John R Shaffer, PhD

Assistant Professor, Human Genetics

Assistant Professor, Oral Biology


3131 Public Health
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

Ekaterina Orlova, Andrew Yeh, Min Shi, Brian Firek, Sarangarajan Ranganathan, 23andMe Research Team, David C. Whitcomb, David N. Finegold, Robert E. Ferrell, M. Michael Barmada, Mary L. Marazita, David A. Hinds, John R. Shaffer (corresponding author), Michael J. Morowitz. Genetic association and differential expression of PITX2 with acute appendicitis.  Human Genetics 2019 138(1), 37-47. PMID: 30392061; PMCID: PMC6514078


John R. Shaffer, Jessica LeClair, Jenna C. Carlson, Eleanor Feingold, Carmen J. Buxó, Kaare Christensen, Frederic W.B. Deleyiannis, L. Leigh Field, Jacqueline T. Hecht, Lina Moreno, Ieda M. Orioli, Carmencita Padilla, Alexandre R. Vieira, George L. Wehby, Jeffrey C. Murray, Seth M. Weinberg, Mary L. Marazita, Elizabeth J. Leslie. Association of Low-Frequency Genetic Variants in Regulatory Regions with Non-Syndromic Orofacial Clefts. American Journal of Medical Genetics Part A 2019 Mar;179(3):467-474. PMID: 30582786; PMCID: PMC6374160


Tamar Sofer, Xiuwen Zheng, Stephanie M. Gogarten, Cecelia A. Laurie, Kelsey Grinde, John R. Shaffer, Dmitry Shungin, Jeffrey R. O’Connell, Ramon A. Durazo-Arvizo, Laura Raffield, Leslie Lange, Solomon Musani, Ramachandran S. Vasan, L. Adrienne Cupples, Alexander P. Reiner, Cathy C. Laurie, Kenneth M. Rice. A Fully-Adjusted Two-Stage Procedure for Rank Normalization in Genetic Association Studies. Genetic Epidemiology 2019 Apr;43(3):263-275. PMID: 30653739; PMCID: PMC6416071


Seth Weinberg, Jasmien Roosenboom, John R. Shaffer, Mark D. Shriver, Joanna Wysocka, Peter Claes. Hunting for genes that shape human faces: initial successes and challenges for the future.  Orthodontics & Craniofacial Research 2019; 22(Suppl. 1):207–212. PMID: 31074157; PMCID: PMC6550302


Agler CS, Shungin D, Ferreira Zandoná AG, Basta PV, Luo J, Cantrell J, Pahel TD, Meyer B, Shaffer JR, Schäefer AS, North KE, Divaris K.  Protocols, methods and tools for genome-wide association studies (GWAS) of dental traits. Methods in Molecular Biology 2019; 1922:493-509. PMID: 30838596.


Jasmien Roosenboom, Karlijne Indencleef, Myoung Keun Lee, Hanne Hoskens, Julie D. White, Dongjing Liu, Jacqueline T. Hecht, George L. Wehby, Lina M. Moreno, Carolyn Hodges-Simeon, Eleanor Feingold, Mary L. Marazita, Stephen Richmond, Mark D. Shriver, Peter Claes, John R. Shaffer, Seth M. Weinberg.  SNPs associated with testosterone levels influence human facial morphology.  Frontiers in Genetics 2018 Oct 23;9:497. PMID: 30405702; PMCID: PMC6206510


Karlijne Indencleef, Jasmien Roosenboom, Hanne Hoskens, Julie D. White, Mark D. Shriver, Stephen Richmond, Hilde Peeters, Eleanor Feingold, Mary L. Marazita, John R. Shaffer, Seth M. Weinberg, Greet Hens, Peter Claes.  Six NSCL/P loci show associations with normal-range craniofacial variation.  Frontiers in Genetics 2018 Oct 25;9:502. PMID: 30410503; PMCID: PMC6210408


Laurence J Howe, Myoung Keun Lee, Gemma C Sharp, George Davey Smith, Beate St Pourcain, John R. Shaffer, Kerstin U Ludwig, Elisabeth Mangold,  Mary L Marazita, Eleanor Feingold, Alexei Zhurov, Evie Stergiakouli, Jonathan Sandy, Stephen Richmond, Seth M Weinberg, Gibran Hemani, Sarah J Lewis. Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology. PLoS Genet. 2018 Aug 1;14(8):e1007501.PMID: 30067744; PMCID: PMC6089455


