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Blood, Vol. 111, Issue 6, 3286-3294, March 15, 2008
Identification of human minor histocompatibility antigens based on genetic association with highly parallel genotyping of pooled DNA
Blood Kawase et al.
111: 3286
Supplemental materials for: Kawase et al
Files in this Data Supplement:
- Document 1. Supplemental materials and methods (PDF, 34.4 KB)
- Table S1. Thresholds of test statistic for various genome-wide p values (PDF, 59.8 KB)
- Table S2. Statistical threshold of ΔRAΔRB for varying genome-wide p values (PDF, 126 KB)
- Table S3. Positive SNPs from pooled DNA analysis (PDF, 42.6 KB)
- Table S4. The linkage disequilibrium (LD) between known SNPs encoding minor H antigens and their flanking SNPs that can be genotyped with Affymetrix® GeneChip® 500K platform* (PDF, 36.4 KB)
- Figure S1. Simulated distribution of the maximum value of the test statistic (ΔRAΔRB) under null hypothesis for 250K NspI arrays (JPG, 33.1 KB)
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A total of 10,000 for CTX+ and CTX− pooled DNA panels were generated by superimposing randomly resampled 44 CEL files from 500 250K NspI experiments to calculate the max ( RARB). The RARB values corresponding to 0.1, 1,and 5 percentile points are indicated by arrows. Similar simulations were performed assuming varying numbers of CTX+ and CTX− pools for all array types.
- Figure S2. Dependence of statistical threshold for genome-wide p value of 0.001 on the sample size in 250K NspI array (JPG, 125 KB)
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Null distributions of maximum RARB values were simulated by generating 10,000 null panels of CEL files for case and control experiments by superimposing varying numbers of individual .CEL files from 250K NspI experiments for 500 normal individuals. For each distribution, the test statistic value for the upper 0.1 percentile point was calculated and plotted for various combinations of number of cases (CTX+ B-LCLs) and controls (CTX− B-LCLs).
- Figure S3. Whole genome association scans performed with pooled DNA constructed based on immunophenotyping with CTL-1B9 (JPG, 78.3 KB)
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Pooled DNAs generated from 57 CTX+ and 38 CTX− B-LCLs (the first pool set) were analyzed with 50K XbaI (A), 50K HindIII (B), 250K NspI (C), and 250K StyI (D) arrays. Test statistics were calculated for all SNPs and plotted in chromosomal order for the first experiment. A positive SNP (rs187894) was uniquely and sensitively pinpointed from more than 500,000 marker SNPs on 250K NspI array as indicated by an arrow, which was reproduced by the other validation pool (see Table S2).
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