Cost-effective analysis of candidate genes using htSNPs: a staged approach.
We have previously shown that the selection of haplotype tag single nucleotide polymorphisms (htSNPs) and their statistical analysis in a multi-locus transmission/disequilibrium test (TDT) results in a more cost-effective genotyping strategy in disease association studies of genes by minimising redundancy due to linkage disequilibrium between SNPs. Further savings can be achieved by the use of a two-stage genotyping strategy. This approach is illustrated here in conjunction with the multi-locus TDT in determining whether common alleles of the immune regulatory genes RANK and its ligand TRANCE (RANKL) are associated with type 1 diabetes (T1D). A saving of approximately 75% of potential genotyping reactions could be made with minimal loss of power. There was little evidence from our analysis for association between the TRANCE and RANK genes and T1D in the populations tested.
Lowe
C E
CE
Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, UK.
Cooper
J D
JD
Chapman
J M
JM
Barratt
B J
BJ
Twells
R C J
RC
Green
E A
EA
Savage
D A
DA
Guja
C
C
Ionescu-Tîrgovişte
C
C
Tuomilehto-Wolf
E
E
Tuomilehto
J
J
Todd
J A
JA
Clayton
D G
DG
D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics / Q000378:metabolism; D005838:Genotype; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D015810:Linkage Disequilibrium; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D053244:Osteoprotegerin; D020641:Polymorphism, Single Nucleotide; D053245:RANK Ligand; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics / Q000378:metabolism; D018124:Receptors, Tumor Necrosis Factor
D002352:Carrier Proteins; D006023:Glycoproteins; D008562:Membrane Glycoproteins; D053244:Osteoprotegerin; D053245:RANK Ligand; D018160:Receptors, Cytoplasmic and Nuclear; D018124:Receptors, Tumor Necrosis Factor