Table 2. Analysis of Framingham Heart Study Data.
| famSKAT | famBT | unrSKAT | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Chr | Start | Stop | Sample Size |
N SNPs |
p- value |
Sample Size |
N SNPs |
p- value |
Sample Size |
N SNPs |
p- value |
| Trait: fasting glucose | ||||||||||||
| ADCY5 | 3 | 124486089 | 124650082 | 6479 | 18 | 0.9125 | 6479 | 18 | 0.5842 | 1924 | 17 | 0.9698 |
| ADRA2A | 10 | 112826911 | 112830560 | 6479 | 5 | 0.9557 | 6479 | 5 | 0.9453 | 1924 | 5 | 0.7293 |
| C2CD4B | 15 | 60243029 | 60244774 | 6479 | 3 | 0.9576 | 6479 | 3 | 0.8209 | 1924 | 3 | 0.7104 |
| CRY2 | 11 | 45825533 | 45861375 | 6479 | 8 | 0.0381 | 6479 | 8 | 0.0085 | 1924 | 7 | 0.7299 |
| DGKB-AGMO | 7 | 14153770 | 15568165 | 6479 | 76 | 0.6579 | 6479 | 76 | 0.3648 | 1924 | 72 | 0.1992 |
| FADS1 | 11 | 61323677 | 61340886 | 6479 | 5 | 0.5245 | 6479 | 5 | 0.3723 | 1924 | 5 | 0.7049 |
| G6PC2 | 2 | 169465996 | 169474756 | 6479 | 24 | 0.0418 | 6479 | 24 | 0.1173 | 1924 | 22 | 0.1373 |
| GCK | 7 | 44150395 | 44165412 | 6479 | 4 | 0.6283 | 6479 | 4 | 0.5864 | 1924 | 4 | 0.2486 |
| GCKR | 2 | 27573210 | 27600054 | 6479 | 7 | 0.2603 | 6479 | 7 | 0.2461 | 1924 | 6 | 0.0930 |
| GLIS3 | 9 | 3814128 | 4290035 | 6479 | 57 | 0.9170 | 6479 | 57 | 0.3920 | 1924 | 56 | 0.9822 |
| MADD | 11 | 47247775 | 47308158 | 6479 | 7 | 0.6571 | 6479 | 7 | 0.5145 | 1924 | 7 | 0.6316 |
| MTNR1B | 11 | 92342437 | 92355596 | 6479 | 11 | 0.8384 | 6479 | 11 | 0.7243 | 1924 | 11 | 0.0833 |
| PROX1 | 1 | 212228483 | 212276385 | 6479 | 34 | 0.2414 | 6479 | 34 | 0.3976 | 1924 | 33 | 0.1082 |
| SLC2A2 | 3 | 172196831 | 172227462 | 6479 | 5 | 0.8383 | 6479 | 5 | 0.7365 | 1924 | 5 | 0.6836 |
| SLC30A8 | 8 | 118216518 | 118258134 | 6479 | 12 | 0.1766 | 6479 | 12 | 0.0970 | 1924 | 12 | 0.7869 |
| TCF7L2 | 10 | 114699999 | 114916060 | 6479 | 7 | 0.1035 | 6479 | 7 | 0.4249 | 1924 | 7 | 0.2147 |
|
| ||||||||||||
| Trait: log-transformed fasting insulin | ||||||||||||
| GCKR | 2 | 27573210 | 27600054 | 6031 | 7 | 0.4878 | 6031 | 7 | 0.1586 | 1840 | 6 | 0.1016 |
| IGF1 | 12 | 101335584 | 101398508 | 6031 | 16 | 0.0232 | 6031 | 16 | 0.0234 | 1840 | 16 | 0.1258 |
Association analysis with fasting glucose and log-transformed fasting insulin from the Framingham Heart Study and genotype data from the Framingham SNP Health Association Resource, using famSKAT, famBT and unrSKAT. Fasting glucose was adjusted for age and sex, and log-transformed fasting insulin was adjusted for age, sex and body mass index. SNPs with MAF less than 5% within 100kb of each gene region were included in the analysis. Gene and SNP locations were reported on NCBI build 36. All individuals with available genotypes and phenotype were analyzed with famSKAT and famBT, while unrSKAT analyses only included a subset of unrelated participants. Wu weights with beta (1, 25) based on the MAF in a subset of unrelated individuals were used for all three methods.