Charles Lee, Ph.D., FACMG

Scientific Director and Professor, The Jackson laboratory for Genomic Medicine

Farmington, CT

The study of structural genomic variation in human biology, evolution and disease

The JAX Cancer Center

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Contact me at: 860-837-2474

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About Charles Lee, Ph.D., FACMG

The research laboratory of Dr. Charles Lee at The Jackson Laboratory for Genomic Medicine develops and applies state-of-the-art technologies to study structural genomic variation and its contribution to human diseases, and vertebrate genome evolution.

Grants, honors and accomplishments

2014 - Thompson Reuters Citation Laureate in Physiology and Medicine

2012 - Fellow, AAAS American Association for the Advancement of Science

2012 - Chen Global Investigator Award, Human Genome Organization (HUGO)

2012 - Vandenberghe Chair Award, Katholic University of Leuven, Belgium

2010 - George W. Brumley, Jr., MD Memorial Award, Duke University, Durham, North Carolina, USA

2008 - C. Thomas Caskey Lectureship, University of South Carolina, Columbia, South Carolina, USA

2007 - American Association for Cancer Research Inaugural Team Award, American Association for Cancer Research

2002 - Stanley L. Robbins Research Award, Department of Pathology, Brigham and Women’s Hospital

1996-1998 - NSERC Postdoctoral Fellowship, Natural Sciences and Engineering Research Council of Canada

1996 - MRC Postdoctoral Fellowship, Medical Research Council of Canada

1994-1996 - AHFMR PhD Studentship, Alberta Heritage Foundation for Medical Research

1994 - 75th Anniversary Faculty of Medicine Scholarship, University of Alberta

Selected Publications

Highlighted Abstract

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Press ReleaseMarch 19, 2020
Announcement: JAX to offer coronavirus testing in Connecticut
The Jackson Laboratory for Genomic Medicine, in partnership with the Connecticut Department of Health, UConn Health and Hartford HealthCare, will provide additional coronavirus testing capacity for Connecticut residents
Research HighlightApril 03, 2018
Calling all structural variants
Structural variants, or SVs, are large DNA sequences that are inserted, inverted, deleted or duplicated within genomes. Finding SVs with short-read seq and analysis methods is difficult, but a new SV identification tool, FusorSV, sets a gold standard for SV detection and analysis.
- Genetic Tools
- Genetics and Genomics
Blog PostMarch 02, 2017
Moving forward with human genomics
HUGO President Charles Lee contemplates HUGO’s place in the global research and clinical communities and its value moving forward.
Research HighlightApril 27, 2016
Know your roots
The Y chromosome is pretty amazing. In humans, it determines male sex, but for a long time it was given short shrift due to its paucity of protein coding, which some researchers found uninteresting. Furthermore, its abundance of short tandem repeats (STRs) made sequencing and subsequent positioning difficult.

Press ReleaseJanuary 30, 2020
Advancing genomics for pediatric orthopedic diseases
Shriners Hospitals for Children and The Jackson Laboratory announce research affiliation for genomic studies of pediatric patients.
- Bones and Joints
- Genetics and Genomics
Search MagazineApril 07, 2017
Addressing gastric cancers, a leading cause of cancer deaths in Asia
Researchers at JAX are making significant breakthroughs in understanding and targeting gastric cancers.
- Cancer/Tumors
- Cancer
Research HighlightSeptember 06, 2016
Benign lung tumors found to have a high rate of mutation in a single gene
A form of benign lung tumor known as pulmonary sclerosing hemangioma (PSH) has been shown to share its origin with malignant lung adenocarcinoma.
Press ReleaseMarch 02, 2016
Charles Lee named president of international Human Genome Organization
The international Human Genome Organisation has named as its new president Charles Lee, Ph.D., FACMG, professor and scientific director of The Jackson Laboratory for Genomic Medicine