Hong-Wen Deng, PhD
Professor and Edward G. Schlieder Endowed Chair
Department of Biostatistics and Bioinformatics
Tulane University School of Public Health and Tropical Medicine
1440 Canal Street, Suite 2001
New Orleans, LA 70112
Phone: (504) 988-5164
Fax: (504) 988-1706
Our research group is interested in genetic dissection of human complex diseases using the state-of-the-art multi- and inter-disciplinary approaches of genomic technologies, and statistical and bioinformatical methods. The complex disease we are focusing on is osteoporosis, which is a prevalent, debilitating disorder characterized by bone fragility and an increased risk of low-trauma fractures. The approaches we are using involve genome-wide association analyses, genome-wide transcriptome analyses, proteome-wide protein expression profiling and in vivo and in vitro functional analyses of specific genes of interest. Currently, we are funded by several NIH grants for genetic, genomic and proteomic research of osteoporosis, including a P50 Specialized Center grant (1 P50 AR055081-01) for studying osteoporosis using the "genomic convergence analyses" approach.
Using the same genomic strategies, we are extending our research to other human complex diseases, including obesity, sarcopenia and periodontitis, and other human complex traits, including age at menarche/menopause and behavior traits, e.g., smoking, drinking and exercise. We are also extending our research of complex diseases from genome to epigenome, e.g., we are performing epigenome-wide profiling of osteoporosis at micro-RNA, DNA phosphorylation and histone modification levels. In particular, we are interested in developing novel statistical methods and bioinformatics tools for analyzing and managing large, complex datasets in genomic and epigenomic research.
Through Louisiana Osteoporosis Study (LOS), we are building a large research cohort and database for human complex disease studies. The LOS will enroll >20,000 subjects of different ethnicities in New Orleans, Baton Rouge and their surrounding areas. Each subject will be phenotyped for body composition (including bone mineral density, lean and fat mass), muscle function, and blood pressure etc., and assayed for important health-related and life-style information. Their blood samples will be collected for extraction of DNA, RNA and proteins and for cell isolation and biobanking. The LOS will become a sample pool for selecting subjects of extreme phenotypes (e.g., extremely high vs. low bone mass) for our ongoing funded and future genomic and epigenomic studies.
- Member, Genetics Society of American
- Member, American Society of Human Genetics (ASHG)
- Member, American Society for Bone and Mineral Research (ASBMR)
- Member, International Genetic Epidemiology Society
- Member, Great Plains States Society for Molecular Biology and Genetics
- Member, International Chinese Hard Tissue Society (ICHTS)
- Member, International Society of Musculoskeletal and Neuronal Interactions (ISMNI)
- Member, International Society of Clinical Densitometry (ISCD)
- Postdoctoral research, molecular and statistical population/quantitative genetics, Human Genetics Center, University of Texas, Houston, TX, 1997
- PhD, quantitative genetics, University of Oregon, Eugene, OR, 1995
- MS, mathematical statistics, University of Oregon, Eugene, OR, 1995
- MS, ecology and entomology, Peking University, Beijing, P. R. China, 1990
- BS, ecology and environmental biology, Peking University, Beijing, P. R. China, 1988
Ongoing Research Supports:
NIH 1R01AR057049-01A1, Hong-Wen Deng (PI) 9/1/09-8/30/14
Title: Identification of proteins important for male osteoporosis
To perform proteomics experiments to identify genes in monocytes and bone marrow mesenchymal stem cells important for male osteoporosis.
NIH 2R01AR050496-06A1, Hong-Wen Deng (PI) 9/01/09-8/30/14
Title: Robust and powerful test of candidate genes to bone mass
Systematically test for association of ten candidate genes for bone mass variation.
NIH R01AG026564, Hong-Wen Deng (PI) 3/1/07-2/28/11
Title: Genomic search for bone mass QTLs
To perform whole genome linkage studies and fine mapping in large pedigrees for bone mass QTLs.
NIH 1P50AR055081-01, Hong-Wen Deng (Program PI) 9/1/07-8/30/12
Title: Genomic Convergence for Female Osteoporosis Risk Genes
To perform a comprehensive study using approaches of genome wide association search for DNA polymorphisms,, RNA and proteins to identify genes and their functions important for female bone mass variation
NIH 1 RC2 DE20756-01, Hong-Wen Deng (Multiple PI) 10/1/09-09/30/10
Title: Genome-wide association study of periodontitis
To perform a pilot study for a large-scale genome-wide association study of periodontitis.
