Research Investigators

Gerard Bouffard, Ph.D.

Gerard Bouffard
Bioinformatics Group

Associate Investigator
NIH Intramural Sequencing Center

B.S. University of Vermont, 1984
Ph.D. George Washington University, 1994

phone (301) 435-6154
fax (301) 435-6170
Room 5N-01L, MSC 9400
ROCKVILLE, MD 20892-9400

Selected Publications

NIH Intramural Sequencing Center []

The Mammalian Gene Collection []

Hembase: Hematopoietic Cell Expression Database []

Dr. Bouffard directs the Bioinformatics Group at the NIH Intramural Sequencing Center (NISC). He oversees many aspects of project management, beginning with initial team contact and developing experimental design strategies with collaborative investigators. He and his staff have built and continue to develop a robust system for recording the receipt of biological samples and relevant metadata, laboratory process tracking, and raw DNA sequence data collection and processing. Working closely with NISC personnel, numerous quality control and integrity monitoring measures have been implemented, allowing for thorough review, reporting and process control.

To cope with NISC's large sequencing throughput and data generation, Dr. Bouffard has directed the development of a customized Laboratory Information Management System (LIMS). This system controls the flow of samples and materials through the laboratory, identifies reagents and equipment with barcodes, and records the people and tools involved at every stage. Efficient flow control, flexibility to prioritize tasks, and backtracking capability are achieved thereby. More recent enhancements have included the capabilities to capture and report the costs of reagents and services used for all projects. As a result, budgeting and cost projections have improved significantly, while allowing true cost comparisons of protocols and projects.

Since NISC's founding in 1997, Dr. Bouffard has played an active leadership role in planning and overseeing operational changes in response to rapid developments in molecular biology, DNA sequencing, and information technologies. The first large-scale sequencing project of the mouse genome using Sanger sequencing of BAC-based (bacterial artificial chromosome) shotgun libraries evolved, over time, into the widely-recognized Comparative Vertebrate Sequencing Program. This project targeted specific subgenomic regions across as many as 80 different species of primates, other mammals, marsupials, monotremes, birds, and fish. In addition, a number of significant scientific publications have been based on NISC's high-quality comparative genomic sequence data in the ENCODE (ENCyclopedia Of DNA Elements) project. Both established and novel technologies were used in identifying all the functional elements in ?1 percent of the human genome.

Shifting its emphasis from interspecies comparisons to the detection of medically significant human genetic variations, NISC established a robust PCR-based medical sequencing pipeline that targets specific genes and regions of interest. Extensive changes were made to the LIMS and DNA sequencing pipeline to accommodate the accurate tracking of over 2.5 million amplicons from over six thousand samples. In ClinSeq, the largest among several well-known projects, ?1,000 volunteers are providing DNA samples and undergoing laboratory tests aimed at understanding the genetic components of cardiovascular disease.

With the start of "NextGen" production DNA sequencing at NISC, attention has shifted from the well-established shotgun clone and PCR amplicon-based Sanger sequencing processes to the rapid design and construction of entirely new pipelines. Years of experience with Sanger sequencing have enabled Dr. Bouffard's group to anticipate the data and metadata collection needs of large-scale sequencing projects, and thereby implement practical approaches to process automation, historical tracking, and real-time quality assurance. The establishment of robust systems has been crucial to the rapid and successful deployment of sequencing technologies into exciting new areas, such as chromatin immunoprecipitation (ChIP-Seq), RNA sequencing, and both whole exome and whole genome sequencing. Use of new and improved interfaces and information technologies has positioned Dr. Bouffard's group to meet future challenges of increased sequence data complexity and volume.

Dr. Bouffard's graduate studies and continued interest are in the microbiological field. As a participant in the NIH Intramural Skin Microbiome Consortium, which endeavors to catalog the variety and relative abundance of microbial populations in and on the skin, he is actively involved with the study's microbial survey, the development of a whole-genome reference sequence, and the metagenomic sequencing of human skin samples.

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Last Updated: May 18, 2014