Harvard Group Develops Low-Cost DNA Sequencing Technique


By Kevin Davies Bio-IT World

A team of researchers at Harvard Medical School led by George Church has developed a new and relatively inexpensive method to DNA sequencing that utilizes readily available tools and reagents.

The Harvard team reported its results in Science in the same week that researchers at 454 Life Sciences published an alternative method for DNA sequencing in Nature. Its technology has been licensed to Agencourt Bioscience Corporation.

Unlike the 454 approach, the method developed by Church and colleagues is a form of DNA resequencing – that is, it requires a reference sequence with which to compare the new sequence, because each fragment of DNA sequenced is so short. Nevertheless, many likely lab applications – from genotyping haplotypes in a disease study, searching for mutations in cancer resistance, or as in the Science paper, identifying microbial strain variants – would fall into this category.

Church calculates that his group’s method offers a ninefold reduction in the theoretical cost of sequencing a human genome – from an estimated $20 million to about $2.2 million. “These developments give the feeling that improvements are coming very quickly,” says Church. “The [desirable] cost of $1,000 for a human genome should allow prioritization of detailed diagnostics and therapeutics, as is already happening with cancer.”

The Harvard group tested its method by sequencing a novel strain of the bacterium Escherichia coli. Similar to 454, the method relies on elongating small DNA fragments on tiny micron-diameter beads. Church’s group packs some 14 million DNA-coated beads onto a slide the size of a dime.

The Church method adapts a commonly available microscope with a digital camera. Short nine-base tags, with each of the four bases present at a specific query location, are ligated onto the bead-attached DNA fragments. Each tag has a different fluorescent dye attached, depending on the base at the query position. The fluorescence data are recorded, and an algorithm aligns the short DNA sequences onto the appropriate reference sequence. The authors append detailed supplemental material, methods, and pricing to allow other researchers to assemble similar sequencing systems.

The Harvard group sees ample room for improvement, in part by increasing the density of beads on a slide. They write: “We collected ~786 gigabits of image data from which we gleaned only ~60 megabits of sequence. This sparsity – one useful bit of information per 10,000 bits collected – is a ripe area for improvement. The natural limit of this direction is single-pixel sequencing, in which the commonplace analogy between bytes and bases will be at its most manifest.”

Featured Report: Shendure, J. et al. “Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome.” Science online 4 August, 2005. DOI: 10.1126/science.1117389 

Click here to login and leave a comment.  

0 Comments

Add Comment

Text Only 2000 character limit

Page 1 of 1

White Papers & Special Reports

thomson reuters image
Biomarkers: An Indispensible Addition to the Drug Development Toolkit
Examining the Potential of Biomarkers
Sponsored by Thomson Reuters

Biomarkers are becoming an essential part of clinical development. In this white paper, Thomson Reuters provides insight from experts in industry and academia, and explores the role of biomarkers as evaluative tools in improving clinical research and the challenges this presents.

Discover the potential of biomarkers to:

  • Improve decision making
  • Accelerate drug development
  • Reduce development costs


BlueArc_Scientific Data
Scientific Data Lifecycle Management: Preparing for Storage in an Uncertain Future
Sponsored by BlueArc

Managing vast and overwhelming streams of gene sequencing data today requires ultra-high performance systems and processes. With continued rapid advancement and improvements in gene sequencing, expect tomorrow’s instruments to output quantities of genomic information that will dwarf current levels. Help your organization maintain data control and prepare for the future of sequencing through this informative paper that discusses:

  • The information technology challenges of gene sequencing
  • “Intelligent” methods for data management and customization
  • System survival tips... Deciding what data to keep or delete
  • New tools to keep scientists ahead of impending data torrents


SAS Managed image
Managed Innovation, Assured Compliance
Developing, executing and managing the transformation, analysis and submission of clinical research data with SAS® Drug Development
Sponsored by SAS
Get better products to market faster. Download this white paper to discover the top ten challenges facing life science executives and how to overcome them. See how SAS Drug Development transforms clinical data into true innovation.


Life Science Webcasts & Podcasts

Presented by Trade Commission of Spain

Spain Biotech: An Engine for Economic Change 

TCS podcastDiscover how Spain is focusing on biotechnology to be an engine for economic change through gradual internationalization, development and technology transfer.

Regional governments are actively investing in public and private biology research and promoting the creation of knowledge-based companies. Spain’s human capital combined with aggressive investment in biotech research and infrastructure has led to the creation of bio-clusters.

Today, there are nearly 700 Spanish companies engaged in biotechnology, with almost 50 percent growth in funding devoted to research. In fact, spending on internal R & D in biotechnology has grown 46 percent and is close to 300 million Euros.

Access the podcast 

 



More Podcasts

Job Openings

saic_logo

MANAGER, SCIENTIFIC COMPUTING & PROGRAMMING
(Bioinformatics Manager)
SAIC-Frederick, Inc has an exciting opportunity for a Manager, Scientific Computing & Programming - Core Genoytyping Facility in Gaithersburg, Maryland.  In this role, you will lead the Bioinformatics & Analysis Group.
Master’s or equivalent required.  PhD preferred. Six years experience in development of scientific programs in high-performance computing environment including five years supporting scientific research in computational chemistry, biology, or genetics, & two years supervisory experience.  View complete job posting & apply: www.saic-frederick.com. Position #146945.

For reprints and/or copyright permission, please contact The YGS Group, 1808 Colonial Village Lane, Lancaster, PA;

(717) 399-1900 ext. 125, or via email to Ashley.Zander@theYGSgroup.com.