Multiplexed analysis of polymorphisms in the HLA gene complex using bead array chips

Rapid phenotypic fingerprinting of cell products by robust measurement of ubiquitous surface markers

Flow cytometry is one of the most versatile and powerful approach for the quantitative analysis of cell suspensions. With widespread applications in basic and clinical research, its commonest use is in the detection of cell populations labelled against markers specific for a particular phenotype. In this study, we aimed to expand the potential of flow cytometry by describing a method based on robust automated quantification of ubiquitous cell surface markers. We demonstrate that automatic fluorescence standardization combined with whole cell population analysis yields highly reproducible results and can alleviate many of the difficulties associated with conventional analyses. This new generic approach is very flexible for quantifying the uniqueness of entire cell populations regardless of their composition. It provides quantitative phenotypic fingerprints rapidly, does not incorporate subjective factors, is more amenable to standardization, and is easily transferable across a wide diversity of applications, such as quality control for cell manufacture and authentication of cell products.

Bacterial identification by 16S rRNA gene PCR-hybridization as a supplement to negative culture results

PCR-hybridization was compared to culture methods for evaluating suspected blood infections. A total of 231 clinical samples from blood culture bottles that were flagged positive by the BacT/Alert system or were negative 1 week after inoculation were tested. When the PCR-hybridization and culture method results were compared, the positive and negative concordance rates were 99.2% (122/123) and 89.5% (94/105), respectively. Of the negative blood cultures, 10.5% (11/105) were positive by PCR-hybridization. Supplemental testing of negative blood cultures may identify bacterial pathogens that are undetectable by culture methods.

Competitive hybridization models

Microarray technology, in its simplest form, allows one to gather abundance data for target DNA molecules, associated with genomes or gene-expressions, and relies on hybridizing the target to many short probe oligonucleotides arrayed on a surface. While for such multiplexed reactions conditions are optimized to make the most of each individual probe-target interaction, subsequent analysis of these experiments is based on the implicit assumption that a given experiment yields the same result regardless of whether it was conducted in isolation or in parallel with many others. It has been discussed in the literature that this assumption is frequently false, and its validity depends on the types of probes and their interactions with each other. We present a detailed physical model of hybridization as a means of understanding probe interactions in a multiplexed reaction. Ultimately, the model can be derived from a system of ordinary differential equations (ODE's) describing kinetic mass action with conservation-of-mass equations completing the system. We examine pairwise probe interactions in detail and present a model of "competition" between the probes for the target--especially, when the target is effectively in short supply. These effects are shown to be predictable from the affinity constants for each of the four probe sequences involved, namely, the match and mismatch sequences for both probes. These affinity constants are calculated from the thermodynamic parameters such as the free energy of hybridization, which are in turn computed according to the nearest neighbor (NN) model for each probe and target sequence. Simulations based on the competitive hybridization model explain the observed variability in the signal of a given probe when measured in parallel with different groupings of other probes or individually. The results of the simulations can be used for experiment design and pooling strategies, based on which probes have been shown to have a strong effect on each other's signal in the in silico experiment. These results are aimed at better design of multiplexed reactions on arrays used in genotyping (e.g., HLA typing, SNP, or CNV detection, etc.) and mutation analysis (e.g., cystic fibrosis, cancer, autism, etc.).

Magnetic assembly of high-density DNA arrays for genomic analyses

A method for rapidly assembling high-density DNA arrays with near-perfect order is described. Photolithography is used to generate a wafer-scale array of microwells in a layer of photoresist on a chemically functionalized glass coverslip. The array is enclosed within a microfluidic device, and a suspension of superparamagnetic microbeads conjugated to DNA molecules is introduced into the chamber. A permanent magnet is used to direct the rapid assembly of the beads into the wells, with each well containing a single bead. These beads are immobilized on the glass surface via affinity binding, and excess beads can be recycled or washed away. Nonspecifically bound beads are removed by dissolving the photoresist. The result is a high-density array of beads with virtually no background. This method can be used to produce protein arrays for chip-based assays and DNA arrays for genotyping or genome sequencing.

