The genotyping facility offers SNP genotyping and Methylation analysis to Institute for Systems Biology (ISB) researches, their collaborators and outside for profit companies and research institutions.
Services offered:
- SNP genotyping
a. Individual DNA samples
b.Pooled DNA samples. - SNP validation
- Microsatellite genotyping
The genotyping facility is equipped with:
- Compact Analyzer Mass Spectrometer (Sequenom) for SNP genotyping and methylation analysis
- One liquid handler (Multimek) to set up the PCR reactions
- MassARRAYTM nanodispenser to prepare the spectroCHIPs
- Five dual 384-well Gene Amp PCR system 9700 (PE)
- One dual 96-well Gene Amp PCR system 9700
- Robbins Scientific Work Station (Robbins Scientific)
Procedures:
We use the MassARRAY™ technology developed by Sequenom (San Diego, CA) for SNP genotyping and Methylation analysis. The same equipment can be used for other applications (http://www.sequenom.com/Genetic-Analysis/
Applications/iPLEX-Genotyping/iPLEX-Overview.aspx ).
Examples of projects that use the services of the ISB genotyping facility:
- Polymorphisms in Toll-like Receptor 4 Are Associated with Protection Against Leprosy (Bochud et al., 2009).
- Association of Donor Toll-like receptor 4 polymorphisms with Susceptibility to Invasive Aspergilliosis in Hematopoietic Cell Transplant Recipients (Bochud et al., 2008).
- Toll-like receptor 2 (TLR2) polymorphisms are associated with reversal reaction in Leprosy (Bochud et al., 2008).
- Glutamate Cysteine Ligase Catalytic Subunit Promoter Polymorphisms and associations with Type 1 Diabetes Age-at-onset and GAD65 Autoantibody Levels. Exp Clin Endocrinol Diabetes (Bekris et al., 2007).
- IA-2 autoantibodies in incident type I diabetes patients are associated with a polyadenylation signal polymorphism in GIMAP5 (Shin et al., 2007)
- A common human TLR1 polymorphism regulates the innate immune response to lipopeptides (Hawn et al., 2007).
- Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. (Roach et al, 2006)
- A polymorphism in Toll-interleukin 1 receptor domain containing adaptor protein is associated with susceptibility to meningeal tuberculosis (Hawn et al, 2006).
- Toll-like receptor 4 polymorphisms are associated with resistance to Legionnaires' disease (Hawn et al, 2005).
Bochud PY, Chien JW, Marr KA, Leisenring WM, Upton A, Janer M, Rodrigues SD, Li S, Hansen JA, Zhao LP, Aderem A, Boeckh M (2008) Toll-like receptor 4 polymorphisms and aspergillosis in stem-cell transplantation. N Engl J Med. 23; 359(17):1766-77.
Bochud PY, Hawn TR, Siddiqui MR, Saunderson P, Britton S, Abraham I, Argaw AT, Janer M, Zhao LP, Kaplan G, Aderem A (2008) Toll-like receptor 2 (TLR2) polymorphisms are associated with reversal reaction in leprosy. J Infect Dis. 15; 197(2):253-61.
Hawn TR, Misch EA, Dunstan SJ, Thwaites GE, Lan NT, Quy HT, Chau TT, Rodrigues S, Nachman A, Janer M, Hien TT, Farrar JJ, Aderem A (2007) A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. Eur J Immunol.; 37(8):2280-9.
Roach JC, Deutsch K, Li S, Siegel AF, Bekris LM, Einhaus DC, Sheridan CM, Glusman G, Hood L, Lernmark Å, Janer M on behalf of the Swedish Childhood Diabetes Study Group and the Diabetes Incidence in Sweden Study Group (2006) Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet; 79(4):614-27.
