Tara Matise

Tara Matise
Tara Matise
Professor-Chair, Department of Genetics
604 Allison Road, Piscataway, NJ 08854-8082
Computational Human Genetics
(848) 445-3125
(732) 445-1636
Nelson C205

I head the Laboratory of Computational Genetics, in the Department of Genetics at Rutgers University. Computational Genetics represents my joint interests in human genetics, data science, statistical genetics, and bioinformatics. The goal of our projects is to contribute to the identification of human disease genes. I am also head of the Computational Genetics Program in the Human Genetics Institute of New Jersey (HGINJ.org).

Since 2015 I have been co-director, with Dr. Steve Buyske, of the Coordinating Center (CC) for the NHGRI Genome Sequencing Program.  The National Human Genome Research Institute (NHGRI) Genome Sequencing Program (GSP) uses genome sequencing to identify genes and genomic variants underlying human inherited disease across its full spectrum, including rare diseases likely to be due to rare variants with strong effects (Mendelian), and common genetically complex diseases that are caused by many variants. Novel methods, tools, and knowledge gained through the GSP will be rapidly shared to enhance the ability of the community to pursue other human inherited diseases. The GSP Coordinating Center provides scientific leadership and expertise for specific cross-program objectives and coordination for administrative, logistical, and outreach activities.

Since 2008 I have been co-director, with Dr. Steve Buyske, of the Coordinating Center (CC) for The PAGE Study (PAGE I 2008-2012; PAGE II 2013-2017). This study investigates population-specific variation in genetic disease susceptibility, focusing on non-European populations. You can read a 2013 press announcement here. For this NIH-funded project the Rutgers coordinating center manages the quality control, integration, and dissemination of the large-scale genotype data generated in PAGE, performs genotype imputation and ancestry deconvolution, organizes group discussions and meetings, facilitates collaborations, and oversees the logistics of the PAGE study. Our work is facilitated by collaborators at the USC/Information Sciences Institute and Stanford University. The CC team members bring expertise in population, statistical, and quantitative human genetics, computer science, genome sequencing and bioinformatics. The CC's combined expertise will help advance PAGE II's research on understanding the global relevance of disease-associated alleles across diverse human populations.

My lab also maintains The Rutgers Maps. An extension of our early work constructing genetic linkage maps using my MultiMap map-building software, the Rutgers Maps incorporate marker physical positions into a novel mapping approach to create combined physical-linkage maps. These maps contain over 28,000 markers genoytped in pedigrees and represent very comprehensive linkage maps. The Rutgers Maps also serve as a framework for interpolating the genetic map position of any marker, gene, or physical position in the genome. We have interpolated positions for over 50M SNPs onto the Rutgers Maps.


PUBMED link to all articles

Selected articles:

Lindsay Fernández-Rhodes, L., Malinowski, J.R., ..., Matise, T. ... Franceschini, N., North, N.E. 2018. The genetic underpinnings of variation in ages at menarche and natural menopause among women from the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) Study: A trans-ethnic meta-analysis. PLoS One, https://doi.org/10.1371/journal.pone.0200486.

Gong, J., Nishimura, K. K., Fernandez-Rhodes, L., Haessler, J., Bien, S., Graff, M., . . . Matise, T.C., North K.E., Peters, U. (2018). Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI. Int J Obes (Lond), 42(3), 384-390. doi:10.1038/ijo.2017.304

Yoneyama, S., Yao, J., Guo, X., Fernandez-Rhodes, L., Lim, U., Boston, J., . . . North, K. E. (2017). Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations. [obesity]. Int J Obes (Lond), 41(2), 324-331. doi:10.1038/ijo.2016.207

Fernandez-Rhodes, L., Gong, J., Haessler, J., Franceschini, N., Graff, M., Nishimura, K. K., . . . Matise, T.C., Peters, U., North, K. E. (2017). Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci. Hum Genet, 136(6), 771-800. doi:10.1007/s00439-017-1787-6

Locke, A.E., Kahali, B., Berndt, S.I., Justice, A.E., ... Matise TC (author # 357 of 499 authors) ..., Hirschhorn, J.N., Loos, R.J., and Speliotes, E.K. (2014). Large-scale genetic studies of body mass index provide insight into the biological basis of obesity. Accepted at Nature.

