John J Connolly

The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Electronic address:

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January 2020

GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network.

BMC Med 2019 07 17;17(1):135. Epub 2019 Jul 17.

Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, USA.

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July 2019

Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel.

Genet Med 2019 09 20;21(9):2135-2144. Epub 2019 Mar 20.

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

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September 2019

Enrichment sampling for a multi-site patient survey using electronic health records and census data.

J Am Med Inform Assoc 2019 03;26(3):219-227

Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, USA.

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March 2019

Novel locus for atopic dermatitis in African Americans and replication in European Americans.

Authors:

Berta Almoguera Lyam Vazquez Frank Mentch Michael E March John J Connolly Peggy L Peissig James G Linneman María Del Carmen Plaza-Serón Maria Pino-Yanes Esteban G Burchard Murray Brilliant Patrick Sleiman Hakon Hakonarson

J Allergy Clin Immunol 2019 03 9;143(3):1229-1231. Epub 2018 Nov 9.

Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa.

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March 2019

Leveraging electronic health records to assess the role of ADRB2 single nucleotide polymorphisms in predicting exacerbation frequency in asthma patients.

Authors:

Nikita Sood John J Connolly Frank D Mentch Lyam Vazquez Patrick M A Sleiman Erik B Hysinger Hakon Hakonarson

Pharmacogenet Genomics 2018 11;28(11):256-259

Center for Applied Genomics, Children's Hospital of Philadelphia.

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November 2018

Harmonizing Outcomes for Genomic Medicine: Comparison of eMERGE Outcomes to ClinGen Outcome/Intervention Pairs.

Authors:

Janet L Williams Wendy K Chung Alex Fedotov Krzysztof Kiryluk Chunhua Weng John J Connolly Margaret Harr Hakon Hakonarson Kathleen A Leppig Eric B Larson Gail P Jarvik David L Veenstra Christin Hoell Maureen E Smith Ingrid A Holm Josh F Peterson Marc S Williams

Healthcare (Basel) 2018 Jul 13;6(3). Epub 2018 Jul 13.

Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA.

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July 2018

Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience.

J Pers Med 2018 Jan 3;8(1). Epub 2018 Jan 3.

Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA.

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January 2018

Erratum: A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling.

Sci Rep 2017 08 21;7(1):8379. Epub 2017 Aug 21.

Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

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August 2017

Healthcare provider education to support integration of pharmacogenomics in practice: the eMERGE Network experience.

Authors:

Carolyn R Rohrer Vitek Noura S Abul-Husn John J Connolly Andrea L Hartzler Terrie Kitchner Josh F Peterson Luke V Rasmussen Maureen E Smith Sarah Stallings Marc S Williams Wendy A Wolf Cynthia A Prows

Pharmacogenomics 2017 Jul 22;18(10):1013-1025. Epub 2017 Jun 22.

Departments of Pediatrics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3039, USA.

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July 2017

A genome-wide association study of anorexia nervosa suggests a risk locus implicated in dysregulated leptin signaling.

Sci Rep 2017 06 19;7(1):3847. Epub 2017 Jun 19.

Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.

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June 2017

Conducting a large, multi-site survey about patients' views on broad consent: challenges and solutions.

BMC Med Res Methodol 2016 11 24;16(1):162. Epub 2016 Nov 24.

Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.

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November 2016

Association of a rare NOTCH4 coding variant with systemic sclerosis: a family-based whole exome sequencing study.

Authors:

Christopher J Cardinale Dong Li Lifeng Tian John J Connolly Michael E March Cuiping Hou Fengxiang Wang James Snyder Cecilia E Kim Rosetta M Chiavacci Patrick M Sleiman Jon M Burnham Hakon Hakonarson

BMC Musculoskelet Disord 2016 11 9;17(1):462. Epub 2016 Nov 9.

Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA.

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November 2016

Mendelian randomization analysis demonstrates that low vitamin D is unlikely causative for pediatric asthma.

Authors:

Erik B Hysinger Jeffrey D Roizen Frank D Mentch Lyam Vazquez John J Connolly Jonathan P Bradfield Berta Almoguera Patrick M Sleiman Julian L Allen Michael A Levine Hakon Hakonarson

J Allergy Clin Immunol 2016 12 20;138(6):1747-1749.e4. Epub 2016 Aug 20.

Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Pulmonary Medicine, the Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa. Electronic address:

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December 2016

Systematic data-querying of large pediatric biorepository identifies novel Ehlers-Danlos Syndrome variant.

Authors:

Akshatha Desai John J Connolly Michael March Cuiping Hou Rosetta Chiavacci Cecilia Kim Gholson Lyon Dexter Hadley Hakon Hakonarson

BMC Musculoskelet Disord 2016 Feb 16;17:80. Epub 2016 Feb 16.

Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, 3615 Civic center Blvd, Philadelphia, PA, 19104, USA.

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February 2016

Genetic sharing and heritability of paediatric age of onset autoimmune diseases.

Authors:

Yun R Li Sihai D Zhao Jin Li Jonathan P Bradfield Maede Mohebnasab Laura Steel Julie Kobie Debra J Abrams Frank D Mentch Joseph T Glessner Yiran Guo Zhi Wei John J Connolly Christopher J Cardinale Marina Bakay Dong Li S Melkorka Maggadottir Kelly A Thomas Haijun Qui Rosetta M Chiavacci Cecilia E Kim Fengxiang Wang James Snyder Berit Flatø Øystein Førre Lee A Denson Susan D Thompson Mara L Becker Stephen L Guthery Anna Latiano Elena Perez Elena Resnick Caterina Strisciuglio Annamaria Staiano Erasmo Miele Mark S Silverberg Benedicte A Lie Marilynn Punaro Richard K Russell David C Wilson Marla C Dubinsky Dimitri S Monos Vito Annese Jane E Munro Carol Wise Helen Chapel Charlotte Cunningham-Rundles Jordan S Orange Edward M Behrens Kathleen E Sullivan Subra Kugathasan Anne M Griffiths Jack Satsangi Struan F A Grant Patrick M A Sleiman Terri H Finkel Constantin Polychronakos Robert N Baldassano Eline T Luning Prak Justine A Ellis Hongzhe Li Brendan J Keating Hakon Hakonarson

Nat Commun 2015 Oct 9;6:8442. Epub 2015 Oct 9.

Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.

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October 2015

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.

Authors:

Yun R Li Jin Li Sihai D Zhao Jonathan P Bradfield Frank D Mentch S Melkorka Maggadottir Cuiping Hou Debra J Abrams Diana Chang Feng Gao Yiran Guo Zhi Wei John J Connolly Christopher J Cardinale Marina Bakay Joseph T Glessner Dong Li Charlly Kao Kelly A Thomas Haijun Qiu Rosetta M Chiavacci Cecilia E Kim Fengxiang Wang James Snyder Marylyn D Richie Berit Flatø Øystein Førre Lee A Denson Susan D Thompson Mara L Becker Stephen L Guthery Anna Latiano Elena Perez Elena Resnick Richard K Russell David C Wilson Mark S Silverberg Vito Annese Benedicte A Lie Marilynn Punaro Marla C Dubinsky Dimitri S Monos Caterina Strisciuglio Annamaria Staiano Erasmo Miele Subra Kugathasan Justine A Ellis Jane E Munro Kathleen E Sullivan Carol A Wise Helen Chapel Charlotte Cunningham-Rundles Struan F A Grant Jordan S Orange Patrick M A Sleiman Edward M Behrens Anne M Griffiths Jack Satsangi Terri H Finkel Alon Keinan Eline T Luning Prak Constantin Polychronakos Robert N Baldassano Hongzhe Li Brendan J Keating Hakon Hakonarson

Nat Med 2015 Sep 24;21(9):1018-27. Epub 2015 Aug 24.

The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.

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September 2015

The Philadelphia Neurodevelopmental Cohort: constructing a deep phenotyping collaborative.

Authors:

Monica E Calkins Kathleen R Merikangas Tyler M Moore Marcy Burstein Meckenzie A Behr Theodore D Satterthwaite Kosha Ruparel Daniel H Wolf David R Roalf Frank D Mentch Haijun Qiu Rosetta Chiavacci John J Connolly Patrick M A Sleiman Ruben C Gur Hakon Hakonarson Raquel E Gur

J Child Psychol Psychiatry 2015 Dec 8;56(12):1356-1369. Epub 2015 Apr 8.

University of Pennsylvania, Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine, PA, United States.

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December 2015

The Philadelphia Neurodevelopmental Cohort: A publicly available resource for the study of normal and abnormal brain development in youth.

Authors:

Theodore D Satterthwaite John J Connolly Kosha Ruparel Monica E Calkins Chad Jackson Mark A Elliott David R Roalf Ryan Hopson Karthik Prabhakaran Meckenzie Behr Haijun Qiu Frank D Mentch Rosetta Chiavacci Patrick M A Sleiman Ruben C Gur Hakon Hakonarson Raquel E Gur

Neuroimage 2016 Jan 31;124(Pt B):1115-1119. Epub 2015 Mar 31.

Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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January 2016

The psychosis spectrum in a young U.S. community sample: findings from the Philadelphia Neurodevelopmental Cohort.

