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John R Shaffer, PhD

Assistant Professor, Human Genetics

Contact

R-znvy: wbua.e.funssre@cvgg.rqh
Primary Phone: 967-179-8563


Personal Statement

Dr. Shaffer's research program involves the application of statistical and bioinformatics approaches to understand the genetic contributors to common complex human diseases. In particular, Dr. Shaffer is interested in heritability, linkage analysis, genetic association, epigenetics, and gene-by-environment interactions. His current research interests are focused on oral health outcomes, birth defects, and recovery from brain injury.


Education

2008 | University of Pittsburgh, Pittsburgh, PA | Ph.D. in Human Genetics
2003 | The Pennsylvania State University, University Park, PA | B.S. in Biology


Teaching

2008-present | HUGEN 2022 Human Population Genetics | offered each Fall semester


Selected Publications

Shaffer JR, Carlson J, Stanley BOC, Feingold E, Cooper M, Vanyukov MM, Maher BS, Slayton RL, Willing MC, Rein SE, McNeil DW, Crout RJ, Weyant RJ, Levy SM, Vieira AR, Marazita ML.  Effects of enamel matrix genes on dental caries are moderated by fluoride exposures.  Human Genetics 2015 134(2):159-167.  [PMID: 25373699]

Shaffer JR, Wang X, McNeil DW, Weyant RJ, Crout RJ, Marazita ML.  Genetic susceptibility to dental caries differs between the sexes: A family-based study.  Caries Research 2015 49(2):133-140.  [PMID: 25612913]

Wolf ZT*, Brand HA*, Shaffer JR*, *joint first authors, Leslie EJ, Willet C, McHenry T, Ariz B, Narayan N, Feingold E, Wang X, Sliskovic S, Karmi N, Safra N, Sanchez C, Deleyiannis FWB, Murray JC, Wade CM, Marazita ML, Bannasch DL. Genetic studies in human and canines implicate ADAMTS20 as a novel risk gene for nonsyndromic cleft lip and palate.  PLoS Genetics 2015 11(3):e1005059. [PMID: 25798845]

Neiswanger K, McNeil DW, Foxman B, Govil M, Cooper ME, Weyant RJ, Shaffer JR, Crout RJ, Simhan HN, Beach SR, Chapman S, Zovko JG, Brown LJ, Strotmeyer SJ, Maurer JL, Marazita ML. Oral Health in a Sample of Pregnant Women from Northern Appalachia (2011-2015).  Intl J Dent 2015 469376:1-12.  [Full text]

Shaffer JR, Leslie EJ, Feingold EF, Govil M, McNeil DW, Crout RJ, Weyant RJ, Marazita ML. Caries experience differs between females and males across age groups in Northern Appalachia.  Intl J Dent 2015 938213:1-8. [Full text]

Shungin D, Cornelis M, Divaris K, Holtfreter B, Shaffer JR, Yu Y, Barros SP, Beck JD, Biffar R,  Boerwinkle EA, Crout RJ, Ganna A, Hallmans G, Hindy G, Hu FB, McNeil DW, Melander S, Moss KL, North KE, Orho-Melander M, Pedersen NJ, Ridker PM, Rose LM, Rukh G, Teumer A, Weyant RJ, Chasman DI, Joshipura K,  Kocher T, Magnusson PKE, Marazita ML, Nilsson P, Offenbacher S, Smith GD, Lundberg P, Palmer TM, Timpson NJ, Johansson I, Franks PW.  Is Body Mass Index Causally Related with Periodontitis? Results from the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium.  Intl J Epidemiol 2015 44(2):638-50  [PMID: 26050256]

McNeil DW, Hayes S, Randall CL, Polk DE, Neiswanger K, Shaffer JR, Weyant RJ, Foxman B, Crout RJ, Chapman S, Brown LJ, Maurer JL, Marazita ML.  Depression and a rural environment are associated with poor oral health among pregnant women in Northern Appalachia.  Behav Modif 2016 40(1-2):325-40. [PMID 26643277]