Shungin, D., Winkler, T.W., Croteau-Chonka, D.C., ... Matise TC (author # 295 of 419 authors) ..., Morris, A.P., Lindgren, C.M., and Mohlke, K.L. (2014). New genetic loci link adipose and insulin biology to body fat distribution. Accepted at Nature.

Park SL, Caberto CP, Lin Y, Goodloe RJ, Dumitrescu L, Love SA, Matise TC, Hindorff LA, Fowke JH, Schumacher FR, Beebe-Dimmer J, Chen C, Hou L, Thomas F, Deelman E, Han Y, Peters U, North KE, Heiss G, Crawford DC, Haiman CA, Wilkens LR, Bush WS, Kooperberg C, Cheng I, Le Marchand L. (2014) Association of Cancer Susceptibility Variants with Risk of Multiple Primary Cancers: The Population Architecture using Genomics and Epidemiology Study. Cancer Epidemiol Biomarkers Prev. 2014 Nov;23(11):2568-78.

Restrepo, N.A., Spencer, K.L., Goodloe, R., Garrett, T.A., Heiss, G., B?žková, P., Jorgensen, N., Jensen, R.A., Matise, T.C., Hindorff, L.A., Klein, B.E.K., Klein, R., Wong, T.Y., Cheng, C.-Y., Cornes, B.K., Tai, E.S., Ritchie, M.D., Haines, J.L., and Crawford, D.C. (2014). Genetic determinants of age-related macular degeneration in diverse populations from the PAGE Study. Invest Ophthalmol Vis Sci. 2014 Sep 9;55(10):6839-50.

Wood, A.R., Esko, T., Yang, J., ... Matise TC (author # 300 of 446 authors) ..., Visscher, P.M., Hirschhorn, J.N., and Frayling, T.M. (2014). Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet. 2014 Nov;46(11):1173-86.  

Lim, U., Kocarnik, J.M., Bush, W.S., Matise, T.C., Caberto, C., Park, S.L., Carlson, C.S., Deelman, E., Duggan, D., Fesinmeyer, M., Haiman, C.A., Henderson, B.E., Hindorff, L.A., Kolonel, L.N., Peters, U., Stram, D.O., Tiirikainen, M., Wilkens, L.R., Wu, C., Kooperberg, C., and Le Marchand, L. (2014). Pleiotropy of Cancer Susceptibility Variants on the Risk of Non-Hodgkin Lymphoma: The PAGE Consortium. PLoS One 9, e89791. 3943855

Zhang, L., Spencer, K.L., Voruganti, V.S., Jorgensen, N.W., Fornage, M., Best, L.G., Brown-Gentry, K.D., Cole, S.A., Crawford, D.C., Deelman, E., Franceschini, N., Gaffo, A.L., Glenn, K.R., Heiss, G., Jenny, N.S., Kottgen, A., Li, Q., Liu, K., Matise, T.C., North, K.E., Umans, J.G., and Kao, W.H. (2013a). Association of Functional Polymorphism rs2231142 (Q141K) in the ABCG2 Gene With Serum Uric Acid and Gout in 4 US Populations: The PAGE Study. American Journal of Epidemiol. 177:923-32.

