput detection of specific nucleic acid sequences becomes apparent. Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can greatly reduce the time, cost and labor associated with single reaction detection technologies.

Methods

The Luminex® xMAP™ system is a multiplexed microsphere-based suspension array platform capable of analyzing and reporting up to 100 different reactions in a single reaction vessel. This technology provides a new platform for high-throughput nucleic acid detection and is being utilized with increasing frequency. Here we review specific applications of xMAP technology for nucleic acid detection in the areas of single nucleotide polymorphism (SNP) genotyping, genetic disease screening, gene expression profiling, HLA DNA typing and microbial detection.

Conclusions

These studies demonstrate the speed, efficiency and utility of xMAP technology for simultaneous, rapid, sensitive and specific nucleic acid detection, and its capability to meet the current and future requirements of the molecular laboratory for high-throughput nucleic acid detection.

Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification

BACKGROUND

Complex mixtures of DNA may be found in environmental and medical samples. There is a need for techniques that can measure low concentrations of target DNAs. For a multiplexed, flow cytometric assay, we show that the signal-to-noise ratio for fluorescence detection may be increased with the use of 3DNA dendrimers. A single fluorescent DNA molecule per bead could be detected with conventional flow cytometry instrumentation.

METHODS

The analyte consisted of single-stranded (ss) DNA amplicons that were hybridized to capture probes on the surface of fluorescent polystyrene microspheres (beads) and initially labeled with streptavidin-R-phycoerythrin (single-step labeling). These beads have a low reporter fluorescence background and high efficiency of DNA hybridization. The DNA/SA-RPE complex was then labeled with 3DNA dendrimers and SA-RPE. The bead complexes were detected with a Luminex 100 flow cytometer. Bead standards were developed to convert the intensity to the number of SA-RPE labels per bead and the number of dendrimers per bead.

RESULTS

The dendrimer assay resulted in 10-fold fluorescence amplification compared with single-step SA-RPE labeling. Based on concentration curves of pure target ss-amplicons, the signal-to-noise ratio of the dendrimer assay was greater by a factor of 8.5 over single-step SA-RPE labeling. The dendrimer assay was tested on 16S ribosomal DNA amplified from filter retentates of contaminated groundwater. Multiplexed detection of a single dendrimer-labeled DNA molecule per bead was demonstrated.

CONCLUSIONS

Multiplexed detection of DNA hybridization on a single molecule level per bead was achieved with conventional flow cytometry instrumentation. This assay is useful for detecting target DNAs at low concentrations.

Technical standards and guidelines: Venous thromboembolism (Factor V Leiden and prothrombin 20210G>A testing): A disease-specific supplement to the standards and guidelines for clinical genetics laboratories

These standards and guidelines are designed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to this statement does not necessarily ensure a successful medical outcome. These standards and guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical molecular geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the laboratory record the rationale for any significant deviation from these standards and guidelines.

Microsphere bead arrays and sequence validation of 5/7/9T genotypes for multiplex screening of cystic fibrosis polymorphisms

The development of simple and rapid methods for the detection of the common genetic mutations associated with cystic fibrosis (CF) requires access to positive-control samples including the 5/7/9T variants of intron 8. We used PCR and a simple multiplex bead-array assay to identify 5/7/9T control samples from 29 commercially available DNA samples. Unpurified PCR products were directly hybridized to color-coded beads containing allele-specific capture probes for 5/7/9T detection. The performance of the assay was investigated using reverse-complement oligonucleotides, individual PCR products, and multiplex PCR products for 5/7/9T detection within a complex CFTR screening assay. Samples were genotyped by grouping the relative signal intensities from each capture probe. Of 29 commercially available DNA samples analyzed, 2 5T/7T, 2 5T/9T, 9 7T/9T, 11 7T/7T, and 5 9T/9T genotypes were identified. The genotype within each sample group was confirmed by DNA sequencing. The assay was compatible with the analysis of 10 to 1000 ng of genomic DNA isolated from whole blood and allowed for the separate identification of primary CFTR mutations from reflex variants. The correct identification of positive controls demonstrated the utility of a simple bead-array assay and provided accessible samples for assay optimization and for routine quality control in the clinical laboratory.

