Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification

Ye, F; Li, M S; Taylor, J D; Nguyen, Quoc-Tuan; Colton, Heidi M.; Casey, Warren; Wagner, Michael J.; Weiner, Michael P.; Chen, J

doi:10.1002/humu.28

Cited by 136 publications

(84 citation statements)

References 30 publications

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“…Nevertheless, the m.12706T4C mutation is expected to be detected even in the presence of mtSNP m.12705C4T, because four probes were designed to detect the mutant and wild-type mtDNA with or without the polymorphic sites. Therefore, this system can be used for the screening of various mtDNA point mutations, even in the presence of 23,24 Both the MFI values for the two corresponding alleles were displayed on scatter diagrams. The mutations were considered to be heteroplasmic when both the mutant and wild-type signal intensities were detected above the cutoff values.…”

Section: Materials and Methods Patientsmentioning

confidence: 99%

Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss

et al. 2010

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Sensorineural hearing loss (HL) is one of the most frequent clinical features in patients with mitochondrial diseases caused by mitochondrial DNA (mtDNA) mutations, and hearing is impaired in over half of all cases with mitochondrial disorders. This study analyzed 373 patients with suspected hereditary HL using an extensive and rapid suspension-array screening system for 29 major mtDNA mutations, including the m.1555A4G homoplasmic mutation in the MT-RNR1 gene, which causes non-syndromic sensorineural HL and aminoglycoside-induced HL, and the m.3243A4G heteroplasmic mutation in the MT-TL1 gene. This method is rapid and suitable for large-scale screening because universal 96-well plates are available for use, and because an analysis of each plate can be completed within 1 h. This system detected five different mtDNA mutations in 24 of the 373 (6.4%) patients. The m.1555A4G and m.3243A4G mutations were detected in 11 (2.9%) and 9 (2.7%) patients, respectively. In addition, three mutations, that is, m.8348A4G in the MT-TK gene, m.11778G4A in the MT-ND4 gene and 15498G4A in the MT-CYB gene were detected in one patient for each. This screening system is useful for the genetic diagnosis and epidemiological study of both syndromic and non-syndromic HL.

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Section: Materials and Methods Patientsmentioning

confidence: 99%

Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss

et al. 2010

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“…The microspheres can be purchased in 100 machine-readable fluorescent colors for the Luminex xMAP platform used in this study, and each can be bound to a unique molecular probe so that up to 100 different probes can be employed in a single assay. As with microarrays, bulk genomic DNA can be labeled with a single fluorophore and hybridized simultaneously with a set of different probes (Ye et al 2001). Bead array technology employs a flow cytometer to draw up the thousands of microspheres used in each hybridization (hundreds of each bead color/probe combination) and individually determine 2 fluorescent signals from each: (1) the microsphere color, which identifies the probe; (2) the fluorescent intensity of the reporter fluorophore, attached to that bead via hybridization of fluorescently labeled DNA, which quantitatively informs as to the presence of specifically targeted DNA in the sample.…”

Section: Introductionmentioning

confidence: 99%

Application of bead array technology to community dynamics of marine phytoplankton

Ellison

Burton²

2005

Mar. Ecol. Prog. Ser.

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Studies of the dynamics of marine microplanktonic systems have been hampered by a lack of high-throughput technologies for the simultaneous identification and quantification of the many taxa comprising such communities. To address this problem, we describe a DNA-hybridizationbased method of analysis employing bead array technology. Species-and/or genus-specific probes for 8 phytoplankton taxa were designed and applied to the microplankton community sampled from coastal waters off La Jolla, California, over an exploratory time series 10 d in length. Bulk DNA extractions from 1 l of seawater were used without PCR amplification. Taxa analyzed comprised 4 dinoflagellates, 3 diatoms, and 1 coccolithophorid. The results demonstrated that specifically targeted oligonucleotide probes can be used in this fashion with a high degree of binding-specificity, dependent on hybridization temperature, and that standard curves relative to target-cell concentration can be constructed. The use of 2 different probes for each taxon can provide added confidence that probes are taxon-specific. Further, single-species assays and multiplexed assays were generally in good agreement, as were assays of replicate seawater samples. Once sets of probes are developed for particular groups of taxa, the bead array system appears to provide a technological platform with great promise for high-throughput analyses of microplanktonic communities.

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“…Most solid-phase-mediated methods require a clean-up because the substrates of the allele-specific reaction can produce false-positive signals and complicate genotype scoring. Examples are mass spectrometry, 12,[16][17][18][19][20][21] zip-code technology, 22,23 Illumina color beads, 24,25 Orchid SNP-IT technology 11 and all hybridization based methods. 26,27 Product detection and identification can be performed in many different ways.…”

Section: Detection and Identification Of Allele-specific Productsmentioning

confidence: 99%

“…22,24,25,84 After allele-specific reactions products are hybridized to the microbeads. The hybridization links the products of an SNP to microbeads with a unique signature.…”

Section: Fluorescence Coded Microbeads As Supportersmentioning

confidence: 99%

Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput

2003

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The large number of single nucleotide polymorphism (SNP) markers available in the public databases makes studies of association and fine mapping of disease loci very practical. To provide information for researchers who do not follow SNP genotyping technologies but need to use them for their research, we review here recent developments in the fields. We start with a general description of SNP typing protocols and follow this with a summary of current methods for each step of the protocol and point out the unique features and weaknesses of these techniques as well as comparing the cost and throughput structures of the technologies. Finally, we describe some popular techniques and the applications that are suitable for these techniques.

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Fluorescent microsphere-based readout technology for multiplexed human single nucleotide polymorphism analysis and bacterial identification

Cited by 136 publications

References 30 publications

Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss

Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss

Application of bead array technology to community dynamics of marine phytoplankton

Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput

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