NIH 1R03TW008221-01A1, Hong-Wen Deng (PI) 9/1/09-06/30/12
Title: Genetics of Osteoporotic Fractures in Chinese
To perform a candidate gene-based association study for osteoporotic fractures in Chinese.
Butcher D and Deng HW. 1994. Hypothetical "Sister Killer". Nature 369: 26.
Shen H, Qiu C, Li J, Tian Q, Deng HW. Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes. Epigenomics. 2013 Jun;5(3):255-69.
Cao H, Lei S, Deng HW, Wang YP. Identification of genes for complex diseases using integrated analysis of multiple types of genomic data. PLoS One. 2012;7(9):e42755.
Chen J, Zhang JG, Li J, Pei YF, Deng HW. On combining reference data to improve imputation accuracy. PLoS One. 2013;8(1):e55600. doi: 10.1371/journal.pone.0055600.
Liu YZ, Li J, Pan R, Shen H, Tian Q, Zhou Y, Liu YJ, Deng HW. Genome-wide copy number variation association analyses for age at menarche. J Clin Endocrinol Metab. 2012 Nov;97(11):E2133-9. doi: 10.1210/jc.2012-1145.
Deng FY, Dong SS, Xu XH, Liu YJ, Liu YZ, Shen H, Tian Q, Li J, Deng HW. Genome-Wide Association Study Identified UQCC Locus for Spine Bone Size in Humans. Bone. 2012 Nov 30. doi:pii: S8756-3282(12)01390-7. 10.1016/j.bone.2012.11.028.
Yang TL, Guo Y, Shen H, Li J, Glessner JT, Qiu C, Deng FY, Tian Q, Yu P, Liu YZ, Liu YJ, Hakonarson H, Grant SF, Deng HW. Copy Number Variation on Chromosome 10q26.3 for Obesity Identified by a Genome-Wide Study. J Clin Endocrinol Metab. 2012 Nov 21.
Gu SS, Zhang Y, Wu SY, Diao TY, Gebru YA, Deng HW. Early molecular responses of bone to obstructive nephropathy induced by unilateral ureteral obstruction in mice. Nephrology (Carlton). 2012 Sep 4. doi: 10.1111/j.1440-1797.2012.01656.x.
Li J, Gui YF, Pei Y, Deng HW. The impact of imputation on meta-analysis of genome-wide association studies. PLoS One. 2012;7(3):34486. Epub 2012 Apr 5.
Yang TL, Chen XD, ..., Deng HW. 2008. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet 83:663-674.
Xiong DH, Liu XG, ..., Deng HW. 2009 Genome-wide association and follow-up replication studies identified ADAMTS18 and TGFBR3 as bone mass candidate genes in different ethnic groups. Am J Hum Genet. 84:388-398.
Liu YZ, Pei YF, ..., Deng HW. 2009 Genome-wide association analyses suggested a novel mechanism for smoking behavior regulated by IL15. Mol Psychiatry Feb [Epub ahead of print]
Liu XG, Tan LJ, ..., Deng HW. 2009 Genome-wide association and replication studies identified TRHR as an important gene for lean body mass. Am J Hum Genet. 84:418-423.
Liu YZ, Guo YF, ..., Deng HW. et al. 2009. Genome-wide association analyses identify SPOCK as a key novel gene underlying age at menarche. PLoS.Genet. 5, e1000420.
Chen XD, ..., Deng HW. 2009. Gene expression profiling in monocytes and SNP association suggest the importance of STAT1 gene for osteoporosis in both Chinese and Caucasians. J Bone Miner Res, July 13 [Epub ahead of print]
Hultgren S, Goldstein JM, Delancey JO, Bandstra ES, Brady KT, Brown JS, Deng HW, Dunaif A, Ehrmann DA, Mayer EA, Sinha R, Tobet S, Levine JE. 2009 The vital role of ORWH. Science 323:1009-1010.