Comparison of four flow cytometric SNP detection assays and their use in plant improvement

Single nucleotide polymorphisms (SNPs) are attractive DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed, but it is unclear which assays are best suited and most efficient for various types of plant improvement research. The objective of this study was to compare the accuracy, efficiency, and cost of four SNP genotyping assays: single-base extension (SBE), allele-specific primer extension (ASPE), oligonucleotide ligation (OL), and direct hybridization (DH). All four assay methods used the same Luminex 100 flow cytometer platform. Fifty-eight F(2)-derived soybean [Glycine max (L.) Merr.] lines from a cross between inbred lines G99-G725 and N00-3350 were genotyped at four SNPs. SBE and ASPE clearly differentiated between the two homozygotes and the heterozygote at each SNP. Results were in agreement with those identified using the SNaPshot minisequencing assay as a control. In contrast, the OL and DH assays were unable to differentiate between genotypes at some of the SNPs. However, when the cost per data point for the four different assays was compared, the cost of OL and DH was only about 70% of that for SBE, with DH requiring the least time of the four assays. On the basis of cost and labor, ASPE is more cost-effective and simpler than SBE, and would therefore be a good method for genetic mapping and diversity studies which require a large number of markers and a high level of multiplexing. DH appears to be the most economical assay for marker-assisted selection, though optimization for DH would be required for some SNP markers.

Analytical validation of the tag-it high-throughput microsphere-based universal array genotyping platform: application to the multiplex detection of a panel of thrombophilia-associated single-nucleotide polymorphisms

BACKGROUND

We have developed a novel, microsphere-based universal array platform referred to as the Tag-It platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs).

METHODS

Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP system. Genotypes were also determined by sequencing.

RESULTS

Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations.

CONCLUSIONS

The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.

Multiplexed genetic analysis using an expanded genetic alphabet

Background: All states require some kind of testing for newborns, but the policies are far from standardized. In some states, newborn screening may include genetic tests for a wide range of targets, but the costs and complexities of the newer genetic tests inhibit expansion of newborn screening. We describe the development and technical evaluation of a multiplex platform that may foster increased newborn genetic screening.

Methods: MultiCode® PLx involves three major steps: PCR, target-specific extension, and liquid chip decoding. Each step is performed in the same reaction vessel, and the test is completed in ∼3 h. For site-specific labeling and room-temperature decoding, we use an additional base pair constructed from isoguanosine and isocytidine. We used the method to test for mutations within the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The developed test was performed manually and by automated liquid handling. Initially, 225 samples with a range of genotypes were tested retrospectively with the method. A prospective study used samples from >400 newborns.

Results: In the retrospective study, 99.1% of samples were correctly genotyped with no incorrect calls made. In the perspective study, 95% of the samples were correctly genotyped for all targets, and there were no incorrect calls.

Conclusions: The unique genetic multiplexing platform was successfully able to test for 31 targets within the CFTR gene and provides accurate genotype assignments in a clinical setting.

Preparation, physical properties, on-bead binding assay and spectroscopic reliability of 25 barcoded polystyrene-poly(ethylene glycol) graft copolymers

Here we describe the preparation of 25 beaded polystyrene-poly(ethylene glycol) graft copolymers from six spectroscopically active styrene monomers: styrene, 2,5-dimethylstyrene, 4-methylstyrene, 2,4-dimethylstyrene, 4-tert-butylstyrene, and 3-methylstyrene. These polymers were thoroughly characterized by Raman, infrared, and (1)H/(13)C NMR spectroscopies, and differential scanning calorimetry. Determination of the swelling properties, peptide synthesis, and on-bead streptavidin-alkaline phosphatase (SAP) binding assay further established that their physical and chemical properties where not significantly altered by the diversity of their encoded polystyrene core. Each of the 25 resins displayed a unique Raman and infrared vibrational fingerprint, which was converted into a "spectroscopic barcode". The position of each bar matches the peak wavenumber in the corresponding spectrum but is independent of its intensity. From this simplified representation similarity maps comparing 35 000 resin pairs were generated to establish the spectroscopic barcoding as a reliable encoding methodology. In effect, in 99% of the cases, the highest similarity coefficients were obtained for resin pairs prepared from the same styrene derivatives even after SAP binding assay. We have also shown that a small but unique combination of a resin's vibrations (30-40%) is sufficient for its identification. However, in rare cases where a resin's vibrational signature has been severely compromised, both the Raman and infrared barcodes were synergistically and reliably utilized to unequivocally identify its chemical make up.