An Overview of HLA Typing for Hematopoietic Stem Cell Transplantation

Selection of a related or unrelated haematopoietic stem cell donor for a patient requires accurate matching of human leukocyte antigen (HLA) genes in order to maximise the beneficial effects of the transplant. There are a number of different approaches that can be made in order to achieve HLA type depending on the number of samples being processed, the level of resolution to be achieved, and the cost of providing the various tests. Each method has its advantages and disadvantages and in most laboratories, a combination of methods may be used.

Rapid discrimination of single-nucleotide mismatches using a microfluidic device with monolayered beads

A microfluidic device incorporating monolayered beads is developed for the discrimination of single-nucleotide mismatches, based on the differential dissociation kinetics between perfect match (PM) and mismatched (MM) duplexes. The monolayered beads are used as solid support for the immobilization of oligonucleotide probes containing a single-base variation. Target oligonucleotides hybridize to the probes, forming either PM duplexes or MM duplexes containing a single mismatch. Optimization studies show that PM and MM duplexes are easily discriminated based on their dissociation but not hybridization kinetics under an optimized buffer composition of 100mM NaCl and 50% formamide. Detection of single-nucleotide polymorphism (SNP) using the device is demonstrated within 8 min using four probes containing all the possible single-base variants. The device can easily be modified to integrate multiplexed detection, making high-throughput SNP detection possible.

Miniaturized platforms for the detection of single-nucleotide polymorphisms

Conventional methods for detecting single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in human beings, are mostly limited by their analysis time and throughputs. In contrast, advances in microfabrication technology have led to the development of miniaturized platforms that can potentially provide rapid high-throughput analysis at small sample volumes. This review highlights some of the recent developments in the miniaturization of SNP detection platforms, including microarray-based, bead-based microfluidic and microelectrophoresis-based platforms. Particular attention is paid to their ease of fabrication, analysis time, and level of throughput.

A flexible array format for large-scale, rapid blood group DNA typing

BACKGROUND

Typing for blood group antigens is currently performed by hemagglutination. The necessary reagents are becoming costly and limited in availability, and the methods are labor-intensive. The purpose of this study was to determine the feasibility of the use of large-scale DNA analysis in a microarray as a substitute for blood group typing.

STUDY DESIGN AND METHODS

DNA, extracted from blood samples that had been phenotyped for some of the red blood cell antigens, was analyzed for selected blood group alleles by bead array (BeadChip, (BioArray Solutions Ltd., Warren, NJ) Illumina) [corrected] and by manual polymerase chain reaction (PCR)-based assays. Selected alleles were identified by enzyme-mediated elongation of probes, which were on color-encoded beads assembled into arrays on silicon chips. The performance of a prototype BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] (BLOOD-1) containing single-nucleotide polymorphisms (SNPs) for FYA/B, FY-GATA, DOA/B, COA/B, LWA/B, DIA/B, and SC1/SC2 was verified with DNA from serologically characterized donors. It was then used to analyze more than 400 samples of partially defined phenotype. Samples from Chinese, Ashkenazi, and Thai donors (total n = 227) were tested with BLOOD-1. An expanded BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] with a total of 18 SNPs (36 alleles; SNPs in BLOOD-1 and M/N, S/s, Lu(a)/Lu(b), K/k, FY265[for the Fy(X) polymorphism], Jk(a)/Jk(b), DO323[for Hy], DO350[for Jo(a)], and HgbS) was then evaluated with a subset of previously tested samples from Chinese, Ashkenazi, and New York blood donors (127) and an additional set of samples from Israeli donors (total n = 188).

RESULTS

Results obtained by BeadChip (BioArray Solutions Ltd., Warren, NJ) [corrected] analysis were concordant with those obtained with the manual PCR-restriction fragment length polymorphism, allele-specific PCR, and hemagglutination assays. The frequencies of the alleles in the samples from different ethnic panels were within the expected ranges; however, two new DO alleles were discovered.

CONCLUSION

It has been shown that microarray technology can be used to type DNA and detect new alleles in donor cohorts.