John R Shaffer, PhD

Assistant Professor, Human Genetics

Vice-chair for Education, Human Genetics

Diretor, MS and PhD Programs, Human Genetics

Director of Graduate Studies, Human Genetics

Assistant Professor, Oral and Craniofacial Sciences

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 (1/2019 to 6/2021)

 

Amery Treble-Barna, Lacey W. Heinsberg, Ava M. Puccio, John R. Shaffer, David  O. Okonkwo, Sue R. Beers, Daniel E. Weeks, Yvette P. Conley. Acute Brain-Derived Neurotrophic Factor DNA Methylation Trajectories in CSF and Associations with Outcomes following Severe Traumatic Brain Injury in Adults. Neurorehabilitation and Neural Repair 2021 Jun 25 (online ahdead of print) PMID: 34167372

 

Hanne Hoskens, Dongjing Liu, Sahin Naqvi, Myoung Keun Lee, Ryan J Eller, Karlijne Indencleef, Julie D. White, Jiarui Li, Greet Hens, Joanna Wysocka, Susan Walsh, Stephen Richmond, Mark D. Shriver, John R. Shaffer, Hilde Peeters, Seth M. Weinberg, Peter Claes. 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies. PLOS Genetics 2021 May 13;17(5):e1009528.  PMID: 33983923; PMCID: PMC8118281

 

Nandita Mukhopadhyay, Eleanor Feingold, Lina Moreno-Uribe, George Wehby, Luz Consuelo Valencia-Ramirez, Claudia Restrepo Muneton, Carmencita Padilla, Frederic Deleyiannis, Kaare Christensen, Fernando Poletta, Ieda Orioli, Jacqueline T. Hecht, Carmen Buxo, Azeez Butali, Wasiu Lanre Adeyemo, Alexandre Vieira, John R Shaffer, Jeff Murray, Seth M Weinberg, Elizabeth Leslie, Mary L Marazita. Genome-wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions. Frontiers in Cell and Developmental Biology. 2021 Apr 9;9:621482.  PMID: 33898419; PMCID: PMC8062975

 

Olubukola O. Olatosi, Azeez A . Alade, Afolabi Oyapero, Tamara Busch, Mary Li, John Pape, Joy Olotu, Waheed Awotoye, Mohaned Hassan, Chinyere Adeleke, Wasiu L. Adeyemo, John R. Shaffer, Mary Mazarita, Azeez Butali. Dental caries severity and nutritional status of Nigerian pre-school children. JDR Clinical and Translational Research. 2021 May 20;21(1):274.  PMID: 34016088; PMCID: PMC8139096

 

Sarah W. Curtis, Daniel Chang, Myoung Keun Lee, John R. Shaffer, Karlijne Indencleef, Michael P. Epstein, David J. Cutler, Jeffrey C. Murray, Eleanor Feingold, Terri H. Beaty, Peter Claes, Seth M. Weinberg, Mary L. Marazita, Jenna C. Carlson, Elizabeth J. Leslie. The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. Human Genetics and Genomics Advances 2021 Apr 8;2(2):100025. PMID: 33817668; PMCID: PMC8018676

 

Karlijne Indencleef, Hanne Hoskens, Myoung Keun Lee, Julie D White, Chenxing Liu (mentee), Ryan J Eller, Sahin Naqvi, George L Wehby, Lina M Moreno Uribe, Jacqueline T. Hecht, Ross E Long, Kaare Christensen, Frederic W Deleyiannis, Susan Walsh, Mark Shriver, Stephen Richmond, Joanna Wysocka, Hilde Peeters, John R Shaffer, Mary L Marazita, Greet Hens, Seth M Weinberg, Peter Claes. The intersection of the genetic architectures of orofacial clefts and normal facial variation. Frontiers in Genetics 2021 Feb 22;12:626403. PMID: 33692830; PMCID: PMC7937973

 

Sahin Naqvi, Yoeri Sleyp, Hanne Hoskens, Karlijne Indencleef, Jeffrey P. Spence, Rose Bruffaerts, Ahmed Radwan, Ryan J. Eller, Stephen Richmond, Mark D. Shriver, John R. Shaffer, Seth M. Weinberg, Susan Walsh, James Thomson,  Jonathan K. Pritchard, Stefan Sunaert, Hilde Peeters, Joanna Wysocka, Peter Claes. Shared heritability of face and brain shape distinct from cognitive traits. Nature Genetics 2021 Jun;53(6):830-839. PMID: 33821002; PMCID: PMC8232039