Zhang, L., Spencer, K.L., Voruganti, V.S., Jorgensen, N.W., Fornage, M., Best, L.G., Brown-Gentry, K.D., Cole, S.A., Crawford, D.C., Deelman, E., Franceschini, N., Gaffo, A.L., Glenn, K.R., Heiss, G., Jenny, N.S., Kottgen, A., Li, Q., Liu, K., Matise, T.C., North, K.E., Umans, J.G., and Kao, W.H. (2013a). Association of Functional Polymorphism rs2231142 (Q141K) in the ABCG2 Gene With Serum Uric Acid and Gout in 4 US Populations: The PAGE Study. American Journal of Epidemiol. 177:923-32. 21. Zhang, L., Buzkova, P., Wassel, C.L., Roman, M.J., North, K.E., Crawford, D.C., Boston, J., Brown-Gentry, K.D., Cole, S.A., Deelman, E., Goodloe, R., Wilson, S., Heiss, G., Jenny, N.S., Jorgensen, N.W., Matise, T.C., McClellan, B.E., Jr., Nato, A.Q., Jr., Ritchie, M.D., Franceschini, N., and Kao, W.H. (2013b). Lack of associations of ten candidate coronary heart disease risk genetic variants and subclinical atherosclerosis in four US populations: the Population Architecture using Genomics and Epidemiology (PAGE) study. Atherosclerosis 228, 390-399. 3717342

Wu, Y., Waite, L.L., Jackson, A.U., Sheu, W.H., Buyske, S., Absher, D., Arnett, D.K., Boerwinkle, E., Bonnycastle, L.L., Carty, C.L., Cheng, I., Cochran, B., Croteau-Chonka, D.C., Dumitrescu, L., Eaton, C.B., Franceschini, N., Guo, X., Henderson, B.E., Hindorff, L.A., Kim, E., Kinnunen, L., Komulainen, P., Lee, W.J., Le Marchand, L., Lin, Y., Lindstrom, J., Lingaas-Holmen, O., Mitchell, S.L., Narisu, N., Robinson, J.G., Schumacher, F., Stancakova, A., Sundvall, J., Sung, Y.J., Swift, A.J., Wang, W.C., Wilkens, L., Wilsgaard, T., Young, A.M., Adair, L.S., Ballantyne, C.M., Buzkova, P., Chakravarti, A., Collins, F.S., Duggan, D., Feranil, A.B., Ho, L.T., Hung, Y.J., Hunt, S.C., Hveem, K., Juang, J.M., Kesaniemi, A.Y., Kuusisto, J., Laakso, M., Lakka, T.A., Lee, I.T., Leppert, M.F., Matise, T.C., Moilanen, L., Njolstad, I., Peters, U., Quertermous, T., Rauramaa, R., Rotter, J.I., Saramies, J., Tuomilehto, J., Uusitupa, M., Wang, T.D., Boehnke, M., Haiman, C.A., Chen, Y.D., Kooperberg, C., Assimes, T.L., Crawford, D.C., Hsiung, C.A., North, K.E., and Mohlke, K.L. (2013). Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained. PLoS Genet 9, e1003379. 3605054

Spencer, K.L., Malinowski, J., Carty, C.L., Franceschini, N., Fernandez-Rhodes, L., Young, A., Cheng, I., Ritchie, M.D., Haiman, C.A., Wilkens, L., Chunyuanwu, Matise, T.C., Carlson, C.S., Brennan, K., Park, A., Rajkovic, A., Hindorff, L.A., Buyske, S., and Crawford, D.C. (2013). Genetic variation and reproductive timing: African American women from the Population Architecture using Genomics and Epidemiology (PAGE) Study. PLoS One 8, e55258. 3570525

Peters, U., North, K.E., Sethupathy, P., Buyske, S., Haessler, J., Jiao, S., Fesinmeyer, M.D., Jackson, R.D., Kuller, L.H., Rajkovic, A., Lim, U., Cheng, I., Schumacher, F., Wilkens, L., Li, R., Monda, K., Ehret, G., Nguyen, K.D., Cooper, R., Lewis, C.E., Leppert, M., Irvin, M.R., Gu, C.C., Houston, D., Buzkova, P., Ritchie, M., Matise, T.C., Le Marchand, L., Hindorff, L.A., Crawford, D.C., Haiman, C.A., and Kooperberg, C. (2013). A systematic mapping approach of 16q12.2/FTO and BMI in more than 20,000 African Americans narrows in on the underlying functional variation: results from the Population Architecture using Genomics and Epidemiology (PAGE) study. PLoS Genet 9, e1003171. 3547789