Conomos MP, Laurie CA, Stilp AM, Gogarten SM, McHugh CP, Nelson SC, Sofer T, Fernández-Rhodes L, Justice AE, Graff M, Young KL, Seyerle AA, Avery CL, Taylor KD, Rotter JI, Talavera GA, Daviglus ML, Wassertheil-Smoller S, Schneiderman N, Heiss G, Kaplan RC, Franceschini N, Reiner AP, Shaffer JR, Barr RG, Kerr KF, Browning SR, Browning BL, Weir BS, Avilés-Santa ML, Papanicolaou GJ, Lumley T, Szpiro AA, North KE, Rice K, Thornton TA, Laurie CC.  Genetic Diversity and Association Studies in U.S. Hispanic/Latino Populations:  Applications in the Hispanic Community Health Study/Study of Latinos. Am J Hum Genet 2016 98(1):165-84. [PMID 26748518]

Morrison J, Laurie CC, Marazita ML, Sander AE, Offenbacher S, Salazar CR, Conomos M, Thornton T, Dain D, Laurie CA, Kerr K, Papanicolaou G, Taylor K, Kaste L, Finlayson TL, Beck J, Shaffer JR.  Genome-wide association study of dental caries in the Hispanic Communities Health Study / Study of Latinos. Human Molecular Genetics 2016 Feb 15;25(4):807-16. [PMID 26662797]

Leslie EJ, Liu H, Carlson JC, Shaffer JR, Feingold E, Wehby G, Laurie CA, Jain D, Laurie CC, Doheny K, McHenry T, Resick J, Sanchez C, Jacobs J, Emanuele B, Neiswanger K, Czeizel AE, Deleyiannis F, Christensen K, Munger R, Lie RT, Willcox A, Romitti P, Field LL, Padilla C, Lidral AC, Valencia-Ramirez LC, Lopez-Palacio AM, Palacio DR, Arcos-Burgos M, Castilla EE, Poletta FA, Orioli IM, Carvalho FM, Hecht JT, Blanton SH, Buxó CJ, Butali A, Mossey PA, Adeyemo WL, James O, Braimah RO, Aregbesola BS, Eshete MA, Deribew M, Vieira AR, Koruyucu M, Seymen F, Ma L, de Salamanca JE, Moreno L, Weinberg S, Cornell RA, Murray JC, Marazita ML. A genome-wide association study of nonsyndromic cleft palate identifies an etiologic missense variant in GRHL3.  Am J Hum Genet 2016 Apr 7;98(4):744-54. [PMID 27018472]

Leslie EJ, Carlson JC, Shaffer JR, Feingold E, Wehby G, Laurie CA, Jain D, Laurie CC, Doheny K, McHenry T, Resick J, Sanchez C, Jacobs J, Emanuele B, Neiswanger K, Lidral AC, Valencia-Ramirez LC, Lopez-Palacio AM, Palacio DR, Arcos-Burgos M, Czeizel AE, Field LL, Padilla C, Deleyiannis F, Christensen K, Munger R, Lie RT, Willcox A, Romitti P, Castilla EE, Poletta FA, Orioli IM, Carvalho FM, Hecht JT, Blanton SH, Buxó CJ, Butali A, Mossey PA, Adeyemo WL, James O, Braimah RO, Aregbesola BS, Eshete MA, Deribew M, Vieira AR, Koruyucu M, Seymen F, Ma L, de Salamanca JE, Moreno L, Weinberg S, Murray JC, Marazita ML. A multi-ethnic genome-wide association study identifies novel loci for nonsyndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q31. Human Molecular Genetics Mar 30. pii: ddw104. [PMID 27033726]

Sofer T, Shaffer JR, Graff M, Qi Q, Stilp AM, Gogarten SM, North KE, Isasi CR, Weir BS, Laurie CC, Szpiro AA.  Meta-analysis of genome-wide association studies with correlated individuals: application to the Hispanic Community Health Study / Study of Latinos (HCHS/SOL).  Genetic Epidemiology 2016 Jun 3. doi: 10.1002/gepi.21981. [Epub ahead of print].  [PMID:27256683]

John R Shaffer
© 2017 by University of Pittsburgh Graduate School of Public Health

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