Simon Haworth, Dmitry Shungin, Justin T van der Tas, Strahinja Vucic, Carolina Medina-Gomez, Victor Yakimov, Bjarke Feenstra, John R Shaffer, Myoung Keun Lee, Marie Standl, Elisabeth Thiering, Carol Wang, Klaus Bønnelykke, Johannes Waage, Leon Eyrich Jessen, Pia Elisabeth Nørrisgaard, Raimo Joro, Ilkka Seppälä, Olli Raitakari, Tom Dudding, Olja Grgic, Edwin Ongkosuwito, Anu Vierola, Aino-Maija Eloranta, Nicola  X West, Steven J Thomas,  Daniel W McNeil, Steven M Levy, Rebecca Slayton, Ellen A Nohr, Terho Lehtimäki, Timo Lakka, Hans Bisgaard, Craig Pennell, Jan Kühnisch, Mary L Marazita, Mads Melbye, Frank Geller, Fernando Rivadeneira, Eppo B Wolvius, Paul W Franks, Ingegerd Johansson, Nicholas J Timpson. Consortium genome-wide meta-analysis for childhood dental caries traits. Human Molecular Genetics. 2018 Sep 1;27(17):3113-3127. PMID: 29931343; PMCID: PMC6097157


Özbek U, Lin H, Lin Y, Weeks DE, Chen W, Shaffer JR, Purcell SM, Feingold E. Statistics for X-chromosome Associations. Genetic Epidemiology 2018 Sep;42(6):539-550. PMID:29900581; PMCID: PMC6394852


Govil M, Mukhopadhyay N, Weeks DE, Feingold E, Shaffer JR, Levy SM, Vieira AR, Slayton RL, McNeil DW, Weyant RJ, Crout RJ, Marazita ML.  Novel caries loci in children and adults implicated by genome-wide linkage.  BMC Oral Health  2018 Jun 1;18(1):98. PMID: 29859070; PMCID: PMC5984765


Roosenboom J, Lee MK, Hecht JT, Heike CL, Wehby GL, Christensen K, Feingold E, Marazita ML, Maga AM, Shaffer JR, Weinberg SM. Mapping genetic variants for cranial vault shape in humans. PLoS One. 2018 Apr 26;13(4):e0196148. doi: 10.1371/journal.pone.0196148. eCollection 2018. PMID: 29698431; PubMed Central PMCID: PMC5919379.

Ballantine JL, Carlson JC, Ferreira Zandoná AG, Agler C, Zeldin LP, Rozier RG, Roberts MW, Basta PV, Luo J, Antonio-Obese ME, McNeil DW, Weyant RJ, Crout RJ, Slayton RL, Levy SM, Shaffer JR, Marazita ML, North KE, Divaris K. Exploring the genomic basis of early childhood caries: a pilot study. Int J Paediatr Dent. 2018 Mar;28(2):217-225. doi: 10.1111/ipd.12344. Epub 2017 Oct 23. PMID 29057527; PubMed Central PMCID: PMC5811369.

Claes P, Roosenboom J, White JD, Swigut T, Sero D, Li J, Lee MK, Zaidi A, Mattern BC, Liebowitz C, Pearson L, González T, Leslie EJ, Carlson JC, Orlova E, Suetens P, Vandermeulen D, Feingold E, Marazita ML, Shaffer JR, Wysocka J, Shriver MD, Weinberg SM. Genome-wide mapping of global-to-local genetic effects on human facial shape. Nat Genet. 2018 Mar;50(3):414-423. doi: 10.1038/s41588-018-0057-4. Epub 2018 Feb 19. PMID 29459680; PubMed Central PMCID: PMC5937280.

Duverger O, Carlson JC, Karacz CM, Schwartz ME, Cross MA, Marazita ML, Shaffer JR, Morasso MI. Genetic variants in pachyonychia congenita-associated keratins increase susceptibility to tooth decay. PLoS Genet. 2018 Jan 22;14(1):e1007168. doi: 10.1371/journal.pgen.1007168. eCollection 2018 Jan. PMID: 29357356; PubMed Central PMCID: PMC5794186.

Shaffer JR, Li J, Lee MK, Roosenboom J, Orlova E, Adhikari K; 23andMe Research Team, Gallo C, Poletti G, Schuler-Faccini L, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, González-José R, Pfeffer PE, Wollenschlaeger CA, Hecht JT, Wehby GL, Moreno LM, Ding A, Jin L, Yang Y, Carlson JC, Leslie EJ, Feingold E, Marazita ML, Hinds DA, Cox TC, Wang S, Ruiz-Linares A, Weinberg SM. Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment. Am J Hum Genet. 2017 Dec 7;101(6):913-924. doi: 10.1016/j.ajhg.2017.10.001. Epub 2017 Nov 30.  PMID: 29198719; PubMed Central PMCID: PMC5812923.

Carlson JC, Standley J, Petrin A, Shaffer JR, Butali A, Buxó CJ, Castilla E, Christensen K, Deleyiannis FW, Hecht JT, Field LL, Garidkhuu A, Moreno Uribe LM, Nagato N, Orioli IM, Padilla C, Poletta F, Suzuki S, Vieira AR, Wehby GL, Weinberg SM, Beaty TH, Feingold E, Murray JC, Marazita ML, Leslie EJ. Identification of 16q21 as a modifier of nonsyndromic orofacial cleft phenotypes. Genet Epidemiol. 2017 Dec;41(8):887-897. doi: 10.1002/gepi.22090. Epub 2017 Nov 10.  PMID: 29124805; PubMed Central PMCID: PMC5728176.

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.

John R Shaffer