 

Yuqiao Zhou, Richard Cuddy, Daniel W. McNeil, Casey Wright, Richard J. Crout, Eleanor Feingold, Katherine Neiswanger, Mary L. Marazita, John R. Shaffer. Oral health and related risk factors in Appalachia differ by rurality. Community Dentistry and Oral Epidemiology 2021 (online ahead of print) PMID: 33368457

 

Ahmed M. El Sergani, Stephanie Brandebura, Carmencita Padilla, Azeez Butali, Wasiu L. Adeyemo, Consuelo Valencia-Ramírez, Claudia P. Restrepo Muñeton, Lina M. Moreno, Carmen J. Buxó, Katherine Neiswanger, John R. Shaffer, Mary L. Marazita, Seth M. Weinberg. The Influence of Sex and Ancestry on Three-dimensional Palate Shape. Cleft Palate Craniofacial Journal. 2021 (online ahead of print) PMID: 34231514

 

Betty Bonfante, Pierre Faux, Nicolas Navarro, Javier Mendoza-Revilla, Morgane Dubied, Charlotte Montillot, Emma Wentworth, Lauriane Poloni, Ceferino Varón-González, Phil Jones, Ziyi Xiong, Macarena Fuentes-Guajardo, Juan Camilo Chacón-Duque, Malena Hurtado, Valeria Villegas, Vanessa Granja, Victor Acuña-Alonzo, Claudia Jaramillo, William Arias, Rodrigo Barquera Lozano, Paola Everardo, Mirsha Sánchez-Quinto, Jorge Gómez-Valdés, Hugo Villamil-Ramírez, Caio C. Silva de Cerqueira, Tábita Hunemeier, Virginia Ramallo, Fan Liu, Seth Weinberg, John R. Shaffer, Evie Stergiakouli, Laurence J. Howe, Pirro G. Hysi, Timothy D. Spector, Lavinia Schuler-Faccini, Rolando Gonzalez-José, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Carla Gallo, Giovanni Poletti, Gabriel Bedoya, Francisco Rothhammer, Christel Thauvin, Laurence Faivre, Caroline Costedoat, David Balding, Timothy Cox, Manfred Kayser, Laurence Duplomb, Binnaz Yalcin, Justin Cotney, Kaustubh Adhikari and Andrés Ruiz- Linares. Archaic Introgression impacts on the human face and VPS13B influences natural facial variation in human and mice. Science Advances. 2021 Feb 5;7(6):eabc6160. PMID: 33547071; PMCID: PMC7864580

 

Dongjing Liu, Nora Alhazmi, Harold Matthews, Myoung Keun Lee, Jiarui Li, Jacqueline T. Hecht, George L. Wehby, Lina M. Moreno, Carrie L. Heike, Jasmien Roosenboom, Eleanor Feingold, Mary L. Marazita, Peter Claes, Eric C. Liao, Seth M. Weinberg, John R. Shaffer. Impact of low-frequency Coding Variants on Human Facial Shape. Scientific Reports. 2021 Jan 12;11(1):748. PMID: 33436952; PMCID: PMC7804299

 

Julie D. White, Karlijne Indencleef, Sahin Naqvi, Ryan J. Eller, Jasmien Roosenboom, Myoung Keun Lee, Jiarui Li, Jaaved Mohammed, Stephen Richmond, Ellen E. Quillen, Heather L. Norton, Eleanor Feingold, Tomek Swigut, Mary L. Marazita, Hilde Peeters, Greet Hens, John R. Shaffer, Joanna Wysocka, Susan Walsh, Seth M. Weinberg, Mark D. Shriver, Peter Claes. Insights into the genetic architecture of the human face. Nature Genetics. 2021 Jan;53(1):45-53. PMID: 33288918; PMCID: PMC7796995

 

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. 2021 Jan-Mar;24(1):44-54.  PMID: 31668963; PMCID: PMC7098844

 

Annie I. Arockiaraj, Dongjing Liu, John R Shaffer, Theresa A. Koleck, Elizabeth A. Crago, Daniel E. Weeks, Yvette P. Conley. Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage. Frontiers in Genetics. 2020 Jun 26;11:671. doi: 10.3389/fgene.2020.00671. eCollection 2020.  PMID: 32670358; PMCID: PMC7332758

 

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

John R Shaffer