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Jonathan Gaffin, MD

Medicine Research
Respiratory Diseases Research
Hospital Title:
Assistant in Medicine
Academic Title:
Assistant Professor in Pediatrics, Harvard Medical School
Contact Via Email
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Research Overview

Jonathan Gaffin, MD, MMSc, is a pediatric pulmonologist and clinical researcher with a particular interest in pediatric asthma and the environment, especially as it may relate to potential interventions.

Dr. Gaffin’s primary research activities are aimed at investigating the epidemic of inner city childhood asthma as part of the School Inner City Asthma Study (SICAS; PI: Wanda Phipatanakul, M.D., M.S.). This study prospectively evaluates the effect of the school environment on asthma symptoms in urban public school children with asthma. Dr. Gaffin is specifically interested in the role of indoor air pollution in the school environment. In this unique study design, classroom air pollution is monitored while children attend school and is then able to be compared from classroom to classroom to determine its effects on asthma symptoms in the students. Preliminary data shows a powerful association between pollution exposure and asthma symptoms. Furthermore, data also suggests that certain indoor pollutants can be predicted from measures of outdoor pollution. Planned studies include the use of geographic information systems (GIS) technology, climate, and ambient pollution to take a novel approach to integrate the home and school-based exposures to fully evaluate the individual health risks posed to at-risk children. This approach to the micro-environment will enable an assessment across multiple settings in relation to health and disease. Additionally, Dr. Gaffin is an investigator in several asthma clinical trials at Boston Children’s Hospital and the site-principle investigator for several cystic fibrosis observational and interventional studies.

About Jonathan Gaffin, MD, MMSc

Dr. Gaffin received his MD from the University of Massachusetts in 2004. He completed residency in Pediatrics at The Yale-New Haven Children’s Hospital in 2007 and subspecialty training in Pediatric Pulmonology at Boston Children’s Hospital from 2007-2010. He also completed a Master’s of Medical Science degree, which provided training in translational and clinical research, from Harvard Medical School (2011). Dr. Gaffin is the founder and co-director of the Boston Children’s Hospital Severe Asthma Clinic and is on staff as a pediatric pulmonologist at Boston Children’s Hospital.

Active Projects

2013-2018 School-based air pollution and asthma morbidity in Inner City School Children
NIAID/NIH K23 1K23AI106945-01
Principal Investigator
The goal of this mentored career development award is to determine the role of indoor air pollution specific to the inner city school classroom environment on asthma morbidity for inner city school children with asthma. This research will provide important information that may lead to specific interventions to improve air quality and health in inner city schools.


