John Connolly

John trained as neuropsychologist at Trinity College Dublin, where he studied stroke rehabilitation and neural correlates of attention deficit hyperactivity disorder (ADHD). Following the completion of his Ph.D., he joined Cold Spring Harbor Laboratory (CSHL) to lead development of Genes to Cognition Online, an online resource that examines how the brain, biochemicals, and genes interact to produce neuropsychiatric disorders such as autism, ADHD, depression, and schizophrenia. He also created 3D Brain, an award-winning app that has been downloaded more than 3 million times.

Since joining CAG in 2010, he has led a range of neuropsychiatric studies, with a focus on autism and ADHD. He also maintained a lead role in the Philadelphia Neurodevelopmental Cohort project, which integrates deeply-characterized data from 9,500 children and young adults that includes electronic health records (EHRs), neuroimaging, genotype, sequencing, and methylation profiles. Similarly, he is a project leader for CHOP as part of our collaboration with the electronic Medical Records and Genomics (eMERGE) Consortium, a major NHGRI 9-Center initiative to integrate EHRs and genomics.


CAG Publications

An updated list of publications is available at My NCBI Collections.
Relevant papers include:

The Philadelphia Neurodevelopmental Cohort: constructing a deep phenotyping collaborative.
Calkins ME, Merikangas KR, Moore TM, Burstein M, Behr MA, Satterthwaite TD, Ruparel K, Wolf DH, Roalf DR, Mentch FD, Qiu H, Chiavacci R, Connolly JJ, Sleiman PM, Gur RC, Hakonarson H, Gur RE.
J Child Psychol Psychiatry. 2015 Apr 8. doi: 10.1111/jcpp.12416. [Epub ahead of print]

The Philadelphia Neurodevelopmental Cohort: A publicly available resource for the study of normal and abnormal brain development in youth.
Satterthwaite TD, Connolly JJ, Ruparel K, Calkins ME, Jackson C, Elliott MA, Roalf DR, Ryan Hopsona KP, Behr M, Qiu H, Mentch FD, Chiavacci R, Sleiman PM, Gur RC, Hakonarson H, Gur RE.
Neuroimage. 2015 Mar 31. doi:pii: S1053-8119(15)00252-9. 10.1016/j.neuroimage.2015.03.056. [Epub ahead of print]

Practical guidance on informed consent for pediatric participants in a biorepository.
Brothers KB, Lynch JA, Aufox SA, Connolly JJ, Gelb BD, Holm IA, Sanderson SC, McCormick JB, Williams JL, Wolf WA, Antommaria AH, Clayton EW.
Mayo Clin Proc. 2014 Nov;89(11):1471-80. doi: 10.1016/j.mayocp.2014.07.006. Epub 2014 Sep 26. No abstract available.

Etiology of autism spectrum disorder: a genomics perspective.
Connolly JJ, Hakonarson H.
Curr Psychiatry Rep. 2014 Nov;16(11):501. doi: 10.1007/s11920-014-0501-9. Review.

The psychosis spectrum in a young U.S. community sample: findings from the Philadelphia Neurodevelopmental Cohort.
Calkins ME, Moore TM, Merikangas KR, Burstein M, Satterthwaite TD, Bilker WB, Ruparel K, Chiavacci R, Wolf DH, Mentch F, Qiu H, Connolly JJ, Sleiman PA, Hakonarson H, Gur RC, Gur RE.
World Psychiatry. 2014 Oct;13(3):296-305. doi: 10.1002/wps.20152.

Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems.
Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ, Brautbar A, Brilliant MH, Carrell DS, Connolly JJ, Crosslin DR, Doheny KF, Gallego CJ, Gottesman O, Kim DS, Leppig KA, Li R, Lin S, Manzi S, Mejia AR, Pacheco JA, Pan V, et al.
Clin Pharmacol Ther. 2014 Oct;96(4):482-9. doi: 10.1038/clpt.2014.137. Epub 2014 Jun 24.

The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism.
Hadley D, Wu ZL, Kao C, Kini A, Mohamed-Hadley A, Thomas K, Vazquez L, Qiu H, Mentch F, Pellegrino R, Kim C, Connolly J; AGP Consortium, Glessner J, Hakonarson H.
Nat Commun. 2014 Jun 13;5:4074. doi: 10.1038/ncomms5074.

Return of genomic results to research participants: the floor, the ceiling, and the choices in between.
Jarvik GP, Amendola LM, Berg JS, Brothers K, Clayton EW, Chung W, Evans BJ, Evans JP, Fullerton SM, Gallego CJ, Garrison NA, Gray SW, Holm IA, Kullo IJ, Lehmann LS, McCarty C, Prows CA, Rehm HL, Sharp RR, Salama J, Sanderson S, Van Driest SL, et al.
Am J Hum Genet. 2014 Jun 5;94(6):818-26. doi: 10.1016/j.ajhg.2014.04.009. Epub 2014 May 8.