Pendergrass, S.A., Brown-Gentry, K., Dudek, S., Frase, A., Torstenson, E.S., Goodloe, R., Ambite, J.L., Avery, C.L., Buyske, S., Buzkova, P., Deelman, E., Fesinmeyer, M.D., Haiman, C.A., Heiss, G., Hindorff, L.A., Hsu, C.N., Jackson, R.D., Kooperberg, C., Le Marchand, L., Lin, Y., Matise, T.C., Monroe, K.R., Moreland, L., Park, S.L., Reiner, A., Wallace, R., Wilkens, L.R., Crawford, D.C., and Ritchie, M.D. (2013). Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genet 9, e1003087. 3561060

Londono, D., Chen, K.M., Musolf, A., Wang, R., Shen, T., Brandon, J., Herring, J.A., Wise, C.A., Zou, H., Jin, M., Yu, L., Finch, S.J., Matise, T.C., and Gordon, D. (2013). A novel method for analyzing genetic association with longitudinal phenotypes. Stat Appl Genet Mol Biol 12, 241-261.

Graff, M., Gordon-Larsen, P., Lim, U., Fowke, J.H., Love, S.A., Fesinmeyer, M., Wilkens, L.R., Vertilus, S., Ritchie, M.D., Prentice, R.L., Pankow, J., Monroe, K., Manson, J.E., Le Marchand, L., Kuller, L.H., Kolonel, L.N., Hong, C.P., Henderson, B.E., Haessler, J., Gross, M.D., Goodloe, R., Franceschini, N., Carlson, C.S., Buyske, S., Buzkova, P., Hindorff, L.A., Matise, T.C., Crawford, D.C., Haiman, C.A., Peters, U., and North, K.E. (2013). The influence of obesity-related single nucleotide polymorphisms on BMI across the life course: the PAGE study. Diabetes 62, 1763-1767. 3636619

Gong, J., Schumacher, F., Lim, U., Hindorff, L.A., Haessler, J., Buyske, S., Carlson, C.S., Rosse, S., Buzkova, P., Fornage, M., Gross, M., Pankratz, N., Pankow, J.S., Schreiner, P.J., Cooper, R., Ehret, G., Gu, C.C., Houston, D., Irvin, M.R., Jackson, R., Kuller, L., Henderson, B., Cheng, I., Wilkens, L., Leppert, M., Lewis, C.E., Li, R., Nguyen, K.D., Goodloe, R., Farber-Eger, E., Boston, J., Dilks, H.H., Ritchie, M.D., Fowke, J., Pooler, L., Graff, M., Fernandez-Rhodes, L., Cochrane, B., Boerwinkle, E., Kooperberg, C., Matise, T.C., Le Marchand, L., Crawford, D.C., Haiman, C.A., North, K.E., and Peters, U. (2013). Fine Mapping and Identification of BMI Loci in African Americans. Am J Hum Genet 93, 661-671. 3791273

Fesinmeyer, M.D., North, K.E., Ritchie, M.D., Lim, U., Franceschini, N., Wilkens, L.R., Gross, M.D., Buzkova, P., Glenn, K., Quibrera, P.M., Fernandez-Rhodes, L., Li, Q., Fowke, J.H., Li, R., Carlson, C.S., Prentice, R.L., Kuller, L.H., Manson, J.E., Matise, T.C., Cole, S.A., Chen, C.T., Howard, B.V., Kolonel, L.N., Henderson, B.E., Monroe, K.R., Crawford, D.C., Hindorff, L.A., Buyske, S., Haiman, C.A., Le Marchand, L., and Peters, U. (2013a). Genetic risk factors for BMI and obesity in an ethnically diverse population: results from the population architecture using genomics and epidemiology (PAGE) study. Obesity 21, 835-846. 3482415