Current challenges in cystic fibrosis screening

CONTENT

This article gives an overview of the symptoms and mutations associated with classic and atypical cystic fibrosis (CF). Current testing methods for mutation detection in CF are discussed.

OBJECTIVES

Review testing for CF, including American College of Medical Genetics and American College of Obstetrics and Gynecology guidelines and recommendations regarding population screening for CF. Describe symptomatic and mutational differences between patients with classic CF and atypical CF, including monosymptomatic conditions such as congenital bilateral absence of the vas deferens, idiopathic pancreatitis, and chronic sinusitis. Explain the concern about predicting the phenotypic expression of the condition from the genotype. Discuss the challenges of CF testing, including the preanalytic, analytic, and postanalytic phases. List the current methods for detecting CF transmembrane conductance regulator gene mutations, specifying the advantages and disadvantages of each. Describe the basic patient information necessary for laboratories to provide accurate risk assessments, such as ethnicity and family history, and reasons for the test being conducted (carrier or affected status).

RESULTS

The technical challenges of detecting the 25 recommended mutations are being met by commercially available reagents. Challenges remain for the preanalytic and postanalytic phases. Only with accurate patient information can laboratories provide specific risk reductions on the basis of a negative genetic test result.

CONCLUSION

As health care providers become better informed about the recommendations for CF testing and laboratories continue to increase the sensitivities of their assays, patients will benefit from increased screening efficiency and accuracy. This will allow affected individuals to receive prompt and effective treatment and carriers to enjoy an expanded number of reproductive options.

Encoding microcarriers by spatial selective photobleaching

Bead-based assays on very large numbers of molecules in gene expression studies, drug screening and clinical diagnostics, require the encoding of each of the microspheres according to the particular ligand bound to its surface. This allows mixing the uniquely encoded microspheres and subjecting them to an assay simultaneously. When a particular microsphere gives a positive reaction, the substance on its surface can be identified by reading the code. Previously reported techniques for colour encoding polymer microspheres only allow for a limited number of unique codes. Graphical encoding methods use metallic particles, which are rather uncommon in screening applications. Here, we demonstrate a new approach to encode polymer microspheres that are commonly used in screening applications, such as polystyrene microspheres, with a method that provides a virtually unlimited number of unique codes. Patterns can be written in fluorescently dyed microspheres by 'spatial selective photobleaching' and can be identified by confocal microscopy. Such encoded microparticles can find broad application in the collection and analysis of genetic information, high-throughput screening, medical diagnostics and combinatorial chemistry, and can also be used for labelling of consumer goods or as security labels to prevent counterfeiting.

Multiplexed microsphere-based flow cytometric assays

Flow cytometry has become an indispensable tool for clinical diagnostics and basic research. Although primarily designed for cellular analysis, flow cytometers can detect any particles in the lower micron range, including inert microspheres of different sizes, dyed with various fluorochromes. Over the past 20 years, microspheres have been used as calibrators for flow cytometers and also as a solid support for numerous molecular reactions quantitated by flow cytometry. Proteins, oligonucleotides, polysaccharides, lipids, or small peptides have been adsorbed or chemically coupled to the surface of microspheres to capture analytes that are subsequently measured by a fluorochrome-conjugated detection molecule. More recently, assays for similar analytes have been multiplexed, or analyzed in the same assay volume, by performing each reaction on a set of microspheres that are dyed to different fluorescent intensities and, therefore, are spectrally distinct. Some recent applications with fluorescent microspheres have included cytokine quantitation, single nucleotide polymorphism genotyping, phosphorylated protein detection, and characterization of the molecular interactions of nuclear receptors. The speed, sensitivity, and accuracy of flow cytometric detection of multiple binding events measured in the same small volume have the potential to replace many clinical diagnostic and research methods and deliver data on hundreds of analytes simultaneously.

