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Todd Thorsen. Kumar, Mayank, S.M. Massachusetts Institute of Technology Massachusetts Institute of Technology. Dept. of Mechanical Engineering. Massachusetts Institute of Technology. Department of Mechanical Engineering 2008-02-27T22:15:30Z 2008-02-27T22:15:30Z 2007 2007 http://hdl.handle.net/1721.1/40371 190863819 Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2007. Includes bibliographical references. This thesis describes the design and development of a microfluidic platform to reduce costs and improve the quality of in the DNA sequencing methodology currently implemented at the Broad Institute in Cambridge, Massachusetts. The Sequencing Center at the Broad Institute currently generates an average of 130 million bases per day with an average read length of 800. This is enabled by the successful preparation and detection of over 97,000 unique samples. Most of the cost per sample is tied up in expensive proprietary reagents utilized in the various reactions comprising the preparation process. Through the application of microfluidics, the possibility of drastically scaling down the amount of proprietary reagents is explored. Stamp-sized elastomeric polydimethylsiloxane (PDMS) microfluidic devices were developed and microfluidic sample manipulation techniques were standardized. Using these devices and techniques, an attempt was made to adapt the various components of the sequencing process to the microfluidic platform. Work within the scope of this thesis is focused on the adaptation of the commercial sequencing protocols, which are labor intensive, consume costly reagents and serve as limitations for high-throughput parallelization of the process. (cont.) The first is the amplification reaction. By scaling down the process from a plate-based format to an integrated microfluidic device, amplification reagent consumption was reduced by two orders of magnitude while maintaining the quality and length of the sequencing reads (with the subsequent sequencing reaction run off chip). As a follow up project, an attempt was made to scale down the Sequencing Reaction, which, in spite of limitations, suggested a good path toward the eventual development of an integrated microfluidic device for the preparation of running the complete sequencing reaction protocol on-chip. by Mayank Kumar. S.M. 91 p. eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Mechanical Engineering. Development of a microfluidic platform for integrated DNA sequencing protocols Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="fe510c5a-192b-4b59-bace-b54620033424"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Development of a microfluidic platform for integrated DNA sequencing protocols</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2007</PublicationDate> <Authors> <Author> <DisplayName>Kumar, Mayank, S.M. Massachusetts Institute of Technology</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Mechanical Engineering.</Keyword> <Abstract>This thesis describes the design and development of a microfluidic platform to reduce costs and improve the quality of in the DNA sequencing methodology currently implemented at the Broad Institute in Cambridge, Massachusetts. The Sequencing Center at the Broad Institute currently generates an average of 130 million bases per day with an average read length of 800. This is enabled by the successful preparation and detection of over 97,000 unique samples. Most of the cost per sample is tied up in expensive proprietary reagents utilized in the various reactions comprising the preparation process. Through the application of microfluidics, the possibility of drastically scaling down the amount of proprietary reagents is explored. Stamp-sized elastomeric polydimethylsiloxane (PDMS) microfluidic devices were developed and microfluidic sample manipulation techniques were standardized. Using these devices and techniques, an attempt was made to adapt the various components of the sequencing process to the microfluidic platform. Work within the scope of this thesis is focused on the adaptation of the commercial sequencing protocols, which are labor intensive, consume costly reagents and serve as limitations for high-throughput parallelization of the process.</Abstract> <Abstract>(cont.) The first is the amplification reaction. By scaling down the process from a plate-based format to an integrated microfluidic device, amplification reagent consumption was reduced by two orders of magnitude while maintaining the quality and length of the sequencing reads (with the subsequent sequencing reaction run off chip). As a follow up project, an attempt was made to scale down the Sequencing Reaction, which, in spite of limitations, suggested a good path toward the eventual development of an integrated microfluidic device for the preparation of running the complete sequencing reaction protocol on-chip.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>