The PCDH1 gene and asthma in early childhood.
Mortensen LJ, Kreiner-Møller E, Hakonarson H, Bønnelykke K, Bisgaard H.
Eur Respir J. 2014 Mar;43(3):792-800. doi: 10.1183/09031936.00021613. Epub 2013 Aug 29.

Imputation of TPMT defective alleles for the identification of patients with high-risk phenotypes.
Almoguera B, Vazquez L, Connolly JJ, Bradfield J, Sleiman P, Keating B, Hakonarson H.
Front Genet. 2014;5:96. doi: 10.3389/fgene.2014.00096.

Return of results in the genomic medicine projects of the eMERGE network.
Kullo IJ, Haddad R, Prows CA, Holm I, Sanderson SC, Garrison NA, Sharp RR, Smith ME, Kuivaniemi H, Bottinger EP, Connolly JJ, Keating BJ, McCarty CA, Williams MS, Jarvik GP.
Front Genet. 2014;5:50. doi: 10.3389/fgene.2014.00050.

Assessing the functional consequence of loss of function variants using electronic medical record and large-scale genomics consortium efforts.
Sleiman P, Bradfield J, Mentch F, Almoguera B, Connolly J, Hakonarson H.
Front Genet. 2014;5:105. doi: 10.3389/fgene.2014.00105.

Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts.
Connolly JJ, Glessner JT, Almoguera B, Crosslin DR, Jarvik GP, Sleiman PM, Hakonarson H.
Front Genet. 2014;5:51. doi: 10.3389/fgene.2014.00051. Review.

The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future.
Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, Crosslin D, Denny JC, Gallego CJ, Haines JL, Hakonarson H, Harley J, Jarvik GP, et al.
Genet Med. 2013 Oct;15(10):761-71. doi: 10.1038/gim.2013.72. Epub 2013 Jun 6. Review.

Practical challenges in integrating genomic data into the electronic health record.
Kho AN, Rasmussen LV, Connolly JJ, Peissig PL, Starren J, Hakonarson H, Hayes MG.
Genet Med. 2013 Oct;15(10):772-8. doi: 10.1038/gim.2013.131. Epub 2013 Sep 26. Review.

Copy number variations in alternative splicing gene networks impact lifespan.
Glessner JT, Smith AV, Panossian S, Kim CE, Takahashi N, Thomas KA, Wang F, Seidler K, Harris TB, Launer LJ, Keating B, Connolly J, Sleiman PM, Buxbaum JD, Grant SF, Gudnason V, Hakonarson H.
PLoS One. 2013;8(1):e53846. doi: 10.1371/journal.pone.0053846. Epub 2013 Jan 30.

A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.
Connolly JJ, Glessner JT, Hakonarson H.
Child Dev. 2013 Jan-Feb;84(1):17-33. doi: 10.1111/j.1467-8624.2012.01838.x. Epub 2012 Aug 30.

The impact of genomics on pediatric research and medicine.
Connolly JJ, Hakonarson H.
Pediatrics. 2012 Jun;129(6):1150-60. doi: 10.1542/peds.2011-3636. Epub 2012 May 7. Review.

The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis.
Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium.
Lancet. 2012 Mar 31;379(9822):1214-24. doi: 10.1016/S0140-6736(12)60110-X. Epub 2012 Mar 14.

Age group and sex differences in performance on a computerized neurocognitive battery in children age 8-21.
Gur RC, Richard J, Calkins ME, Chiavacci R, Hansen JA, Bilker WB, Loughead J, Connolly JJ, Qiu H, Mentch FD, Abou-Sleiman PM, Hakonarson H, Gur RE.
Neuropsychology. 2012 Mar;26(2):251-65. doi: 10.1037/a0026712. Epub 2012 Jan 16.

Rare genomic deletions and duplications and their role in neurodevelopmental disorders.
Glessner JT, Connolly JJ, Hakonarson H.
Curr Top Behav Neurosci. 2012;12:345-60. doi: 10.1007/7854_2011_179. Review.

Role of cytokines in systemic lupus erythematosus: recent progress from GWAS and sequencing.
Connolly JJ, Hakonarson H.
J Biomed Biotechnol. 2012;2012:798924. doi: 10.1155/2012/798924. Epub 2012 May 10. Review.

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder.
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, et al.
Nat Genet. 2011 Dec 4;44(1):78-84. doi: 10.1038/ng.1013.

Other Publications

3D Brain (Smartphone App)
Connolly JJ, Micklos D, Amin S, Kirk-Elleker J, Xuan E, et al.
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2009 March.

Genes to Cognition (G2C) Online
Connolly JJ, MIcklos D, Jeong E, Lauter S, Yang C, et al.
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2010 January.