Publications powered by Harvard Catalyst Profiles
  1. Jhun I, Gaffin JM, Coull BA, Huffaker MF, Petty CR, Sheehan WJ, Baxi SN, Lai PS, Kang CM, Wolfson JM, Gold DR, Koutrakis P, Phipatanakul W. School Environmental Intervention to Reduce Particulate Pollutant Exposures for Children with Asthma. J Allergy Clin Immunol Pract. 2016 Sep 15.
  2. Levy S, Dedeoglu F, Gaffin JM, Garvey KC, Harstad E, MacGinnitie A, Rufo PA, Huang Q, Ziemnik RE, Wisk LE, Weitzman ER. A Screening Tool for Assessing Alcohol Use Risk among Medically Vulnerable Youth. PLoS One. 2016; 11(5):e0156240.
  3. Kanchongkittiphon W, Gaffin JM, Kopel L, Petty CR, Bollinger ME, Miller RL, Perzanowski M, Matsui EC, Phipatanakul W. Association of FEF25%-75% and bronchodilator reversibility with asthma control and asthma morbidity in inner-city children with asthma. Ann Allergy Asthma Immunol. 2016 Jul; 117(1):97-9.
  4. Bacharier LB, Guilbert TW, Mauger DT, Boehmer S, Beigelman A, Fitzpatrick AM, Jackson DJ, Baxi SN, Benson M, Burnham CA, Cabana M, Castro M, Chmiel JF, Covar R, Daines M, Gaffin JM, Gentile DA, Holguin F, Israel E, Kelly HW, Lazarus SC, Lemanske RF, Ly N, Meade K, Morgan W, Moy J, Olin T, Peters SP, Phipatanakul W, Pongracic JA, Raissy HH, Ross K, Sheehan WJ, Sorkness C, Szefler SJ, Teague WG, Thyne S, Martinez FD. Early Administration of Azithromycin and Prevention of Severe Lower Respiratory Tract Illnesses in Preschool Children With a History of Such Illnesses: A Randomized Clinical Trial. JAMA. 2015 Nov 17; 314(19):2034-44.
  5. Gaffin JM. Postnatal environmental tobacco smoke exposure is associated with objective markers of atopy in preschool-aged children. Evid Based Med. 2015 Dec; 20(6):219.
  6. Gaffin JM, Landrum A, Petty CR, Baxi S, Sheehan WJ, Phipatanakul W. Black and Hispanic perceptions of asthma medication in the School Inner-City Asthma Study. Ann Allergy Asthma Immunol. 2015 Jun; 114(6):533-4.
  7. Rao DR, Sordillo JE, Kopel LS, Gaffin JM, Sheehan WJ, Hoffman E, Ozonoff A, Gold DR, Phipatanakul W. Association between allergic sensitization and exhaled nitric oxide in children in the School Inner-City Asthma Study. Ann Allergy Asthma Immunol. 2015 Mar; 114(3):256-257.e1.
  8. Kanchongkittiphon W, Gaffin JM, Phipatanakul W. Child with atopic dermatitis. Ann Allergy Asthma Immunol. 2015 Jan; 114(1):6-11.
  9. Kanchongkittiphon W, Mendell MJ, Gaffin JM, Wang G, Phipatanakul W. Indoor environmental exposures and exacerbation of asthma: an update to the 2000 review by the Institute of Medicine. Environ Health Perspect. 2015 Jan; 123(1):6-20.
  10. Gaffin JM, Kanchongkittiphon W, Phipatanakul W. Reprint of: Perinatal and early childhood environmental factors influencing allergic asthma immunopathogenesis. Int Immunopharmacol. 2014 Nov; 23(1):337-46.
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  12. Gaffin JM, Kanchongkittiphon W, Phipatanakul W. Perinatal and early childhood environmental factors influencing allergic asthma immunopathogenesis. Int Immunopharmacol. 2014 Sep; 22(1):21-30.
  13. Kanchongkittiphon W, Gaffin JM, Phipatanakul W. The indoor environment and inner-city childhood asthma. Asian Pac J Allergy Immunol. 2014 Jun; 32(2):103-10.
  14. Kopel LS, Phipatanakul W, Gaffin JM. Social disadvantage and asthma control in children. Paediatr Respir Rev. 2014 Sep; 15(3):256-62; quiz 262-3.
