SNPを用いた2x3テストに関するメモ

• 関係するRのパッケージはこちら
• This is something on the two types of test for 2x3 tables.
• When we do case-control association test for a SNP, we get a 2x3 table.
• For a 2x3 table from an autosomal SNP, we cat perform
  • (1) 2x3 genotypic test with df 2,
  • (2) dominant test for which we make 2x2 table from the 2x3 table according to the genotypes
  • (3) also we can do recessive test
  • (4) then we can do additive model test (trend test)
  • (5) somebody may make 2x2 table from 2x3 by counting the number of chromosomes with one allele and the other. In this case the total of 4 cells of 2x2 table is 2N where N is the sum of individuals.

• (4) and (5) are both testing allele's effect on the phenotype in the additive model but we should do (4) not (5).
• This can be clear when you apply (4) and (5) to X choromosomal SNPs in male population
• When we genotype males for X chromosomal SNPs, all males have homozygous genotypes. Therefore when we give the 2x3 table as

x,y,z
a,b,c

y=b=0.

• When we perform trend test(4), essentially we perform 2x2 test for a table

x,z
a,c

• But when we make 2x2 table from this by counting number of chromosomes,

2x,2z
2z,2c

• is the table we get.
• Total sample size gets doubled, so chi-square value will be also doubled.
• Actually when autosomal SNPs are in HWE perfectly, trend test and 2x2 of -chromosomal number test are mutually identical...
• You can double-check this by using the excel file (here).
• Input

100,200,90
100,200,110

• in the light blue area.
• Then trend test result is 1.00063 (cell B20) and allele comparison of chromosomal number is 1.0006(cell B 17).
• But when you input

100,200,190
100,200,210

• their values are 0.45733 and 0.5335.
• As in X chromosome for males,

100,0,200
100,0,240

• then their values are 1.14082 and 2.2816 = 1.14082*2