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
2008-2022 | HUGEN 2022 Human Population Genetics
offered each Fall semester
2020-present | HUGEN 2080 Statistical Genetics
offered biennially in the Spring semester
2022-present | HUGEN 2020 Population Genetics and Genetic Epidemiology
offered each Fall semester
Recent published works (1/2020 to 6/2022)
Sahin Naqvi, Hanne Hoskens, Franziska Wilke, Seth M. Weinberg, John R. Shaffer, Susan Walsh, Mark D. Shriver, Joanna Wysocka, Peter Claes. Decoding the human face: challenges and progress in understanding the genetics of craniofacial morphology.Annual Reviews (in press)
Myoung Keun Lee, Zelda T. Dahl, Joel Anderton, Jennifer L. Maurer, Mary L. Marazita, John R. Shaffer, Seth M. Weinberg. Bent Pinkies: Quantifying Fifth Finger Clinodactyly in a Sample of U.S. Adults.PLOS One (in press).
Kimon Divaris, Simon Haworth, John R. Shaffer, Vuokko Anttonen, James D. Beck, Yasushi Furuichi, Birte Holtfreter, Daniel Jönsson, Thomas Kocher, Steven M. Levy, Patrik K.E. Magnusson, Daniel W. McNeil, Karl Michaëlsson, Kari E. North, Ulla Palotie, Panos N. Papapanou, Pirkko J. Pussinen, David Porteous, Kadri Reis, Aino Salminen, Arne S. Schaefer, Takeaki Sudo, Yi-Qian Sun, Anna Liisa Suominen, Toru Tamahara, Seth M. Weinberg, Pernilla Lundberg, Mary L. Marazita, Ingegerd Johansson. Phenotype Harmonization in the GLIDE2 Oral Health Genomics ConsortiumJournal of Dental Research (in press).
Kalo Sokoto, Lisa Platt, Linda Alexander, Betsy Foxman, John R. Shaffer, Mary L. Marazita, Daniel W. McNeil. Racism, Dental Care-Related Fear/Anxiety, and Oral Healthcare Utilization among Black/African American Women in Appalachia.Journal of Public Health Dentistry. 2022 Mar;82 Suppl 1:28-35. PMID: 35726465
Yuqiao Zhou, Daniel W. McNeil, Simon Haworth, Tom Dudding, Jonathan M. Chernus, Chenxing Liu, Dongjing Liu, Casey D. Wright, Jamey Brumbaugh, Cameron L. Randall, Robert J. Weyant, Richard J. Crout, Betsy Foxman, Steven Reis, Nicolas J. Timpson, Mary L. Marazita, John R. Shaffer. Genome-wide scan of dental fear and anxiety nominates novel genes.Journal of Dental Research (in press)
Nandita Mukhopadhyay, Eleanor Feingold, Lina Moreno-Uribe, George Wehby, Luz Consuelo Valencia-Ramirez, Claudia P. Restrepo Muneton, Carmencita Padilla, Frederic Deleyiannis, Kaare Christensen, Fernando A. Poletta, Ieda M Orioli, Jacqueline T. Hecht, Carmen J. Buxo, Azeez Butali, Wasiu L. Adeyemo, Alexandre R. Vieira, John R. Shaffer, Jeffrey C. Murray, Seth M. Weinberg, Elizabeth J. Leslie, Mary L. Marazita. Genome-wide association study of non-syndromic orofacial clefts in a multiethnic sample of families and controls identifies novel regions. Genetic Epidemiology. 2022 Apr;46(3-4):182-198. PMID: 33898419 PMCID: PMC8062975
Jenna Carlson, John R. Shaffer, Fred Deleyiannis, Jacqueline T. Hecht, George L. Wehby, Kaare Christensen, Eleanor Feingold, Seth M. Weinberg, Mary L. Marazita, Elizabeth Leslie. Genome-wide interaction study implicates VGLL2 and alcohol exposure and PRL and smoking in orofacial cleft risk. Frontiers in Cell and Developmental Biology. 2022 Feb 10;10:621261. PMID: 35223824 PMCID: PMC8866867
Dongjing Liu, Benjamin E. Zusman, John R. Shaffer, Yunqi Li, Annie I. Arockiaraj, Shuwei Liu, Daniel E. Weeks, Shashvat M. Desai, Patrick M. Kochanek, Ava M. Puccio, David O. Okonkwo, Yvette P. Conley, Ruchira M. Jha. Decreased DNA methylation of RGMA is associated with intracranial hypertension after severe traumatic brain injury: an exploratory epigenome-wide association study. Neurocricial Care. (in press)
Rasha N. Alotaibi, Brian J. Howe, Lina Moreno Uribe, Consuelo Valencia, Claudia Restrepo, Frederic W. B. Deleyiannis, Carmencita Padilla, Ieda M. Orioli, Carmen J Buxo, Jacqueline T. Hecht, George L. Wehby, Katherine Neiswanger, John R. Shaffer, Seth M. Weinberg, Mary L. Marazita. Genome-wide Association Study (GWAS) of dental caries in diverse populations.BMC Oral Health. 2021 Jul 26;21(1):377. PMID: 34311721 PMCID: PMC8311973
Myoung Keun Lee, Chenxing Liu, Elizabeth J. Leslie, John R. Shaffer, Jamie L. Perry, Seth M. Weinberg. Heritability Analysis in Twins Indicates a Genetic Basis for Velopharyngeal Morphology.Cleft Palate-Craniofacial Journal (in press)
Chenxing Liu, Myoung Keun Lee, Sahin Naqvi, Hanne Hoskens, Dongjing Liu, Julie D. White, Karlijne Indencleef, Harold Matthews, Ryan J. Eller, Jiarui Li, Jaaved Mohammed, Tomek Swigut, Stephen Richmond, Mange Manyama, Benedikt Hallgrímsson, Richard A. Spritz, Eleanor Feingold, Mary L. Marazita, Joanna Wysocka, Susan Walsh, Mark D. Shriver, Peter Claes, Seth M. Weinberg, John R. Shaffer. Genome Scans of Facial Features in East Africans and Cross-Population Comparisons Reveal Novel Associations.PLoS Genet. 2021 Aug 19;17(8):e1009695. PMID: 34411106 PMCID: PMC8375984
Dongjing Liu, Hyo-Jeong Ban, Ahmed El Sergani, Myoung Keun Lee, Jacqueline T. Hecht, George L. Wehby, Lina M. Moreno, Carrie L. Heike, Eleanor Feingold, Mary L. Marazita, Seongwon Cha, Heather Szabo-Rogers, Seth M. Weinberg, John R. Shaffer. PRICKLE1 x FOCAD interaction revealed by genome-wide vQTL analysis of human facial traits. Frontiers in Genetics. 2021 Aug 9;12:674642. PMID: 34434215 PMCID: PMC8381734
Lacey W. Heinsberg, Dongjing Liu,John R. Shaffer, Daniel E. Weeks, Yvette P. Conley. Characterization of Cerebrospinal Fluid DNA Methylation Age During the Acute Recovery Period Following Aneurysmal Subarachnoid Hemorrhage.Epigenetics Communications. (2021) 1:2. PMID: 35083469; PMCID: PMC8787331
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 Sep;35(9):790-800. PMID: 34167372 PMCID: PMC8546867
Olubukola O. Olatosi, Mary Li, Azeez A. Alade, Afolabi Oyapero, Tamara Busch, John Pape, Joy Olotu, Waheed Awotoye, Mohaned Hassan, Chinyere Adeleke, Wasiu L. Adeyemo, Elizabeth O. Sote, John R. Shaffer, Mary Marazita, Azeez Butali. Replication of GWAS significant loci in a Sub-Saharan African Cohort with Early Childhood Caries: a pilot study.BMC Oral Health. 2021 May 20;21(1):274. PMID: 34016088 PMCID: PMC8139096
Dongjing Liu, Annie I. Arockiaraj, John R. Shaffer, Elizabeth A. Crago, Daniel E. Weeks, Yvette P. Conley. ANGPT1 methylation is associated with delayed cerebral ischemia after acute subarachnoid hemorrhage – An epigenome-wide association study. Epigenetics Communications. 2021;1:3.doi: 10.1186/s43682-021-00001-7. PMID: 35359917 PMCID: PMC8967216
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. Oct;49(5):427-436. PMID: 33368457 PMCID: PMC8381283
Ahmed M. El Sergani, Stephanie Brandebura, Carmencita Padilla, Azeez Butali, Wasiu L. Adeyemo, Consuelo Valencia-Ramirez, Claudia P. Restrepo Muneton, Lina M. Moreno, Carmen J. Buxo, 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 Nov-Dec 01;32(8):2883-2887. PMID: 34231514 PMCID: PMC8563422
Ahmed M El Sergani, Stephanie Brandebura, Carmencita Padilla, Azeez Butali, Wasiu L Adeyemo, Consuelo Valencia-Ramirez, Claudia P Restrepo Muneton, Lina M Moreno, Carmen J Buxo, Ross E Long Jr, Katherine Neiswanger, John R Shaffer, Mary L Marazita, Seth M Weinberg. Parents of Children With Nonsyndromic Orofacial Clefting Show Altered Palate Shape.Cleft Palate Craniofacial Journal.2021 Jul;58(7):847-853. PMID: 33111571; PMCID: PMC8079510
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
Yueyao Wang, Dipankar Bandyopadhyay, John R. Shaffer, Xiaowei Wu. Gene-based association mapping for dental caries in the GENEVA program. Journal of Dentistry and Dental Medicine 2020; 3(4):156. PMID: 34622142 PMCID: PMC8494074
