This work is licensed under a Table 2.
Number of gastroenteropancreatic (GEP) neuroendocrine neoplasia (NEN) patients with and without missense variants in the TSC2 and RET genes compared to unaffected individuals from the ExAC database.
| TSC2 missense variants | RET missense variants | |||||||
|---|---|---|---|---|---|---|---|---|
| Carriers | Non-carriers | Odds ratio (Pvalue) | CI (95%) | Carriers | Non-carriers | Odds ratio (Pvalue) | CI (95%) | |
| GEP NEN group | 8 | 85 | 1 | 92 | ||||
| ExAC (European non-Finnish) | 107 | 3958 | OR = 3.5 (P = 0.004) | Lower: 1.42 Upper: 7.42 |
127 | 11,742 | OR = 1 (P = 1) | Lower: 0.02 Upper: 5.84 |
| ExAC (Latin American) | 52 | 2480 | OR = 4.48 (P = 0.001) | Lower: 1.78 Upper: 9.90 |
11 | 789 | OR = 0.78 (P = 1) | Lower: 0.01 Upper: 5.48 |
| ExAC (all populations) | 340 | 9491 | OR = 2.63 (P = 0.016) | Lower: 1.09 Upper: 5.47 |
145 | 10,833 | OR = 0.81 (P = 1) | Lower: 0.02 Upper: 4.71 |
The European non-Finnish samples are considered the closest ancestry population to our series. Because the sample size of the ExAC database varies among genes and sites, we conservatively inferred the number of individuals with and without deleterious variants by multiplying the frequency of the variants of interest and the sample size of the least sampled site for each of the three partitions of the data: European non-Finnish, Latin American and unfiltered. For example, in the European ExAC dataset, the TSC2 genomic region with the lowest sample size has 2N = 8130 alleles, corresponding to 4065 individuals. As there are 107 rare variants in this sample, we assumed they represent 107 individuals within the group. All analyses were statistically significant (Fisher’s exact test).