BioMed Central Page 1 of 1 (page number not for citation purposes) BMC Bioinformatics Open Access Poster presentation NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping Colin Clarke*, Michael Malecha and Selly Saini Address: Cranfield University, Department of Analytical Science and Informatics (DASI). Cranfield University, Barton Rd, Silsoe, Bedfordshire, MK45 4DT, UK. Email: Colin Clarke* - [email protected] * Corresponding author We report the development of a novel computational system, NanoSNP. The system is based around semiconduc- tor nanocrystals or quantum dots (QDs), QDs herald the arrival of bio-nanotechnology and due to inherent advantages are currently replacing organic dyes as the probe of choice in fluorescent measurement for biology. QD encoded microspheres consist of various sizes of QD at various intensities polymerized within a latex or polysty- rene bead to yield a unique spectral signature. To facilitate high-throughput SNP genotyping using QD encoded microspheres we have integrated bioinformatics and spectral analysis to create a user friendly system. Features of the system include SNP selection, QD microsphere design, oligonucleotide conjugate sequence output and QD microsphere identification. For experimental design the system is integrated with HGVbase allowing the user to select the SNPs of interest for a population. A panel of QD encoded microspheres is designed by the system, each microsphere assigned to a SNP allele. Once the QD encoded microspheres have been prepared in the laboratory. An allele specific oligonucleotide is prepared and conjugated to its respective QD encoded microsphere. During the experimental stage of the procedure described by Mahoney et al 2003, DNA is extracted from the sample, purified and subjected to multiplex PCR around each SNP location. The QD encoded microspheres are added to the amplified PCR products, the oligo conjugates on the sur- face of the QD microsphere hybridise to complementary PCR product only when there is a prefect match. Hybridi- sation is detected via a biotinstreptavidin system and QD encoded microsphere spectra are resolved using a flow cytometer. NanoSNP identifies hybridised spectra from a database of theoretical spectra thus identifying the allele present creating a SNP profile for each sample. We believe that this system and integration with bioinformatics recourses represents the future of real time, automated and user friendly genetic determination due to advantages such throughput, accuracy, automation and simplified instrumentation. from BioSysBio: Bioinformatics and Systems Biology Conference Edinburgh, UK, 14–15 July 2005 Published: 21 September 2005 BMC Bioinformatics 2005, 6(Suppl 3):P5 <supplement> <title><p>BioSysBio: Bioinformatics and Systems Biology Conference</p></title> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/files/pdf/1471-2105-6-S3-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1471-2105-6-S3-info.pdf</url> </supplement>

NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping

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Page 1: NanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotyping

BioMed Central

Page 1 of 1(page number not for citation purposes)

BMC Bioinformatics

Open AccessPoster presentationNanoSNP: A computational platform for high throughput Quantum Dot encoded microsphere SNP genotypingColin Clarke*, Michael Malecha and Selly Saini

Address: Cranfield University, Department of Analytical Science and Informatics (DASI). Cranfield University, Barton Rd, Silsoe, Bedfordshire, MK45 4DT, UK.

Email: Colin Clarke* - [email protected]

* Corresponding author

We report the development of a novel computational sys-tem, NanoSNP. The system is based around semiconduc-tor nanocrystals or quantum dots (QDs), QDs herald thearrival of bio-nanotechnology and due to inherent advan-tages are currently replacing organic dyes as the probe ofchoice in fluorescent measurement for biology. QDencoded microspheres consist of various sizes of QD atvarious intensities polymerized within a latex or polysty-rene bead to yield a unique spectral signature. To facilitatehigh-throughput SNP genotyping using QD encodedmicrospheres we have integrated bioinformatics and spec-tral analysis to create a user friendly system. Features ofthe system include SNP selection, QD microspheredesign, oligonucleotide conjugate sequence output andQD microsphere identification.

For experimental design the system is integrated withHGVbase allowing the user to select the SNPs of interestfor a population. A panel of QD encoded microspheres isdesigned by the system, each microsphere assigned to aSNP allele. Once the QD encoded microspheres havebeen prepared in the laboratory. An allele specific oligo-nucleotide is prepared and conjugated to its respectiveQD encoded microsphere.

During the experimental stage of the procedure describedby Mahoney et al 2003, DNA is extracted from the sample,purified and subjected to multiplex PCR around each SNPlocation. The QD encoded microspheres are added to theamplified PCR products, the oligo conjugates on the sur-face of the QD microsphere hybridise to complementaryPCR product only when there is a prefect match. Hybridi-sation is detected via a biotinstreptavidin system and QDencoded microsphere spectra are resolved using a flow

cytometer. NanoSNP identifies hybridised spectra from adatabase of theoretical spectra thus identifying the allelepresent creating a SNP profile for each sample. We believethat this system and integration with bioinformaticsrecourses represents the future of real time, automatedand user friendly genetic determination due to advantagessuch throughput, accuracy, automation and simplifiedinstrumentation.

from BioSysBio: Bioinformatics and Systems Biology ConferenceEdinburgh, UK, 14–15 July 2005

Published: 21 September 2005

BMC Bioinformatics 2005, 6(Suppl 3):P5<supplement> <title><p>BioSysBio: Bioinformatics and Systems Biology Conference</p></title> <note>Meeting abstracts – A single PDF containing all abstracts in this Supplement is available <a href="http://www.biomedcentral.com/content/files/pdf/1471-2105-6-S3-full.pdf">here</a>.</note> <url>http://www.biomedcentral.com/content/pdf/1471-2105-6-S3-info.pdf</url> </supplement>

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