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Hakon Hakonarson, MD, PhD
Hakon Hakonarson Headshot
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.



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Dr. Hakonarson is the founding director of the Center for Applied Genomics (CAG). With an extensive track record in genomics and translational medicine, and more than 750 peer-reviewed published manuscripts, including over 50 in Nature and Nature Genetics combined (H-index 134; citations >82,600), Dr. Hakonarson has served as principal investigator on several significant NIH awards. Under Dr. Hakonarson’s direction, CAG leads or is a principal investigator of numerous consortium efforts, including TOPMed, KidsFirst, eMERGE, EGG, IIBDGC, AGP, EAGLE, and PGC-ADHD. CAG has received more than $200 million in sponsored research funding. 

Prior to founding CAG, Dr. Hakonarson co-created the Icelandic biobank at deCODE genetics, serving as Head of Inflammatory and Pharmacogenomics Research and Vice President of Clinical Sciences at deCODE, and as Chief Scientific Officer for its subsidiary, enCODE. 

Dr. Hakonarson has built the CAG’s research strategy on the foundation of the multi-phase study, A Study of the Genetic Causes of Complex Pediatric Disorders. The study has established broad consent to recruit pediatric patients and their families to participate in genomics research coupled with longitudinal data-collection based on electronic health records and surveys. To date, it has recruited more than 100,000 children and 30,000 parents from CHOP and gathered an additional 450,000 samples through multiple collaborations.

Notable career achievements include:

  • Founded CAG Biobank in 2006, which has become one of the world’s largest and most diverse pediatric biorepositories, hosting 600,000 samples, including more than 130,000 CHOP patients and family members.
  • Senior-authored CAG’s autism gene discovery project, reported in Nature in 2009 and subsequently included among Time magazine’s Top 10 medical breakthroughs of that year.
  • Launched CAG’s Rare Disease sequencing program in 2015, which has since revealed more than 200 rare disorders.
  • Based on several high-profile translational studies, founded NeuroFix in 2014, which included the compound Fasoracetam (NFC-1), an activator of metabotropic glutamate receptors (mGluR). NeuroFix was subsequently acquired by Aevi Genomics, and Fasoracetam has advanced into clinical trials for several neuropsychiatric conditions, including ADHD and autism.

Education and Training

MD, University of Iceland, Reykjavik (1986)

PhD, University of Iceland, Reykjavik (Molecular Biology), 2002

Titles and Academic Titles

Director, Center for Applied Genomics

Endowed Chair in Genomics Research

Professor of Pediatrics

Professional Memberships

Icelandic Medical Association in the United States, President, 1992 -1998; Board Member, 1998 –

Frontiers in Bioscience, Editorial Board Member, 2000 –

Discovery Medicine, Editorial Board Member, 2010 –

Human Genetics and Genomics, Editor in Chief on 300 chapter publication in journal, 2018

Professional Awards

Outstanding Third Year Resident Award for Teaching and Role Model, University of Connecticut, 1992

The James Kangos Memorial Teaching Award for “Excellence in Patient Care by a Pediatric Resident,” Hartford Hospital, University of Connecticut, 1992

Parker B. Francis Science Award, Parker B. Francis Foundation, 1995

Excellence in Science Award for Pediatric Research, University of Iceland, 2002

The 2009 Scripps Genomics Medicine Award: Pioneering Discoveries in Pediatric Genomics, Scripps Research Institute, 2009

