Center for Applied Genomics Laboratory



Subscribe to be notified of changes or updates to this page.

11 + 3 =
Solve this simple math problem and enter the result. E.g. for 1+3, enter 4.

CAG has analyzed genetic data from more than 600,000 individuals, including more than 100,000 CHOP patients/family members. CAG's suite of services covers every major vendor and technology, its research program spans the gamut of the complex/rare disease spectrum, and its translational medicine program has several projects in advanced clinical trials. CAG currently has over 60 active disease projects, including ADHD, asthma and autoimmune disease, autism, Crohn's disease and ulcerative colitis, diabetes and obesity. The lab has 12,000 rare disease samples, and it has resolved the causes for more than 200 rare diseases.

CAG's gene discovery pipeline runs from genotype-sequencing-Sanger/TaqMan through validation, and all steps are CAP/CLIA compliant.

CLIA Laboratory: CAG's sequencing laboratory is CLIA-certified and fully integrated with its CAP/CLIA clinical genotyping program. In one laboratory, CAG operates every major technology and sequencing/genotyping platform from Illumina (including NovaSeq, HiSeq and MiSeq), Thermo Fisher, 10X Chromium systems, Oxford Nano and Bionano, and PacBio.

Omics Services: CAG conducts WES, WGS, 10x-, RNASeq, ChIP-seq, PacBio and Oxford Nanopore long-range sequencing, Bionano, and many more.

Analysts and Software: The team includes 28 doctoral-level analysts whose work is complemented and supported by a suite of research tools, many of which remain industry standard (e.g. ANNOVAR, PennCNV, PennCNV-Seq, ParseCNV).

Throughput: CAG's current capacity is more than 3,000 samples/week across its omics suite, including more than 250 whole genomes per week.

Ancestry and Diversity: In contrast to every other major genome center in the United States, CAG is the only group whose biorepository is not majority Caucasian. African American samples alone constitute more than 35 percent of CAG's cohort.  

Project Highlights

  • Biorepository: Fully-automated biorepository with >600,000 samples
  • Disease Studies: Numerous prominent studies, including novel causal discoveries for ADHD, asthma and autoimmune diseases, autism, IBD, and rare diseases (>200 resolved)
  • Clinical Trials: Mature translational program, with the lead drug, NFC-1 (fasoracetam monohydrate), in advanced trials with several neuro-phenotypes
Hakon Hakonarson Headshot

Hakon Hakonarson, MD, PhD

Director, Center for Applied Genomics
Dr. Hakonarson is director of the Center for Applied Genomics and professor of Pediatrics at the Perelman School of Medicine, University of Pennsylvania. He leads a $40 million commitment from Children’s Hospital of Philadelphia to genomically characterize approximately 100,000 children, an initiative that has gained nationwide attention in the Wall Street Journal, New York Times, Time Magazine, Nature, and Science.