Bouffard Group

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services

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-01G

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). In this role, he oversees many aspects of project management, beginning with initial team contact with collaborative investigators, through sample tracking in the laboratory, processing of raw data from several DNA sequencing platforms, to the final delivery of high quality and value-added DNA sequence data.

Several NISC staff scientists meet with each investigator to review project proposals and select experimental strategies that are technically feasible, cost-effective and designed to generate sufficient quantities of data to properly address the biological questions of interest. Staying abreast of current advances in molecular biology allows NISC to use the most powerful tools to tackle some of today's most challenging medical and biological questions.

Over the past four years, NISC has successfully transformed from a highly productive Sanger DNA sequencing center to a contemporary operation using the best of current next-generation, or NextGen, sequencing and optical mapping technologies. NextGen DNA sequencing technologies bring challenges associated with large increases in data volume and complexity that are being met with significant investments in leading edge information storage and computing technologies. As laboratory and computational methods evolve, the Bioinformatics Group works continuously assimilates them into a production environment where stability must be balanced with potential improvements in data quality and quantity. A sophisticated Laboratory Information Management System (LIMS) allows tracking of samples and derivatives, such as libraries, through the extensive use of barcoded containers and reagents, ensuring that the final sequence data can be connected to the original DNA or RNA source as accurately as possible. A customized workflow insures the prioritization and efficient, timely processing of an increasing number of samples. Numerous tools that capture primary analysis statistics that allow for both manual and automated quality review processes complement the LIMS.

The end results of the primary DNA sequence analysis are DNA basecalls and associated quality scores. Numerous secondary analysis pipelines are being developed to connect the sequence data to biological insights. Among these is a high-throughput whole exome sequencing (WES) process that results in reporting of statistically significant genetic variants that can be linked to medical phenotypes of interest. Another area of active development is the use of NextGen sequencing for microbiome population survey and microbial genome sequencing and annotation, particularly in response to clinical outbreaks of antibiotic-resistant pathogens.

The Bioinformatics Group is integral to NISC's maintenance of an extremely productive DNA sequencing pipeline that optimizes current technologies to deliver large quantities of high-quality data in the most cost-effective manner.


Dr. Gerard Bouffard began his career in the biological sciences with an interest in Veterinary Medicine.  After graduating cum laude with a B.S. in animal sciences from the University of Vermont, his focus shifted towards research in molecular biology. Several years as a laboratory technician in the Pathology Department of the University of Vermont motivated him to pursue graduate studies.

In 1994, he earned a Ph.D. in microbiology from the George Washington University, where he combined his interests in early genome sequencing of the Escherichia coli genome with the nascent field of bioinformatics. He used restriction endonuclease mapping data with published DNA sequence fragments to target and close gaps in the genomic sequence, leading to the discovery of two new genes, which he synthesized and biochemically characterized.

As a postdoctoral fellow in the laboratory of Eric D. Green, M.D., Ph.D., currently NHGRI director, Dr. Bouffard performed data management and analysis for a YAC-based, STS content physical map of human chromosome 7, which greatly expedited gene discovery on this chromosome, and directed sequencing efforts in the early days of the Human Genome Project.

In 1997, he co-founded the NIH Intramural Sequencing Center (NISC) as director of the Bioinformatics Group, where he quickly established tools for sample tracking, data management and data analysis for a state-of-the-art DNA production facility. In the 14 years since its establishment, Dr. Bouffard has worked closely with colleagues to insure that NISC bioinformatics capabilities remain at the cutting edge to meet the demands and exercise the capabilities of revolutionary DNA sequencing technologies and advanced information technologies. NISC remains a premier facility for the rapid, accurate and cost-effective generation of DNA sequence data.

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Last Updated: January 5, 2015