Fesinmeyer, M.D., North, K.E., Lim, U., Buzkova, P., Crawford, D.C., Haessler, J., Gross, M.D., Fowke, J.H., Goodloe, R., Love, S.A., Graff, M., Carlson, C.S., Kuller, L.H., Matise, T.C., Hong, C.P., Henderson, B.E., Allen, M., Rohde, R.R., Mayo, P., Schnetz-Boutaud, N., Monroe, K.R., Ritchie, M.D., Prentice, R.L., Kolonel, L.N., Manson, J.E., Pankow, J., Hindorff, L.A., Franceschini, N., Wilkens, L.R., Haiman, C.A., Le Marchand, L., and Peters, U. (2013b). Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study. BMC Med Genet 14, 6. 3564691

Duan, Q., Liu, E.Y., Auer, P.L., Zhang, G., Lange, E.M., Jun, G., Bizon, C., Jiao, S., Buyske, S., Franceschini, N., Carlson, C.S., Hsu, L., Reiner, A.P., Peters, U., Haessler, J., Curtis, K., Wassel, C.L., Robinson, J.G., Martin, L.W., Haiman, C.A., Le Marchand, L., Matise, T.C., Hindorff, L.A., Crawford, D.C., Assimes, T.L., Kang, H.M., Heiss, G., Jackson, R.D., Kooperberg, C., Wilson, J.G., Abecasis, G.R., North, K.E., Nickerson, D.A., Lange, L.A., and Li, Y. (2013). Imputation of coding variants in African Americans: better performance using data from the exome sequencing project. Bioinformatics 29, 2744-2749. 3799474

Carty, C.L., Spencer, K.L., Setiawan, V.W., Fernandez-Rhodes, L., Malinowski, J., Buyske, S., Young, A., Jorgensen, N.W., Cheng, I., Carlson, C.S., Brown-Gentry, K., Goodloe, R., Park, A., Parikh, N.I., Henderson, B., Le Marchand, L., Wactawski-Wende, J., Fornage, M., Matise, T.C., Hindorff, L.A., Arnold, A.M., Haiman, C.A., Franceschini, N., Peters, U., and Crawford, D.C. (2013). Replication of genetic loci for ages at menarche and menopause in the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) study. Human Reprod 28, 1695-1706. 3657124

Carlson, C.S., Matise, T.C., North, K.E., Haiman, C.A., Fesinmeyer, M.D., Buyske, S., Schumacher, F.R., Peters, U., Franceschini, N., Ritchie, M.D., Duggan, D.J., Spencer, K.L., Dumitrescu, L., Eaton, C.B., Thomas, F., Young, A., Carty, C., Heiss, G., Le Marchand, L., Crawford, D.C., Hindorff, L.A., Kooperberg, C.L., and Consortium, P. (2013). Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study. PLoS Biology 11, e1001661. 3775722

Liu EY, Buyske S, Aragaki AK, Peters U, Boerwinkle E, Carlson C, Carty C, Crawford DC, Haessler J, Hindorff LA, Marchand LL, Manolio TA, Matise T, Wang W, Kooperberg C, North KE, Li Y. 2012. Genotype imputation of Metabochip SNPs using a study-specific reference panel of ~4,000 haplotypes in African Americans from the Women's Health Initiative. Genet Epidemiol. 2012 Feb;36(2):107-17. PMID: 22851474

Fesinmeyer MD, North KE, Ritchie MD, Lim U, Franceschini N, Wilkens LR, Gross MD, B?žková P, Glenn K, Quibrera PM, Fernández-Rhodes L, Li Q, Fowke JH, Li R, Carlson CS, Prentice RL, Kuller LH, Manson JE, Matise TC, Cole SA, Chen CT, Howard BV, Kolonel LN, Henderson BE, Monroe KR, Crawford DC, Hindorff LA, Buyske S, Haiman CA, Le Marchand L, Peters U. 2012. Genetic Risk Factors for BMI and Obesity in an Ethnically Diverse Population: Results From the Population Architecture Using Genomics and Epidemiology (PAGE) Study. Obesity (Silver Spring). 2012 Jun 22. PMID: 22810976

