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
Equipment and procedures:
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)
The facility operates on a fee for service basis for internal ISB and external users.
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).
Representative publication(s):
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.
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