Microfabricated integrated DNA analysis system

Abstract

Methods and apparatus for genome analysis are provided. A microfabricated structure including a microfluidic distribution channel is configured to distribute microreactor elements having copies of a sequencing template into a plurality of microfabricated thermal cycling chambers. A microreactor element may include a microcarrier element carrying the multiple copies of the sequencing template. The microcarrier element may comprise a microsphere. An autovalve at an exit port of a thermal cycling chamber, an optical scanner, or a timing arrangement may be used to ensure that only one microsphere will flow into one thermal cycling chamber wherein thermal cycling extension fragments are produced. The extension products are captured, purified, and concentrated in an integrated oligonucleotide gel capture chamber. A microfabricated component separation apparatus is used to analyze the purified extension fragments. The microfabricated structure may be used in a process for performing sequencing and other genetic analysis of DNA or RNA.

Description

CROSS REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation of and claims priority to U.S. application Ser. No. 11 / 139,018, filed May 25, 2005 (Atty. Docket No. UCALP054), titled “MICROFABRICATED INTEGRATED DNA ANALYSIS SYSTEM,” which claims the benefit under 35 U.S.C. 119(e) from Provisional U.S. Patent Application No. 60 / 576,102, filed Jun. 1, 2004 (Atty. Docket No. UCALP054P), entitled “MICROBEAD INTEGRATED DNA ANALYSIS SYSTEM (MINDS),” all of which are incorporated herein by reference for all purposes.STATEMENT REGARDING GOVERNMENTAL SUPPORT[0002]The invention was made with government support under Grant Numbers AI056472, CA77664, and HG001399 awarded by the National Institute of Health. The government has certain rights in this invention.BACKGROUND[0003]1. Field of Invention[0004]The present invention relates to microfabricated and microfluidic structures. In one example, the present invention relates to a microfabricated system and method for genome sequenc...

AI Technical Summary

Benefits of technology

This approach automates and integrates laborious steps, reducing the need for robotic operations, significantly lowering costs, time, and space requirements while enabling efficient production and analysis of sequencing extension fragments.

Problems solved by technology

The plate and grow (step 108), and the pick, grow and extract steps (step 110), however, are problematic.

These steps have remained refractory to miniaturization and integration.

However, this is a problem because no less than 30 million colonies must be picked and grown to produce a sequencing template for a genome.

Furthermore, the minimum quantities of materials prepared by such robotic technologies are orders of magnitude more than that required by modern microfabricated CE analysis systems.

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