Authors:

Monica E Calkins Tyler M Moore Kathleen R Merikangas Marcy Burstein Theodore D Satterthwaite Warren B Bilker Kosha Ruparel Rosetta Chiavacci Daniel H Wolf Frank Mentch Haijun Qiu John J Connolly Patrick A Sleiman Hakon Hakonarson Ruben C Gur Raquel E Gur

World Psychiatry 2014 Oct;13(3):296-305

Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, 9 Maloney, 3600 Spruce Street, Philadelphia, PA, 19104, USA.

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October 2014

Practical guidance on informed consent for pediatric participants in a biorepository.

Authors:

Kyle B Brothers John A Lynch Sharon A Aufox John J Connolly Bruce D Gelb Ingrid A Holm Saskia C Sanderson Jennifer B McCormick Janet L Williams Wendy A Wolf Armand H M Antommaria Ellen W Clayton

Mayo Clin Proc 2014 Nov 26;89(11):1471-80. Epub 2014 Sep 26.

Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN.

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November 2014

Etiology of autism spectrum disorder: a genomics perspective.

Authors:

John J Connolly Hakon Hakonarson

Curr Psychiatry Rep 2014 Nov;16(11):501

Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia (CHOP), Philadelphia, PA, 19104, USA,

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November 2014

Imputation of TPMT defective alleles for the identification of patients with high-risk phenotypes.

Authors:

Berta Almoguera Lyam Vazquez John J Connolly Jonathan Bradfield Patrick Sleiman Brendan Keating Hakon Hakonarson

Front Genet 2014 12;5:96. Epub 2014 May 12.

Center for Applied Genomics, The Children's Hospital of Philadelphia Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA.

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May 2014

Return of results in the genomic medicine projects of the eMERGE network.

Authors:

Iftikhar J Kullo Ra'ad Haddad Cynthia A Prows Ingrid Holm Saskia C Sanderson Nanibaa' A Garrison Richard R Sharp Maureen E Smith Helena Kuivaniemi Erwin P Bottinger John J Connolly Brendan J Keating Catherine A McCarty Marc S Williams Gail P Jarvik

Front Genet 2014 26;5:50. Epub 2014 Mar 26.

Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington Seattle, WA, USA.

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May 2014

Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts.

Authors:

John J Connolly Joseph T Glessner Berta Almoguera David R Crosslin Gail P Jarvik Patrick M Sleiman Hakon Hakonarson

Front Genet 2014 18;5:51. Epub 2014 Mar 18.

The Center for Applied Genomics, Children's Hospital of Philadelphia Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine Philadelphia, PA, USA.

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June 2014

A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project.

Authors:

Casey L Overby Luke V Rasmussen Andrea Hartzler John J Connolly Josh F Peterson RoseMary E Hedberg Robert R Freimuth Brian H Shirts Joshua C Denny Eric B Larson Christopher G Chute Gail P Jarvik James D Ralston Alan R Shuldiner Justin Starren Iftikhar J Kullo Peter Tarczy-Hornoch Marc S Williams

AMIA Annu Symp Proc 2014 14;2014:944-53. Epub 2014 Nov 14.

Genomic Medicine Institute, Geisinger Health System, Danville, PA.

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September 2015

Practical challenges in integrating genomic data into the electronic health record.

Authors:

Abel N Kho Luke V Rasmussen John J Connolly Peggy L Peissig Justin Starren Hakon Hakonarson M Geoffrey Hayes

Genet Med 2013 Oct 26;15(10):772-8. Epub 2013 Sep 26.

Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

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October 2013

The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future.

Genet Med 2013 Oct 6;15(10):761-71. Epub 2013 Jun 6.

Mount Sinai School of Medicine, New York, New York, USA.

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October 2013

A genome-wide association study of autism incorporating autism diagnostic interview-revised, autism diagnostic observation schedule, and social responsiveness scale.

Authors:

John J Connolly Joseph T Glessner Hakon Hakonarson

Child Dev 2013 Jan-Feb;84(1):17-33. Epub 2012 Aug 30.

The Children's Hospital of Philadelphia.

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July 2013

Role of cytokines in systemic lupus erythematosus: recent progress from GWAS and sequencing.

Authors:

John J Connolly Hakon Hakonarson

J Biomed Biotechnol 2012 10;2012:798924. Epub 2012 May 10.

Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

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December 2012

The impact of genomics on pediatric research and medicine.

Authors:

John J Connolly Hakon Hakonarson

Pediatrics 2012 Jun 7;129(6):1150-60. Epub 2012 May 7.

Center for Applied Genomics, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Research Center, Suite 1216E, Philadelphia, PA 19104, USA.

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June 2012