Guo Y, ..., Deng HW. 2009 Genome-wide Association Study Identifies ALDH7A1 as a Novel Susceptibility Gene for Osteoporosis. PLoS Genetics In press
Guo Y, Yang TL, Liu YZ, Shen H, Lei SF, Yu N, Chen J, Xu T, Cheng Y, Tian Q, Yu P, Deng HW. 2011. Mitochondria-wide association study of common variants in osteoporosis. Ann Human Genet, July 18 [Epub ahead of print]
Liu JF, Papasian C, Deng HW. 2007 Incorporating Single Locus Tests into Haplotype Cladistic Analysis in Case Control Studies. Plos Genetics 3(3):e46.
Liu JF, Liu YJ, Liu XG, Deng HW. 2007. Bayesian Mapping of Quantitative Trait Loci for Multiple Complex Traits under Variance Component Model. Am J Hum Genet. 81(2):304-20.
Zhang J, Li J, Deng HW. 2008. Class-specific correlations of gene expressions: identification and their effects on clustering analyses. Am J Hum Genet 83:269-277
Li JL, Deng H, Lai DB, Xu F, Chen J, Gao G, Recker RR, Deng HW 2001 Toward high-throughput genotyping: Dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers. Genome Research 11:1304-1314
Lin Y, Li J,...Deng HW. et al. 2011. Comparative Studies of de novo Assembly Tools for Next-generation Sequencing Technologies. Bioinformatics. 27(12): 1093
Zhao LJ, Li MX, Guo YF, Xu FH, Li JL, Deng HW 2005 SNPP: Automating large-scale SNP genotype data management. Bioinformatics 21:266-268
Molecular cell biology:
Cao H, Deng HW, Li M, Wang YP. Classification of multicolor fluorescence in situ hybridization (M-FISH) images with sparse representation. IEEE Trans Nanobioscience. 2012 Jun;11(2):111-8.
Liu YZ, Dvornyk V, Lu Y, Shen H, Lappe JM, Recker RR, Deng HW 2005 A novel pathophysiological mechanism for osteoporosis suggested by an in vivo gene expression study of circulating monocytes. Journal of Biological Chemistry 280:29011-29016
Deng FY, Liu YZ,...., Xiao G, Liang SP, Deng HW. 2008 Proteomic analysis of circulating monocytes in Chinese premenopausal females with extremely discordant bone mineral density. Proteomics. 8(20):4259-72.
Deng FY, Lei SF, Chen XD, Tan LJ, Zhu XZ, Deng HW. 2011. An integrative study ascertained SOD2 as a susceptibility gene for osteoporosis in Chinese. J Bone Miner Res, July 19 [Epub ahead of print]
Deng FY, Lei SF, Zhang Y, Zhang YL, Zheng YP, Zhang LS, Pan R, Wang L, Tian Q, Shen H, Zhao M, Lundberg YW, Liu YZ, Papasian CJ, Deng HW. 2011. Peripheral blood monocyte-expressed ANXA2 gene is involved in pathogenesis of osteoporosis in humans. Mol Cell Proteomics. 2011 Nov;10(11):M111.011700. Epub 2011 Aug 4.
Chen J, Zhang JG, Li J, Pei YF, Deng HW. On combining reference data to improve imputation accuracy. PLoS One. 2013;8(1):e55600. doi: 10.1371/journal.pone.0055600. Epub 2013 Jan 30.
Liu YJ, Zhang L, Pei Y, Papasian CJ, Deng HW. On Genome-Wide Association Studies and Their Meta-Analyses: Lessons Learned From Osteoporosis Studies. J Clin Endocrinol Metab. 2013 Jun 19.
Zhao LJ, Zhou Y, Bu F, Travers-Gustafson D, Ye A, Xu X, Hamm L, Gorsage DM, Fang X, Deng HW, Recker RR, Lappe JM. Factors predicting vitamin D response variation in non-Hispanic white postmenopausal women. J Clin Endocrinol Metab. 2012 Aug;97(8):2699-705. doi: 10.1210/jc.2011-3401. Epub 2012 May 14.
Sun L, Tan L, Yang F, Luo Y, Li X, Deng HW, Dvornyk V. 2011. Meta-analysis suggests that smoking is associated with an increased risk of early natural menopause. Menopause. Sept 19. [Epub ahead of print]
Level of Instruction:
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