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I am interested in developing statistical methods for complex disease research. Many complex diseases such as diabetes, breast cancer, chronic fatigue and obesity result from a combination of inheriting susceptibility alleles and exposure to environmental factors. One explanation for the high prevalence of many complex diseases is that risk alleles are common but each confers only a small genetic effect. The disease develops when an individual inherits several of these common risk alleles. Common small-effect alleles are difficult to study because it can be difficult to distinguish true signal from noise. While rare large-effect alleles resulting in Mendelian diseases can be tracked through pedigrees, this strategy has proven less effective for complex diseases. Instead, it may be more beneficial to study the genetics of individuals at the population level.
Preliminary study of complex disease etiology might require 1,000's to 10,000's of subjects for genome-wide association analysis. The large number of subjects, coupled with modern high-throughput genotyping (with 500k - 1 million SNP chips) and expression profiling (60k microarrays) technology can exceed the capacity of many modern genetic analysis software.
Genetic networks, which identify higher order structures within genetic data, may offer a means for a more tractable analysis. This approach identifies clusters of genes that have similar properties and then relates these clusters rather than the individual genes to clinical traits of interest. The thought is that these gene clusters represent biological pathways, and by identifying a disease related pathway, one can then target the genes that have risk alleles. My work here has mostly involved using correlation to construct gene co-expression networks and integrate them with other genetic and clinical data. Possible future work includes developing models for this algorithmic approach.
1. Presson AP, Partyka G, Jensen KM, Devine OJ, Rasmussen S, McCabe L, McCabe ERB (2013). "Current estimate of Down syndrome population prevalence in the United States." J Pediatr 163(4): 1163-1168. PMID: 23885965
Supplementary material for Presson et al. 2013 available here: Supplement.
2. Cheng P, Shih W, Alberto M, Presson AP, Licudine A, Mayer EA, Naliboff BD, Chang L (2013) "Autonomic Response to a Visceral Stressor is Dysregulated in Irritable Bowel Syndrome and Correlates with Duration of Disease." Neurogastroenterology and Motility 2013 Jul 3. PMID: 23822743
3. Myers JB, Taylor MB, Brant WO, Stevens M, Presson AP, Lowrance W, Willis C, Nirula R, Morris S (2013) "Process Improvement in Trauma: Traumatic Bladder Injuries and Compliance with Recommended Imaging Evaluation." J Trauma Acute Care Surg 74(1):264-9. PMID: 23147187
4. Hardee MJ, Lowrance W, Brant WO, Presson AP, Stevens MH, Myers JB (2012) "High Grade Renal Injuries: Application of Parkland Hospital’s Predictors of Intervention for Renal Hemorrhage to a Large Series of Patients with Blunt Renal Trauma." Journal of Urology 2012 Dec 3. PMID: 23219543
5. Chang L, Adeyemo M, Karagiannidis I, Videlock EJ, Bowe C, Shih W, Presson AP, Yuan P, Cortina G, Gong H, Singh S, Licudine A, Mayer M, Tache Y,Pothoulakis C, Mayer EA (2012) "Serum and colonic mucosal immune markers in irritable bowel syndrome." American Journal of Gastroenterology 107(2):262-72. PMID: 22158028
6. Bradford K, Shih W, Videlock E, Presson AP, Naliboff BD, Mayer EA, Chang L (2012) "Association between Early Life Trauma Events and Irritable Bowel Syndrome." Clinical Gastroenterology and Hepatology 10(4):385-90. PMID: 22178460
7. Presson AP, Yoon NK, Mah V, Alavi M, Maresh E, Goodglick L, Chia D, Horvath S (2011) "Protein expression based multimarker analysis of breast cancer patients." BMC Cancer 11(1):230. PMID: 21651811
8. Presson AP, Kim N, Xiaofei Y, Chen ISY and Kim S (2011) "Methodology and software to detect viral integration site hot-spots." BMC Bioinformatics 12:367. PMID: 21914224
9. Presson AP, Moore T, Kempert P (2010) "Efficacy of High Dose Chemotherapy and Autologous Stem Cell transplant for Recurrent Wilms' Tumor: A Meta-Analysis." Journal of Pediatric Hematology/Oncology 32(6):454-61. PMID: 20505538
10. Loo KK, Li Y, Tan Y, Luo X, Presson A, Shih W (2010) "Prenatal Anxiety is Associated with Male Child Preference among Expectant Mothers at 10-20 Weeks Gestation in Xiangyun County, Yunnan, China." International Journal of Gynecology & Obstetrics 111(3):229-32. PMID: 20817176
11. Kim S, Kim N, Presson AP, An DS, Mao SH, Bonifacino AC, Donahue RE, Chow SA, Chen ISY (2010) "High-throughput, sensitive quantification of repopulating hematopoietic stem cell clones." Journal of Virology 84(22):11771-80. PMID: 20844053
12. 12. Henderson-MacLennan NK, Papp JC, Talbot CC, McCabe ERB, Presson AP (2010) "Pathway Analysis Software: Annotation Errors and Solutions." Molecular Genetics and Metabolism 101(2-3):134-40. PMID: 20663702
13. Nickerson DW, Presson AP, Weigt SS, Gregson AL, Belperio JA, and Gomperts BN (2009) "Quantification of Cytokeratin 5 mRNA Expression in the Circulation of Healthy Human Subjects and after Lung Transplantation." PLoS One 4(6): e5925. PMID: 19529775
14. Loo KK, Luo X, Su H, Presson A, Li Y (2009) "Dreams of Tigers and Flowers: Child Gender Predictions and Preference in an Urban Mainland Chinese Sample during Pregnancy." Women & Health 49(1): 50–65. PMID: 19485234
15. Presson AP, Sobel E, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD and Horavth S (2008) "Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome." BMC Systems Biology, 2:95. PMID: 18986552
16. Presson AP, Sobel E, Pajukanta P, Plaisier C, Weeks DE, Alberg K, Papp JC (2008) "Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis." BMC Bioinformatics. 9:318. PMID: 18644149
17. Presson AP, Sobel E, Lange K, Papp JC (2006) "Merging microsatellite data." Journal of Computational Biology. 13:1131-1147. PMID: 16901233
For a full list please see: Publications