Development of a microfluidic platform for integrated DNA sequencing protocols

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Mechanical Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2007

Author dc:creator

• Kumar, Mayank, S.M. Massachusetts Institute of Technology

Advisor dc:contributor.advisor

• Todd Thorsen.

• Mechanical Engineering.

Statement dc:rights

• 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/40371

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/40371