  15. Kanchongkittiphon W, Sheehan WJ, Friedlander J, Chapman MD, King EM, Martirosyan K, Baxi SN, Permaul P, Gaffin JM, Kopel L, Bailey A, Fu C, Petty CR, Gold DR, Phipatanakul W. Allergens on desktop surfaces in preschools and elementary schools of urban children with asthma. Allergy. 2014 Jul; 69(7):960-3.
  16. Kopel LS, Gaffin JM, Ozonoff A, Rao DR, Sheehan WJ, Friedlander JL, Permaul P, Baxi SN, Fu C, Subramanian SV, Gold DR, Phipatanakul W. Perceived neighborhood safety and asthma morbidity in the school inner-city asthma study. Pediatr Pulmonol. 2015 Jan; 50(1):17-24.
  17. Gaffin JM, Raby BA, Petty CR, Hoffman EB, Baccarelli AA, Gold DR, Phipatanakul W. ß-2 adrenergic receptor gene methylation is associated with decreased asthma severity in inner-city schoolchildren: asthma and rhinitis. Clin Exp Allergy. 2014; 44(5):681-9.
  18. Gaffin JM, Phipatanakul W. Beta-2-Adrenergic Receptor Methylation Influences Asthma Phenotype in The School Inner City Asthma Study. Receptors Clin Investig. 2014; 1(1).
  19. Baxi SN, Muilenberg ML, Rogers CA, Sheehan WJ, Gaffin J, Permaul P, Kopel LS, Lai PS, Lane JP, Bailey A, Petty CR, Fu C, Gold DR, Phipatanakul W. Exposures to molds in school classrooms of children with asthma. Pediatr Allergy Immunol. 2013 Nov; 24(7):697-703.
  20. Gaffin JM, Bouzaher A, McCown M, Larabee Tuttle K, Israel E, Phipatanakul W. Rethinking the prevalence of exercise-induced bronchoconstriction in patients with asthma. Ann Allergy Asthma Immunol. 2013 Dec; 111(6):567-8.
  21. Friedlander JL, Sheehan WJ, Baxi SN, Kopel LS, Gaffin JM, Ozonoff A, Fu C, Gold DR, Phipatanakul W. Food allergy and increased asthma morbidity in a School-based Inner-City Asthma Study. J Allergy Clin Immunol Pract. 2013 Sep-Oct; 1(5):479-84.
  22. Permaul P, Sheehan WJ, Baxi SN, Gaffin JM, Fu C, Petty CR, Gold DR, Phipatanakul W. Predictors of indoor exposure to mouse allergen in inner-city elementary schools. Ann Allergy Asthma Immunol. 2013 Oct; 111(4):299-301.e1.
  23. Rao DR, Gaffin JM, Baxi SN, Sheehan WJ, Hoffman EB, Phipatanakul W. The utility of forced expiratory flow between 25% and 75% of vital capacity in predicting childhood asthma morbidity and severity. J Asthma. 2012 Aug; 49(6):586-92.
  24. Permaul P, Hoffman E, Fu C, Sheehan W, Baxi S, Gaffin J, Lane J, Bailey A, King E, Chapman M, Gold D, Phipatanakul W. Allergens in urban schools and homes of children with asthma. Pediatr Allergy Immunol. 2012 Sep; 23(6):543-9.
  25. Cortot CF, Sheehan WJ, Permaul P, Friedlander JL, Baxi SN, Gaffin JM, Dioun AF, Hoffman EB, Schneider LC, Phipatanakul W. Role of specific IgE and skin-prick testing in predicting food challenge results to baked egg. Allergy Asthma Proc. 2012 May-Jun; 33(3):275-81.
  26. Baxi SN, Sheehan WJ, Gaffin JM, Yodying J, Panupattanapong S, Lane JP, Fu C, Hoffman EB, Gold DR, Phipatanakul W. Agreement between parent and student responses to an asthma and allergy questionnaire in a diverse, inner-city elementary school population. Ann Allergy Asthma Immunol. 2011 Oct; 107(4):371-3.
  27. Gaffin JM, Sheehan WJ, Morrill J, Cinar M, Borras Coughlin IM, Sawicki GS, Twarog FJ, Young MC, Schneider LC, Phipatanakul W. Tree nut allergy, egg allergy, and asthma in children. Clin Pediatr (Phila). 2011 Feb; 50(2):133-9.
