Identification of Type 2 Diabetes-associated combination of SNPs using Support Vector Machine

Hyo-Jeong Ban; Jee Yeon Heo; Kyung-Soo Oh; Keun-Joon Park
January 2010
BMC Genetics;2010, Vol. 11, p26
Academic Journal
Background: Type 2 diabetes mellitus (T2D), a metabolic disorder characterized by insulin resistance and relative insulin deficiency, is a complex disease of major public health importance. Its incidence is rapidly increasing in the developed countries. Complex diseases are caused by interactions between multiple genes and environmental factors. Most association studies aim to identify individual susceptibility single markers using a simple disease model. Recent studies are trying to estimate the effects of multiple genes and multi-locus in genome-wide association. However, estimating the effects of association is very difficult. We aim to assess the rules for classifying diseased and normal subjects by evaluating potential gene-gene interactions in the same or distinct biological pathways. Results: We analyzed the importance of gene-gene interactions in T2D susceptibility by investigating 408 single nucleotide polymorphisms (SNPs) in 87 genes involved in major T2D-related pathways in 462 T2D patients and 456 healthy controls from the Korean cohort studies. We evaluated the support vector machine (SVM) method to differentiate between cases and controls using SNP information in a 10-fold cross-validation test. We achieved a 65.3% prediction rate with a combination of 14 SNPs in 12 genes by using the radial basis function (RBF)-kernel SVM. Similarly, we investigated subpopulation data sets of men and women and identified different SNP combinations with the prediction rates of 70.9% and 70.6%, respectively. As the high-throughput technology for genome-wide SNPs improves, it is likely that a much higher prediction rate with biologically more interesting combination of SNPs can be acquired by using this method.


Related Articles

  • Insulin Resistance And Syndrome X.  // Health & Stress;2002, Issue 5, p4 

    Reports on the link between insulin resistance and metabolic syndrome X. Symptoms and etiology of the syndrome; Prevalence of insulin resistance in patients with Type 2 diabetes; Factors mediating the complications of non-insulin dependent patients.

  • The Insulin-sensitizing Role of the Fat Derived Hormone Adiponectin. Heilbronn, L.K.; Smith, S.R.; Ravussin, E. // Current Pharmaceutical Design;Jul2003, Vol. 9 Issue 17, p1411 

    Adiponectin is an insulin-sensitizing hormone whose blood concentration is reduced in obesity and type 2 diabetes. Administration of recombinant adiponectin in rodents increases glucose uptake and increases fat oxidation in muscle, reduces fatty acid uptake and hepatic glucose production in...

  • Reduced Expression of Nuclear-Encoded Genes Involved in Mitochondrial Oxidative Metabolism in Skeletal Muscle of Insulin-Resistant Women With Polycystic Ovary Syndrome. Skov, Vibe; Glintborg, Dorte; Knudsen, Steen; Jensen, Thomas; Kruse, Torben A.; Tan, Qihua; Brusgaard, Klaus; Beck-Nielsen, Henning; Højlund, Kurt // Diabetes;Sep2007, Vol. 56 Issue 9, p2349 

    Insulin resistance in skeletal muscle is a major risk factor for the development of type 2 diabetes in women with polycystic ovary syndrome (PCOS). In patients with type 2 diabetes, insulin resistance in skeletal muscle is associated with abnormalities in insulin signaling, fatty acid...

  • Prevalence of co-morbid depression in out-patients with type 2 diabetes mellitus in Bangladesh. Roy, Tapash; Lloyd, Cathy E.; Parvin, Masuma; Mohiuddin, Khondker Galib B.; Rahman, Mosiur // BMC Psychiatry;2012, Vol. 12 Issue 1, p123 

    Background: Little is known about the prevalence of depression in people with diabetes in Bangladesh. This study examined the prevalence and factors associated with depression in out-patients with Type 2 diabetes in Bangladesh. Methods: In this cross-sectional study a random sample of 483...

  • An economic evaluation of adaptive e-learning devices to promote weight loss via dietary change for people with obesity. Miners, Alec; Harris, Jody; Felix, Lambert; Murray, Elizabeth; Michie, Susan; Edwards, Phil // BMC Health Services Research;2012, Vol. 12 Issue 1, p190 

    Background: The prevalence of obesity is over 25 % in many developed countries. Obesity is strongly associated with an increased risk of fatal and chronic conditions such as cardiovascular disease and type 2 diabetes. Therefore it has become a major public health concern for many economies....

  • Perceived need to increase physical activity levels among adults at high risk of type 2 diabetes. A cross-sectional analysis within a community-based diabetes prevention project FIN-D2D. Vähäsarja, Kati; Salmela, Sanna; Villberg, Jari; Rintala, Pauli; Vanhala, Mauno; Saaristo, Timo; Peltonen, Markku; Keinänen-Kiukaanniemi, Sirkka; Korpi-Hyövälti, Eeva; Kujala, Urho M.; Moilanen, Leena; Niskanen, Leo; Oksa, Heikki; Poskiparta, Marita // BMC Public Health;2012, Vol. 12 Issue 1, p514 

    Background: Increased physical activity is a cornerstone of type 2 diabetes prevention. The perception of a need to change is considered essential in behaviour change processes. However, the existing literature on individuals' perceived need to change health behaviour is limited. In order to...

  • Insulin Resistance Associated Genes and miRNAs. Honardoost, Maryam; Sarookhani, Mohammad; Arefian, Ehsan; Soleimani, Masoud // Applied Biochemistry & Biotechnology;Sep2014, Vol. 174 Issue 1, p63 

    Type 2 diabetes mellitus is the result of resistance to insulin function along with inadequate insulin secretion, leading to a number of dysfunctions characterized by hyperglycemia, and it is associated with microvascular, macrovascular, and neuropathic complications. There is compelling...

  • The evolving definitions and increasing prevalence of the metabolic syndrome. Desroches, Sophie; Lamarche, Benoît // Applied Physiology, Nutrition & Metabolism;Feb2007, Vol. 32 Issue 1, p23 

    The metabolic syndrome (MetS) represents a cluster of metabolic abnormalities that predisposes an individual to a greater risk of developing coronary heart disease and type 2 diabetes. The condition is widespread among adults from developed nations, and progresses in frequency with age. In...

  • Case Study: Treating New-Onset Catabolic Type 2 Diabetes With Glargine and Lispro. DeWitt, Dawn E. // Clinical Diabetes;Fall2006, Vol. 24 Issue 4, p180 

    The article focuses on the treatment of catabolic type 2 diabetes in a 38-year-old African American woman with glargine and lispro. There was a combination of insulin resistance because of the patient's obesity and evidenced by her acanthosis nigricans and decreased insulin output. Once it...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics