Nathan Pankratz, PhD
Associate Professor, Department of Laboratory Medicine and Pathology
Associate Professor, Department of Laboratory Medicine and Pathology
PhD, Indiana University (Medical and Molecular Genetics), 2003
Purdue University (Genetic Biology), 1999
Dr. Pankratz is director of the Division of Computational Pathology and a member of the Division of Molecular Pathology and Genomics who conducts research at the intersection of genetics, epidemiology, statistics, and computer science in the context of population studies. After a decade of focus on the neurogenetics of Parkinson and Alzheimer disease, Pankratz has expanded his research efforts to investigate genes and biomarkers associated with cardiovascular disease and cancer. He conducts meta-analyses of data sets from large-scale studies of these diseases using linkage analysis, genome-wide association studies (GWAS), analysis of copy number variation (CNV), and analysis of targeted whole-exome and whole-genome sequencing data produced by next-generation sequencing (NGS) technologies.
NIH-sponsored cohort studies such as the Atherosclerosis Risk in Communities (ARIC) study and the Coronary Artery Risk Development in Young Adults (CARDIA) study give Pankratz and his fellow collaborators large data sets to analyze in their search for genetic factors involved in cardiovascular disease (CVD). These meta-analyses usually involve multiple institutions and collaborators, often under the banner of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Pankratz has led exome-wide meta-analyses for the CHARGE working groups focused on hemostatic factors, hematology markers, and inflammatory biomarkers of CVD, using data from as many as a hundred thousand research participants. Advanced software tools are required to manage the resulting large datasets and perform genetic analyses, and developing such software is a major focus of the Pankratz lab.
One of the Java software packages that the lab is actively developing is designed to more reliably identify copy number variants (CNVs) in the human genome. CNVs are gains or losses of large DNA segments that vary from one individual to the next. CNVs are associated with many common diseases, but they can be difficult to detect and measure with the most commonly used genomic platforms. Software that is easy to use, automatically implements best practices, and allows for the meta-analysis of multiple datasets will allow investigators to identify CNVs associated with complex diseases, such as those being studied by the CHARGE consortium. Large-scale genome-wide association studies focused on CNVs will go a long way toward clarifying their role in health and disease.
- Tang W, Stimson MR, Basu S, Heckbert SR, Cushman M, Pankow JS, Folsom AR, Pankratz N. Burden of rare exome sequence variants in PROC gene is associated with venous thromboembolism: a population-based study. J Thromb Haemost. 2019 Nov 4. doi: 10.1111/jth.14676.
- Pankratz N, Schick UM, Zhou Y, Zhou W, Ahluwalia TS, Allende ML, Auer PL, Bork-Jensen J, Brody JA, Chen MH, Clavo V, Eicher JD, Grarup N, Hagedorn EJ, Hu B, Hunker K, Johnson AD, Leusink M, Lu Y, Lyytikäinen LP, Manichaikul A, Marioni RE, Nalls MA, Pazoki R, Smith AV, van Rooij FJ, Yang ML, Zhang X, Zhang Y, Asselbergs FW, Boerwinkle E, Borecki IB, Bottinger EP, Cushman M, de Bakker PI, Deary IJ, Dong L, Feitosa MF, Floyd JS, Franceschini N, Franco OH, Garcia ME, Grove ML, Gudnason V, Hansen T, Harris TB, Hofman A, Jackson RD, Jia J, Kähönen M, Launer LJ, Lehtimäki T, Liewald DC, Linneberg A, Liu Y, Loos RJ, Nguyen VM, Numans ME, Pedersen O, Psaty BM, Raitakari OT, Rich SS, Rivadeneira F, Di Sant AM, Rotter JI, Starr JM, Taylor KD, Thuesen BH, Tracy RP, Uitterlinden AG, Wang J, Wang J, Dehghan A, Huo Y, Cupples LA, Wilson JG, Proia RL, Zon LI, O'Donnell CJ, Reiner AP, Ganesh SK. Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nat Genet. 2016 Aug;48(8):867-76. doi: 10.1038/ng.3607
- Chartier-Harlin MC, Dachsel JC, Vilariño-Güell C, Lincoln SJ, Leprêtre F, Hulihan MM, Kachergus J, Milnerwood AJ, Tapia L, Song MS, Le Rhun E, Mutez E, Larvor L, Duflot A, Vanbesien-Mailliot C, Kreisler A, Ross OA, Nishioka K, Soto-Ortolaza AI, Cobb SA, Melrose HL, Behrouz B, Keeling BH, Bacon JA, Hentati E, Williams L, Yanagiya A, Sonenberg N, Lockhart PJ, Zubair AC, Uitti RJ, Aasly JO, Krygowska-Wajs A, Opala G, Wszolek ZK, Frigerio R, Maraganore DM, Gosal D, Lynch T, Hutchinson M, Bentivoglio AR, Valente EM, Nichols WC, Pankratz N, Foroud T, Gibson RA, Hentati F, Dickson DW, Destée A, Farrer MJ (2011) Translation Initiator EIF4G1 Mutations in Familial Parkinson Disease. Am J Hum Genet 89(3):398-406
- Pankratz N, Dumitriu A, Hetrick K, Sun M, Latourelle JC, Wilk JB, Halter CH, Doheny KF, Gusella JF, Nichols WC, Myers RH, Foroud T, DeStefano AL, PSG–PROGENI and GenePD Investigators, Coordinators and Molecular Genetic Laboratories (2011) Copy Number Variation in Familial Parkinson Disease PLoS One 6(8):e20988
- Kirkpatrick, Robert M.; McGue, Matt K.; Iacono, William G.; Miller, Michael B.; Basu, Saonli; Pankratz, Nathan D. Low-frequency copy-number variants and general cognitive ability: No evidence of association. Intelligence (2014) Jan 42(1):98-106.
- Gong, Jian; Schumacher, Fredrick R.; Lim, Unhee; Hindorff, Lucia A.; Haessler, Jeff; Buyske, Steven G.; Carlson, Christopher S.; Rosse, Stephanie A.; B?žková, Petra; Fornage, Myriam; Gross, Myron D.; Pankratz, Nathan D.; Pankow, James S.; Schreiner, Pamela J.; Cooper, Richard S.; Ehret, Georg B.; Gu, C. Charles; Houston, Denise K.; Irvin, Marguerite Ryan; Jackson, Rebecca D.; Kuller, Lew H.; Hendersön, Brian E.; Cheng, Iona; Wilkens, Lynne Ross; Leppert, Mark F.; Lewis, Cora Elizabeth; Li, Rongling; Nguyen, Khanh Dung H; Goodloe, Robert J.; Farber-Eger, Eric; Boston, Jonathan; Dilks, Holli Hutcheson; Ritchie, Marylyn D.; Fowke, Jay H.; Pooler, Loreall C.; Graff, Misa; Fernández-Rhodes, Lindsay E.; Cochrane, Barbara; Boerwinkle, Eric Eric; Kooperberg, Charles L.; Matise, Tara Cox; Le Marchand, Loïc; Crawford, Dana C.; Haiman, Christopher A.; North, Kari E.; Peters, Ulrike. Fine mapping and identification of BMI loci in African Americans. American Journal of Human Genetics (2013) Oct 93(4):661-671.
- Schubert, Carla R.; Cruickshanks, Karen J.; Fischer, Mary E.; Huang, Guanhua; Klein, Ronald E.; Pankratz, Nathan D.; Zhong, Wenjun; Nondahl, David M. Odor identification and cognitive function in the beaver dam offspring study. Journal of Clinical and Experimental Neuropsychology (2013) Aug 35(7):669-676.
- Dumitriu, Alexandra; Latourelle, Jeanne C.; Hadzi, Tiffany C.; Pankratz, Nathan D.; Garza, Dan A.; Miller, John Paul; Vance, Jeffery M.; Foroud, Tatiana M.; Beach, Thomas Gerald; Myers, Richard H M. Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation. PLoS Genetics (2012) June 8(6):
- Pankratz, Nathan D.; Beecham, Gary W.; Destefano, Anita L.; Dawson, Ted Murray; Doheny, Kimberly Floy; Factor, Stewart A.; Hamza, Taye H.; Hung, Albert Y.; Hyman, Bradley T.; Ivinson, Adrian J.; Krainc, Dimitri; Latourelle, Jeanne C.; Clark, Lorraine N.; Marder, Karen S.; Martin, Eden R.; Mayeux, Richard P.; Ross, Owen A.; Scherzer, Clemens R.; Simon, David K.; Tanner, Caroline M.; Vance, Jeffery M.; Wszo?ek, Zbigniew K.; Zabetian, Cyrus P.; Myers, Richard H M; Payami, Haydeh; Scott, William K.; Foroud, Tatiana M. Meta-analysis of Parkinson's Disease: Identification of a novel locus, RIT2. Annals of Neurology (2012) 71(3):370-384.