Inaugural Mentor Award at CHOP, 2016

Children’s Hospital of Philadelphia Endowed Chair in Genomics Research, 2017 

Publication Highlights

Elia J, Glessner JT, Wang K, Takahashi N, Shtir CJ, Hadley D, Sleiman PM, Zhang H, Kim CE, Robison R, Lyon GJ, Flory JH, Bradfield JP, Imielinski M, Hou C, Frackelton EC, Chiavacci RM, Sakurai T, Rabin C, Middleton FA, Thomas KA, Garris M, Mentch F, Freitag CM, Steinhausen HC, Todorov AA, Reif A, Rothenberger A, Franke B, Mick EO, Roeyers H, Buitelaar J, Lesch KP, Banaschewski T, Ebstein RP, Mulas F, Oades RD, Sergeant J, Sonuga-Barke E, Renner TJ, Romanos M, Romanos J, Warnke A, Walitza S, Meyer J, Pálmason H, Seitz C, Loo SK, Smalley SL, Biederman J, Kent L, Asherson P, Anney RJ, Gaynor JW, Shaw P, Devoto M, White PS, Grant SF, Buxbaum JD, Rapoport JL, Williams NM, Nelson SF, Faraone SV, Hakonarson H. Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet. 2011 Dec; 44(1):78-84. PMID: 22138692
Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA, Wang K, Rafaels NM, Michel S, Bonnelykke K, Zhang H, Kim CE, Frackelton EC, Glessner JT, Hou C, Otieno FG, Santa E, Thomas K, Smith RM, Glaberson WR, Garris M, Chiavacci RM, Beaty TH, Ruczinski I, Orange JM, Allen J, Spergel JM, Grundmeier R, Mathias RA, Christie JD, von Mutius E, Cookson WO, Kabesch M, Moffatt MF, Grunstein MM, Barnes KC, Devoto M, Magnusson M, Li H, Grant SF, Bisgaard H, Hakonarson H. Variants of DENND1B Associated with Asthma in Children. N Engl J Med. 2010 Jan; 7;362 (1):36-44.PMID: 20032318
Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, Game RM, Rudd DS, Zurawiecki D, McDougle CJ, Davis LK, Miller J, Posey DJ, Michaels S, Kolevzon A, Silverman JM, Bernier R, Levy SE, Schultz RT, Dawson G, Owley T, McMahon WM, Wassink TH, Sweeney JA, Nurnberger JI, Coon H, Sutcliffe JS, Minshew NJ, Grant SF, Bucan M, Cook EH, Buxbaum JD, Devlin B, Schellenberg GD, Hakonarson H. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature. 2009 May; 459(7248):569-573. PMID: 19404257; PMC2925224
Wang K, Zhang H, Ma D, Bucan M, Glessner JT, Abrahams BS, Salyakina D, Imielinski M, Bradfield JP, Sleiman PM, Kim CE, Hou C, Frackelton E, Chiavacci R, Takahashi N, Sakurai T, Rappaport E, Lajonchere CM, Munson J, Estes A, Korvatska O, Piven J, Sonnenblick LI, Alvarez Retuerto AI, Herman EI, Dong H, Hutman T, Sigman M, Ozonoff S, Klin A, Owley T, Sweeney JA, Brune CW, Cantor RM, Bernier R, Gilbert JR, Cuccaro ML, McMahon WM, Miller J, State MW, Wassink TH, Coon H, Levy SE, Schultz RT, Nurnberger JI, Haines JL, Sutcliffe JS, Cook EH, Minshew NJ, Buxbaum JD, Dawson G, Grant SF, Geschwind DH, Pericak-Vance MA, Schellenberg GD, Hakonarson H. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature. 2009 May; 459(7246):528-33. PMID: 19404256; PMC2943511
Kugathasan S, Baldassano RN, Bradfield JP, Sleiman PM, Imielinski M, Guthery SL, Cucchiara S, Kim CE, Frackelton EC, Annaiah K, Glessner JT, Santa E, Willson T, Eckert AW, Bonkowski E, Shaner JL, Smith RM, Otieno FG, Peterson N, Abrams DJ, Chiavacci RM, Grundmeier R, Mamula P, Tomer G, Piccoli DA, Monos DS, Annese V, Denson LA, Grant SF, Hakonarson H. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Nature Genet. 2008 Oct; 40:1211-1215 (2008), PMCID: PMC2770437

Personal Interests

Dr. Hakonarson is a keen cyclist, skier, rider, angler, guitarist, and former Icelandic underage soccer player.

Links of Interest