Buyske S, Wu Y, Carty CL, Cheng I, Assimes TL, Dumitrescu L, Hindorff LA, Mitchell S, Ambite JL, Boerwinkle E, Buzkova P, Carlson CS, Cochran B, Duggan D, Eaton CB, Fesinmeyer MD, Franceschini N, Haessler J, Jenny N, Kang HM, Kooperberg C, Lin Y, Le Marchand L, Matise TC, Robinson JG, Rodriguez C, Schumacher FR, Voight BF, Young A, Manolio TA, Mohlke KL, Haiman CA, Peters U, Crawford DC, North KE. 2012. Evaluation of the metabochip genotyping array in African Americans and implications for fine mapping of GWAS-identified loci: the PAGE study. PLoS One. 2012;7(4):e35651. PMID: 22539988

Carty CL, Buzková P, Fornage M, Franceschini N, Cole S, Heiss G, Hindorff LA, Howard BV, Mann S, Martin LW, Zhang Y, Matise TC, Prentice R, Reiner AP, Kooperberg C. 2012. Associations between incident ischemic stroke events and stroke and cardiovascular disease-related genome-wide association studies single nucleotide polymorphisms in the Population Architecture Using Genomics and Epidemiology study. Circ Cardiovasc Genet. 2012 Apr 1;5(2):210-6. PMID: 22403240

Pendergrass SA, Brown-Gentry K, Dudek SM, Torstenson ES, Ambite JL, Avery CL, Buyske S, Cai C, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Moreland L, Monroe K, Reiner AP, Wallace R, Wilkens LR, Crawford DC, Ritchie MD. 2011. The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery. Genet Epidemiol. 2011 Jul;35(5):410-22

Matise TC, Ambite JA, Buyske S, Carlson C, Cole SA, Crawford DC, Haiman CA, Heiss G, Kooperberg C, Le Marchand L, Manolio TA, North KE, Peters U, Ritchie MD, Hindorff LA, Haines JL, for The PAGE Study. 2011. The next PAGE in understanding complex traits: design for the analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study. Am J Epidemiol 174: 849-859. PMC3176830

Mehta G., Deelman E., Knowles J.A., Chen T., Wang Y., Vöckler J., Buyske S., and Matise T.C. (2011). Enabling Data and Compute Intensive Workflows in Bioinformatics. High Performance Bioinformatics and Biomedicine (HiBB) 2011, Bordeaux, France.

He C, Weeks DE, Buyske S, Abecasis GR, Stewart WC, Matise TC. 2010. Enhanced Linkage Maps from Family-based Studies: population-specific comparisons. BMC Med Genet. 2011 Jan 19;12(1):15. 

Clark AG, Wang X, Matise T. 2010. Contrasting Methods of Quantifying fine Structure of Human Recombination. Annu Rev Genomics Hum Genet. http://highwire.stanford.edu/cgi/medline/pmid;20690817

Chen C, Yang G, Buyske S, Matise T, Finch SJ, Gordon D. 2009. Transmission disequilibrium test power and sample size in the presence of locus heterogeneity. Stat Appl Genet Mol Biol. 8(1):Article 44.

Buyske S, Yang G, Matise TC, Gordon D. 2009. When a case is not a case: effects of phenotype misclassification on power and sample size requirements for the disequilibrium test with affected child trios. Hum Hered. 67(4):287-92.

Matise TC, Chen F, Chen W, De La Vega FM, Hansen M, He C, Hyland FC, Kennedy GC, Kong X, Murray SS, Ziegle JS, Stewart WC, Buyske S. 2007. A second-generation combined linkage physical map of the human genome. Genome Res. 17(12):1783-6.