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John R Shaffer, PhD

Assistant Professor, Human Genetics

Assistant Professor, Oral Biology,


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 projects include studies of oral health, craniofacial phenotypes, and recovery from brain injury.


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


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

Selected Publications

Lee MK, Shaffer JR, Leslie EJ, Orlova E, Carlson JC, Feingold E, Marazita ML, Weinberg SM. Genome-wide association study of facial morphology reveals novel associations with FREM1 and PARK2. PLoS One. 2017 Apr 25;12(4):e0176566. doi: 10.1371/journal.pone.0176566. eCollection 2017. PubMed PMID: 28441456; PubMed Central PMCID: PMC5404842.

Leslie EJ, Carlson JC, Shaffer JR, Buxó CJ, Castilla EE, Christensen K, Deleyiannis FWB, Field LL, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Feingold E, Weinberg SM, Murray JC, Marazita ML. Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Am J Med Genet A. 2017 Jun;173(6):1531-1538. doi: 10.1002/ajmg.a.38210. Epub 2017 Apr 19. PubMed PMID: 28425186; PubMed Central PMCID: PMC5444956.

Wright CD, McNeil DW, Edwards CB, Crout RJ, Neiswanger K, Shaffer JR, Marazita ML. Periodontal Status and Quality of Life: Impact of Fear of Pain and Dental Fear. Pain Res Manag. 2017;2017:5491923. doi: 10.1155/2017/5491923. Epub 2017 Mar 9. PubMed PMID: 28377670; PubMed Central PMCID: PMC5362723.

Lewis DD, Shaffer JR, Feingold E, Cooper M, Vanyukov MM, Maher BS, Slayton RL, Willing MC, Reis SE, McNeil DW, Crout RJ, Weyant RJ, Levy SM, Vieira AR, Marazita ML. Genetic Association of MMP10, MMP14, and MMP16 with Dental Caries. Int J Dent. 2017;2017:8465125. doi: 10.1155/2017/8465125. Epub 2017 Feb 28. PubMed PMID: 28348596; PubMed Central PMCID: PMC5350286.

Eckert S, Feingold E, Cooper M, Vanyukov MM, Maher BS, Slayton RL, Willing MC, Reis SE, McNeil DW, Crout RJ, Weyant RJ, Levy SM, Vieira AR, Marazita ML, Shaffer JR. Variants on chromosome 4q21 near PKD2 and SIBLINGs are associated with dental caries. J Hum Genet. 2017 Apr;62(4):491-496. doi: 10.1038/jhg.2016.161. Epub 2017 Jan 19. PubMed PMID: 28100911; PubMed Central PMCID: PMC5367940.

Sanders AE, Jain D, Sofer T, Kerr KF, Laurie CC, Shaffer JR, Marazita ML, Kaste LM, Slade GD, Fillingim RB, Ohrbach R, Maixner W, Kocher T, Bernhardt O, Teumer A, Schwahn C, Sipilä K, Lähdesmäki R, Männikkö M, Pesonen P, Järvelin M, Rizzatti-Barbosa CM, Meloto CB, Ribeiro-Dasilva M, Diatchenko L, Serrano P, Smith SB. GWAS Identifies New Loci for Painful Temporomandibular Disorder: Hispanic Community Health Study/Study of Latinos. J Dent Res. 2017 Mar;96(3):277-284. doi: 10.1177/0022034516686562. Epub 2017 Jan 12. PubMed PMID: 28081371; PubMed Central PMCID: PMC5298397.

Leslie EJ, Carlson JC, Shaffer JR, Butali A, Buxó CJ, Castilla EE, Christensen K, Deleyiannis FW, Leigh Field L, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Feingold E, Weinberg SM, Murray JC, Beaty TH, Marazita ML. Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with
or without cleft palate. Hum Genet. 2017 Mar;136(3):275-286. doi: 10.1007/s00439-016-1754-7. Epub 2017 Jan 4. PubMed PMID: 28054174; PubMed Central PMCID: PMC5317097.

Randall CL, Shaffer JR, McNeil DW, Crout RJ, Weyant RJ, Marazita ML. Toward a genetic understanding of dental fear: evidence of heritability. Community Dent Oral Epidemiol. 2016 Oct 11. doi: 10.1111/cdoe.12261. [Epub ahead of print] PubMed PMID: 27730664; PubMed Central PMCID: PMC5388586.

Sanders AE, Sofer T, Wong Q, Kerr KF, Agler C, Shaffer JR, Beck JD, Offenbacher S, Salazar CR, North KE, Marazita ML, Laurie CC, Singer RH, Cai J, Finlayson TL, Divaris K. Chronic Periodontitis Genome-wide Association Study in the Hispanic Community Health Study / Study of Latinos. J Dent Res. 2017 Jan;96(1):64-72. doi: 10.1177/0022034516664509. Epub 2016 Oct 1. PubMed PMID: 27601451; PubMed Central PMCID: PMC5347427.

Shaffer JR, Orlova E, Lee MK, Leslie EJ, Raffensperger ZD, Heike CL, Cunningham ML, Hecht JT, Kau CH, Nidey NL, Moreno LM, Wehby GL, Murray JC, Laurie CA, Laurie CC, Cole J, Ferrara T, Santorico S, Klein O, Mio W, Feingold E, Hallgrimsson B, Spritz RA, Marazita ML, Weinberg SM. Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology. PLoS Genet. 2016 Aug 25;12(8):e1006149. doi: 10.1371/journal.pgen.1006149. eCollection 2016 Aug. PubMed PMID: 27560520; PubMed Central PMCID: PMC4999139.

Randall CL, McNeil DW, Shaffer JR, Crout RJ, Weyant RJ, Marazita ML. Fear of Pain Mediates the Association between MC1R Genotype and Dental Fear. J Dent Res. 2016 Sep;95(10):1132-7. doi: 10.1177/0022034516661151. PubMed PMID: 27555332; PubMed Central PMCID: PMC5004243.

Sofer T, Shaffer JR, Graff M, Qi Q, Stilp AM, Gogarten SM, North KE, Isasi CR, 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). Genet Epidemiol. 2016 Sep;40(6):492-501. doi: 10.1002/gepi.21981. Epub 2016 Jun 3. PubMed PMID: 27256683; PubMed Central PMCID: PMC4981554.

Leslie EJ, Carlson JC, Shaffer JR, Feingold E, Wehby G, Laurie CA, Jain D, Laurie CC, Doheny KF, McHenry T, Resick J, Sanchez C, Jacobs J, Emanuele B, Vieira AR, Neiswanger K, Lidral AC, Valencia-Ramirez LC, Lopez-Palacio AM, Valencia DR, Arcos-Burgos M, Czeizel AE, Field LL, Padilla CD, Cutiongco-de la Paz EM, Deleyiannis F, Christensen K, Munger RG, Lie RT, Wilcox A, Romitti PA, Castilla EE, Mereb JC, 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, Abate F, Koruyucu M, Seymen F, Ma L, de Salamanca JE, Weinberg SM, Moreno L, Murray JC, Marazita ML. A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. Hum Mol Genet. 2016 Jul 1;25(13):2862-2872. Epub 2016 Mar 30. PubMed PMID: 27033726; PubMed Central PMCID: PMC5181632.

John R Shaffer
© 2018 by University of Pittsburgh Graduate School of Public Health

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