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What’s the best thing you’ve done to cut sequencing costs without sacrificing quality?

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A.I run an academic core sequencing lab. Previously, we operated two ABI 3700 sequencers that were purchased primarily with institutional funds. Last year, we upgraded to two ABI 3730/3730xl sequencers but chose to lease the instruments rather than purchase outright. This move has more than paid for itself and we are enjoying substantial improvements in quality, read length, speed, and reliability. At the same time, our reagents costs have dropped significantly, allowing overall costs to users to drop.

Alfred L. George, Jr.

Scientific Director, DNA Sequencing Facility

Vanderbilt University

 

A.In the cost-cutting department, I’d say the most dramatic thing that we’ve done lately is to cut our sequencing reaction volume by 50 percent (6 to 3 µl). As you might predict, this saves us about 50 percent — no quality sacrificed whatsoever.

Elaine R. Mardis

Co-Director,

Genome Sequencing Center

Washington University School of Medicine

 

A.Our core sequencing facility has implemented several technology changes, such as automation (Biomek FX) and advanced instrumentation (ABI 3730xl). With these new methods in place we have decreased our reagent costs dramatically. For our ABI 3730xl, the reagent cost of one single pass sequencing reaction is $1.46 CAD, which is down considerably from $5.00 CAD using an ABI 3700. The key cost-cutting measure is the use of a 1:32 ABI BigDye Terminator mix dilution.

Constantine Christopoulos

DNA Sequencing Facility

Hospital for Sick Children

 

A.The best thing we have done to reduce costs is to use less of the commercial DNA sequencing reagents. On the ABI 3700s one can use ~1/20th while scaling the volume down to 5-8µl, and with the ABI 3730s as little as ~1/32nd can be used routinely. Since this reagent is the major cost of sequencing, the savings is approximately proportional to the fraction of sequencing mix used.

Bruce A. Roe

Advanced Center for Genome Technology

University of Oklahoma

 

A.Outsource to Macrogen. Firstly, it supports one of the facilities that was involved in sequencing the human genome. Secondly, they are very good and cost effective. Thirdly, hands down they have one of the best customer services I have ever experienced in and out of science!

Shu Hui Chen

Dept. of Biological Sciences

University of Illinois at Chicago

 

A.I spent a lot of time to develop various protocols for sequencing difficult templates (GC-rich, all kinds of repeats, hairpins, etc.) This saves us a lot of time and effort when we face such issues.

Jan Kieleczawa

Wyeth Research

 

A.High-throughput analysis using capillary DNA genetic analyzers (such as the ABI 3100) [has] allowed rapid fingerprinting of BAC and cosmid clones. Using specialized software (GenoProfiler) to rapidly type these fingerprints, and to use fluorescence for restriction enzyme pattern differentiation, files sufficient for reading and assembly by the FPC program can be generated to build ordered clone sets. This reduces sequence redundancy several-fold and limits sequencing problems to the ordered clones by location, rather than representing a random non-positioned clone (until further analysis).

Gerard R. Lazo

USDA ARS Western Regional Research Center