A novel TCF7L2 type 2 diabetes SNP identified from fine mapping in African American women

Stephen A. Haddad, Julie R. Palmer, Kathryn L. Lunetta, Maggie C.Y. Ng, Edward A. Ruiz-Narváez, Daniel Shriner, Brian H. Chen, Jiang Li, Wei Min Chen, Xiuqing Guo, Jiankang Liu, Suzette J. Bielinski, Lisa R. Yanek, Michael A. Nalls, Mary E. Comeau, Laura J. Rasmussen-Torvik, Richard A. Jensen, Daniel S. Evans, Yan V. Sun, Ping AnSanjay R. Patel, Yingchang Lu, Jirong Long, Loren L. Armstrong, Lynne Wagenknecht, Lingyao Yang, Beverly M. Snively, Nicholette D. Palmer, Poorva Mudgal, Carl D. Langefeld, Keith L. Keene, Barry I. Freedman, Josyf C. Mychaleckyj, Uma Nayak, Leslie J. Raffel, Mark O. Goodarzi, Y. D.Ida Chen, Herman A. Taylor, Adolfo Correa, Mario Sims, David Couper, James S. Pankow, Eric Boerwinkle, Adebowale Adeyemo, Ayo Doumatey, Guanjie Chen, Rasika A. Mathias, Dhananjay Vaidya, Andrew B. Singleton, Alan B. Zonderman, MEDIA Consortium

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


SNP rs7903146 in the Wnt pathway's TCF7L2 gene is the variant most significantly associated with type 2 diabetes to date, with associations observed across diverse populations. We sought to determine whether variants in other Wnt pathway genes are also associated with this disease. We evaluated 69 genes involved in the Wnt pathway, including TCF7L2, for associations with type 2 diabetes in 2632 African American cases and 2596 controls from the Black Women's Health Study. Tag SNPs for each gene region were genotyped on a custom Affymetrix Axiom Array, and imputation was performed to 1000 Genomes Phase 3 data. Gene-based analyses were conducted using the adaptive rank truncated product (ARTP) statistic. The PSMD2 gene was significantly associated with type 2 diabetes after correction for multiple testing (corrected p = 0.016), based on the nine most significant single variants in the +/- 20 kb region surrounding the gene, which includes nearby genes EIF4G1, ECE2, and EIF2B5. Association data on four of the nine variants were available from an independent sample of 8284 African American cases and 15,543 controls; associations were in the same direction, but weak and not statistically significant. TCF7L2 was the only other gene associated with type 2 diabetes at nominal p <0.01 in our data. One of the three variants in the best gene-based model for TCF7L2, rs114770437, was not correlated with the GWAS index SNP rs7903146 and may represent an independent association signal seen only in African ancestry populations. Data on this SNP were not available in the replication sample.

Original languageEnglish (US)
Article numbere0172577
JournalPloS one
Issue number3
StatePublished - Mar 1 2017

Bibliographical note

Funding Information:
This work was supported by grants R01MD007015 (to EAR) from the National Institute on Minority Health and Health Disparities (http://www.nimhd.nih.gov/); R01CA058420, R01CA098663 (to JRP), and UM1CA164974 from the National Cancer Institute (http://www.cancer.gov/); and 11SDG7390014 (to EAR) from the American Heart Association (http://www.heart.org/HEARTORG/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the Black Women's Health Study participants for their continuing participation in this research effort.

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