A novel monoclonal antibody screening method using the Luminex-100 microsphere system

We describe the development of a robust and sensitive assay system (detection limit <500 pg/ml biotin-IL-6, K(d)=75 ng/ml), using Luminex-100 microspheres, that could effectively screen for neutralizing antibody whenever a soluble form of the receptor for a target molecule is available. As an example, we coupled a recombinant human interleukin-6 soluble receptor to a Luminex carboxylated microsphere and used a biotin-labeled recombinant human interleukin-6 as a probe to assess binding competition. Three anti-human IL-6 monoclonal antibodies that bind distinct IL-6 epitopes were used as test articles to evince the stringency of the screen. Our assay was able to detect antibody concentration as low as 10 ng/ml without interference from hybridoma growth medium or cell supernatant. The time-saving benefits of this assay format make it ideal for high-throughput screening (HTS) applications for neutralizing monoclonal antibodies.

Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides

We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.

Encoding microcarriers: present and future technologies

In answer to the ever-increasing need to carry out many assays simultaneously in drug screening and drug discovery, several microcarrier-based multiplex technologies have arisen in the past few years. The compounds to be screened are attached to the surface of microcarriers, which can be mixed together in a vessel that contains the target analyte. Each microcarrier has to be encoded to know which compound is attached to its surface. In this article, the methods that have been developed for the encoding of microcarriers are reviewed and discussed.

Development of internal controls for the Luminex instrument as part of a multiplex seven-analyte viral respiratory antibody profile

The ability of the Luminex system to simultaneously quantitate multiple analytes from a single sample source has proven to be a feasible and cost-effective technology for assay development. In previous studies, my colleagues and I introduced two multiplex profiles consisting of 20 individual assays into the clinical laboratory. With the Luminex instrument's ability to classify up to 100 distinct microspheres, however, we have only begun to realize the enormous potential of this technology. By utilizing additional microspheres, it is now possible to add true internal controls to each individual sample. During the development of a seven-analyte serologic viral respiratory antibody profile, internal controls for detecting sample addition and interfering rheumatoid factor (RF) were investigated. To determine if the correct sample was added, distinct microspheres were developed for measuring the presence of sufficient quantities of immunoglobulin G (IgG) or IgM in the diluted patient sample. In a multiplex assay of 82 samples, the IgM verification control correctly identified 23 out of 23 samples with low levels (<20 mg/dl) of this antibody isotype. An internal control microsphere for RF detected 30 out of 30 samples with significant levels (>10 IU/ml) of IgM RF. Additionally, RF-positive samples causing false-positive adenovirus and influenza A virus IgM results were correctly identified. By exploiting the Luminex instrument's multiplexing capabilities, I have developed true internal controls to ensure correct sample addition and identify interfering RF as part of a respiratory viral serologic profile that includes influenza A and B viruses, adenovirus, parainfluenza viruses 1, 2, and 3, and respiratory syncytial virus. Since these controls are not assay specific, they can be incorporated into any serologic multiplex assay.

Submicrometer metallic barcodes

We synthesized multimetal microrods intrinsically encoded with submicrometer stripes. Complex striping patterns are readily prepared by sequential electrochemical deposition of metal ions into templates with uniformly sized pores. The differential reflectivity of adjacent stripes enables identification of the striping patterns by conventional light microscopy. This readout mechanism does not interfere with the use of fluorescence for detection of analytes bound to particles by affinity capture, as demonstrated by DNA and protein bioassays.

SNPing in the human genome

More than a million genetic markers in the form of single nucleotide polymorphisms are now available for use in genotype-phenotype studies in humans. The application of new strategies for representational cloning and sequencing from genomes combined with the mining of high-quality sequence variations in clone overlaps of genomic and/or cDNA sequences has played an important role in generating this new resource. The focus of variation analysis is now shifting from the identification of new markers to their typing in populations, and novel typing strategies are rapidly emerging. Assay readouts on oligonucleotide arrays, in microtiter plates, gels, flow cytometers and mass spectrometers have all been developed, but decreasing cost and increasing throughput of DNA typing remain key if high-density genetic maps are to be applied on a large scale.