Rapid Multiplex Single Nucleotide Polymorphism Genotyping Based on Single Base Extension Reactions and Color-Coded Beads

Fujimura, Naoko; Kohara, Yoshinobu; OKANO, KAZUNORI; Yohda, Masafumi; Kambara, Hideki

doi:10.1263/jbb.94.368

Cited by 2 publications

(2 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Once the SNPs were selected, three primers were designed for each sequence (forward, reverse and SBE primer extension) and used with Luminex technology (Fujimura et al 2002). A Luminex system 100 IS at the Biotechnology Unit, Centro Internacional de Agricultura Tropical-CIAT was used for this assay.…”

Section: Single Nucleotide Polymorphism-snpmentioning

confidence: 99%

Strategies to develop polymorphic markers for Coffea arabica L.

Zárate¹,

Cristancho²,

Moncada³

2009

Euphytica

View full text Add to dashboard Cite

This study reports the implementation of three strategies for the development of genetic markers and their evaluation in both progenitors of an F2 population used for the construction of a genetic map of Coffea arabica. The strategies were Cleaved Amplified Polymorphic Sequences (CAPS), Single Strand Conformational Polymorphism (SSCP), and sequence analysis predicted Single Nucleotide Polymorphism (SNP). The methodologies were developed from different sequence sources: For CAPS, we used 25 COS sequences derived from Hedyotis spp. and 29 COSII sequences derived from Solanaceae and Rubiaceae species; for SSCP, we used 111 coffee EST sequences, 50 COSII sequences, and 10 C. arabica BAC end sequences. A low polymorphism was identified with the CAPS and SSCP methodologies. A total of 61 SNPs were identified in silico from 5,371 ESTs of coffee and from amplified, cloned, and sequenced COSII markers. Sixteen of these SNPs were validated with Luminex technology and 2 of them were polymorphic in C. arabica genotypes. This study highlights the difficulties of finding polymorphism in the species C. arabica where SNP identification seems to be the best strategy to search for polymorphic markers for this low diversity plant.

show abstract

Section: Single Nucleotide Polymorphism-snpmentioning

confidence: 99%

Strategies to develop polymorphic markers for Coffea arabica L.

Zárate¹,

Cristancho²,

Moncada³

2009

Euphytica

View full text Add to dashboard Cite

show abstract

“…Because the conjugation of probes can be performed simultaneously on many microspheres, probe molecules are used effectively and probe cost per device is decreased. Techniques reported are on the combination of color-coded microspheres and a flow cytometer − and fixed microspheres mounted on the terminal wells of bundled optical fibers. , On the other hand, one way to achieve the fast hybridization reaction is to use microfluidic devices, i.e., a microchannel and a sample flow, and to limit the reaction to a space small enough that the time needed for target molecules to diffuse to probes on a solid surface is short. Many applications of microfluidic devices have been reported. , …”

mentioning

confidence: 99%

Hybridization Reaction Kinetics of DNA Probes on Beads Arrayed in a Capillary Enhanced by Turbulent Flow

Kohara

2003

Anal. Chem.

Self Cite

View full text Add to dashboard Cite

The hybridization reaction kinetics of DNA probes on beads arrayed in a capillary was investigated experimentally and theoretically by using fluid mechanical methods. A device was prepared to contain DNA probes conjugated on 103-microm-diameter beads that were queued in a 150-microm-diameter capillary. The hybridization experiments were performed by introducing sample into the capillary and moving it with a one-way or a reciprocal flow. From the relation between Reynolds number and the resistance coefficient of the system, we found that the flow in the system was turbulent and not laminar as has been said of other microfluidic devices. The reaction efficiency was estimated using a mass-transfer coefficient derived from Chilton-Colburn's analogy. The estimate agreed well with the experimental data. A diffusion equation under laminar assumption was also solved, but this estimated value was 4.0-10.4 times smaller than the experimental data. Using the device achieved a hybridization efficiency as high as approximately 90% in 10 min. It was concluded that the high hybridization performance of the device resulted from turbulent flow and that the flow compensated the slow molecular diffusion. Using this bead-included structure resulted in a rapid and effective reaction at the solid-liquid interface, and the device seems very promising for many future applications.

show abstract

Rapid Multiplex Single Nucleotide Polymorphism Genotyping Based on Single Base Extension Reactions and Color-Coded Beads

Cited by 2 publications

References 12 publications

Strategies to develop polymorphic markers for Coffea arabica L.

Strategies to develop polymorphic markers for Coffea arabica L.

Hybridization Reaction Kinetics of DNA Probes on Beads Arrayed in a Capillary Enhanced by Turbulent Flow

Contact Info

Product

Resources

About