  28. Gaffin JM, Israel E, Phipatanakul W. The effect of prophylactic palivizumab on recurrent wheezing in children with an atopic family history. J Allergy Clin Immunol. 2011 Jan; 127(1):292-3; author reply 293.
  29. Gaffin JM, Sheehan WJ, Morrill J, Sawicki G, Twarog F, Cinar M, Young M, Schneider LC, Phipatanakul W. Peanut Allergy is Associated with Increased Asthma Prevalence in Food Allergic Children. AAAAI. 2009.
  30. Gaffin JM, Phipatanakul W. Montelukast as Monotherapy for Pediatric Asthma. MP Med Prakt Pediatr. 2009; 3(63):20-23.
  31. Gaffin JM, Gallagher PG. Picture of the month. Blueberry muffin baby (extramedullary hematopoiesis) due to congenital cytomegalovirus infection. Arch Pediatr Adolesc Med. 2007 Nov; 161(11):1102-3.
  32. Jonathan M. Gaffin, MD Sumit Bhargava, MD. Sleep. Yale Curriculum in Primary Care. 2007.
  33. Jonathan M. Gaffin, MD Sumit Bhargava, MD. Sleep. Yale Curriculum in Primary Care. 2006.
  34. Gaffin JM, Shotola NL, Martin TR, Phipatanakul W. Clinically useful spirometry in preschool-aged children: evaluation of the 2007 American Thoracic Society Guidelines. J Asthma. 2010 Sep; 47(7):762-7.
  35. Phipatanakul W, Bailey A, Hoffman EB, Sheehan WJ, Lane JP, Baxi S, Rao D, Permaul P, Gaffin JM, Rogers CA, Muilenberg ML, Gold DR. The school inner-city asthma study: design, methods, and lessons learned. J Asthma. 2011 Dec; 48(10):1007-14.
  36. Gaffin JM, Spergel JM, Boguniewicz M, Eichenfield LF, Paller AS, Fowler JF, Dinulos JG, Tilles SA, Schneider LC, Phipatanakul W. Effect of cat and daycare exposures on the risk of asthma in children with atopic dermatitis. Allergy Asthma Proc. 2012 May-Jun; 33(3):282-8.
  37. Rork JF, Sheehan WJ, Gaffin JM, Timmons KG, Sidbury R, Schneider LC, Phipatanakul W. Parental response to written eczema action plans in children with eczema. Arch Dermatol. 2012 Mar; 148(3):391-2.
  38. Gaffin JM, Phipatanakul W. The role of indoor allergens in the development of asthma. Curr Opin Allergy Clin Immunol. 2009 Apr; 9(2):128-35.
  39. Sheehan WJ, Hoffman EB, Fu C, Baxi SN, Bailey A, King EM, Chapman MD, Lane JP, Gaffin JM, Permaul P, Gold DR, Phipatanakul W. Endotoxin exposure in inner-city schools and homes of children with asthma. Ann Allergy Asthma Immunol. 2012 Jun; 108(6):418-22.
  40. Lai PS, Sheehan WJ, Gaffin JM, Petty CR, Coull BA, Gold DR, Phipatanakul W. School Endotoxin Exposure and Asthma Morbidity in Inner-city Children. Chest. 2015 Nov; 148(5):1251-8.
  41. Sheehan WJ, Mauger DT, Paul IM, Moy JN, Boehmer SJ, Szefler SJ, Fitzpatrick AM, Jackson DJ, Bacharier LB, Cabana MD, Covar R, Holguin F, Lemanske RF, Martinez FD, Pongracic JA, Beigelman A, Baxi SN, Benson M, Blake K, Chmiel JF, Daines CL, Daines MO, Gaffin JM, Gentile DA, Gower WA, Israel E, Kumar HV, Lang JE, Lazarus SC, Lima JJ, Ly N, Marbin J, Morgan WJ, Myers RE, Olin JT, Peters SP, Raissy HH, Robison RG, Ross K, Sorkness CA, Thyne SM, Wechsler ME, Phipatanakul W. Acetaminophen versus Ibuprofen in Young Children with Mild Persistent Asthma. N Engl J Med. 2016 Aug 18; 375(7):619-30.
  42. Gaffin JM, Zhou JS, Cai Q, Petty CR, Fu C, Sheehan WJ, Baxi S, Bailey A, Gold DR, Phipatanakul W. Utility of a portable hand-held forced expiratory volume in 1 second meter for monitoring asthma in an inner-city school setting. Ann Allergy Asthma Immunol. 2016 Sep; 117(3):323-4.
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