John R Shaffer, PhD

Assistant Professor, Human Genetics

Assistant Professor, Oral Biology

Contact

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.


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

2020 | HUGEN 2080 Statistical Genetics


Selected Publications

Recent published works (1/2018 to 6/2020)

 

Lacey W. Heinsberg, Annie I. Arockiaraj, Elizabeth A. Crago, Samuel M. Poloyac, Dianxu Ren, John R. Shaffer, Paula R. Sherwood, Susan M. Sereika, Daniel E. Weeks, Yvette P. Conley. Genetic variability and trajectories of DNA methylation support a role for HAMP in patient outcomes after aneurysmal subarachnoid hemorrhage. Neurocritical Care 2020 Apr;32(2):550-563. PMID: 31346934; PMCID: PMC6981002

 

Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FM, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TE, Palstra RT, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M; International Visible Trait Genetics (VisiGen) Consortium. Novel genetic loci affecting facial shape variation in humans. Elife 2019 Nov 26;8. pii: e49898. PMID: 31763980; PMCID: PMC6905649

 

Camden P. Bay, Steven M. Levy, Kethleen F. Janz, Brian J. Smith, John R. Shaffer, Mary L. Marazita, Trudy L. Burns.  Genome-wide Association Analysis of Longitudinal Bone Mineral Content Data from the Iowa Bone Development Study. Journal of Clinical Densitometry. (online ahead of print) PMID: 31668963; PMCID: PMC7098844

 

Ekaterina Orlova, Jenna C. Carlson, Myoung Keun Lee, Eleanor Feingold,  Daniel W. McNeil, Richard J. Crout, Robert J. Weyant, Mary L. Marazita, John R. Shaffer. Pilot GWAS of Dental Caries in African-Americans shows Genetic Heterogeneity. BMC Oral Health 2019 Sep 18;19(1):215. PMID: 31533690; PMCID: PMC6751797

 

Anna L. Zakas, Claire Leifeste, Beth Dudley, Eve Karloski, Samantha Afonso, Robin E. Grubs, John R. Shaffer, Andrea L. Durst, Michael D. Parkinson, Randall Brand. The Impact of Genetic Counseling on Patient Engagement in a Specialty Cancer Clinic. Journal of Genetic Counseling. 2019 Oct;28(5):9740981. PMID: 31293033; DOI: 10.1002/jgc4.1149

 

Dmitry Shungin, Simon Haworth, Kimon Divaris, Yoichiro Kamatani, Myoung Keun Lee, Kelsey Grinde, George Hindy,Viivi Alaraudanjoki, Paula Pesonen, Alexander Teumer, Birte Holtfreter, Saori Sakaue, Jun Hirata, Franco Giulianini, Daniel I Chasman, Paul M Ridker, Yau-Hua Yu, Patrik Magnusson, Takeaki Sudo, Yukinori Okada, Thomas Kocher, Vuokko Anttonen, Marja-Liisa Laitala, Marju Orho-Melander, John R. Shaffer, Mary Marazita, Michiaki Kubo, Yasushi Furuichi, Steve Offenbacher, Cary Agler, Paul W. Franks, Nicholas Timpson, Ingegerd Johansson.  Understanding dental diseases through combined genome-wide analyses of clinical and self-reported data. Nature Communications 2019 Jun 24;10(1):2773. PMID: 31235808; PMCID: PMC6591304

 

Jenna C. Carlson, Deepti Anand, Carmen J. Buxo, Kaare Christensen, Fred Deleyiannis, Jacqueline T. Hecht, Lina M. Moreno, Ieda M. Orioli, Carmencita Padilla, John R. Shaffer, Alexandre R. Vieira, George L. Wehby, Seth M. Weinberg, Jeffrey C. Murray, Terri H. Beaty, Irfan Saadi, Salil A. Lachke, Mary L. Marazita, Eleanor Feingold, Elizabeth J. Leslie. A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genetic Epidemiology 2019 Sep;43(6):704-716. PMID: 31172578; PMCID: PMC6687557

 

Mengxia Chen, Casey D. Wright, Oluwabunmi Tokede, Alfa Yansane, Alexander Montasem, E. Kalenderian, Terri Beaty, Eleanor Feingold, Richard J. Crout, Katherine Neiswanger, John R. Shaffer, Robert J. Weyant, Mary L. Marazita, Daniel W. McNeil. Predictors of Dental Care Utilization in North Central Appalachia in the USA. Community Dent Oral Epidemiol 2019 Aug;47(4):283-290. PMID: 30993747; PMCID: PMC6631312

 

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. PMCID: PMC6613560

 

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.

 

John R Shaffer